6048 results for "canc*"

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• Testicular Cancer Consortium WES

  We have leveraged our previous collaborative research to better understand the genetic underpinnings of testicular germ cell tumor (TGCT), and have completed whole exome sequencing on the DNA of patients at high risk for TGCT. Specifically, we conducted a study of high-risk individuals using data from Penn Medicine and the NCI. We collected germline DNA from blood or saliva samples from men with bilateral TGCT, and a family history consisting of at least one first to third degree relative diagnosed with the disease. The goal of the study was to identify coding genomic variation associated with predisposition to TGCT. Whole exome sequencing and gene burden analyses were performed on 293 men with a family history of TGCT or bilateral disease. 228 unique families were represented in this sample. Our results found a missense variant in the hinge domain of proto-oncogene PIM1. Several more candidates were identified via gene burden association, including loss-of-function variants in NIN and QRSL1. We also identified an association with variants in CFTR using gene-specific analysis. There was no association with sex and germ cell development pathways or regions identified by GWAS previously. We identified associations with three major pathways including, mitosis/cell cycle, co-translational protein targeting, and sex differentiation. Our results showed associations with variants in several genes, which suggests a multigenic heritability. We also found potential association with CFTR, co-translational protein targeting, and chromosomal segregation in sex determination. Our results suggest potential drug targets for TGCT prevention or treatment, e.g., PIM1, and the co-translational targeting pathway. To our knowledge, our study is the largest to date of men with high risk TGCT.

  Study phs003107

• Urine Cell-Free RNA Analysis for Cancer Detection and Therapy Response Prediction

  The goal of this study was to develop a urine cell-free RNA (cfRNA) liquid biopsy assay for bladder cancer. We developed a method called uRARE-seq, which involves targeted RNA sequencing of urine cfRNA, and applied it to urine samples from bladder cancer patients and non-cancer controls. We evaluated its performance for bladder cancer detection and monitoring. We also developed a pre-treatment urine biomarker to predict the likelihood of response to intravesical therapy.

  Study phs004116

• National Cancer Institute (NCI) Early Onset Malignancies Initiative (EOMI): Molecular profiling of Breast, Colon, Kidney, Liver, Multiple Myeloma, and Prostate among Racially and Ethnically Diverse Populations

  The Early Onset Malignancies Initiative (EOMI) is focused on collecting specimens from racially and ethnically diverse population groups with six different types of cancer (breast, prostate, colon, liver, kidney, and multiple myeloma). This initiative is a partnership between the Center for Research Strategy, the Center for Cancer Genomics and the Division of Cancer (DCP). DCP's NCI Community Oncology Research Program (NCORP) is a critical partner. The acquisition of the cancer and matching normal biospecimens in this initiative are from newly diagnosed early onset cancer patients who identify as Non-Hispanic Black, Hispanic, American Indian or Alaska Native, or Non-Hispanic White. The Minority/Underserved NCORPs sites will collect the samples for this project. By carrying out this initiative in the NCORP's national network of investigators, cancer care providers, and research institutions, the EOMI will harness the community-based partnerships to improve participation among these racial/ethnic groups. The NCORP investigators, as participants in NCI's clinical trials network, will annotate the biologic samples with clinical information that will enhance the ability to answer questions about molecular determinants of early disease, treatment response, and/or prognosis. The EOMI will be a step forward in addressing racial/ethnic disparities and in understanding cancer in underserved populations.

  Study phs001952

• NCTN: A Phase III Randomized Trial for Patients with De Novo AML Using Bortezomib and Sorafenib (NSC# 681239, NSC# 724772) for Patients with High Allelic Ratio FLT3/ITD (AAML1031)

  Study ID: AAML1031NCT Number: NCT01371981 Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Phase III Randomized Trial for Patients with De Novo AML Using Bortezomib and Sorafenib (NSC# 681239, NSC# 724772) for Patients with High Allelic Ratio FLT3/ITD (AAML1031)Trial Description: This randomized phase III trial studies how well bortezomib and sorafenib tosylate work in treating patients with newly diagnosed acute myeloid leukemia. Bortezomib and sorafenib tosylate may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth. Drugs used in chemotherapy work in different ways to stop the growth of cancer cells, either by killing the cells or by stopping them from dividing. Giving bortezomib and sorafenib tosylate together with combination chemotherapy may be an effective treatment for acute myeloid leukemia. Clinical data presented in the following publication(s): PMID 32029509Disease type(s): Hematopoietic Neoplasm/Leukemia - Acute Myeloid LeukemiaClinical Dataset(s) included:NCT01371981-D4 (PMID 32029509): There is one dataset (-D4) for AAML1031's primary publication (PMID 32029509). This dataset is a patient level dataset which contains patient characteristics, consort diagram classifications, abnormal karyotype, CEBP alpha status, NPM status, minimal residual disease, survival, treatment-related mortality, and toxicity data presented in the manuscript for eligible pediatric acute myeloid leukemia (AML) patients enrolled on the AAML1031 clinical trial.Forthcoming Dataset(s): NCT01371981-D1, NCT01371981-D2, NCT01371981-D3, NCT01371981-D5, NCT01371981-D6You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004142

• PCPT and SELECT Cohorts: Core Infrastructure Support for Cancer Research

  SELECT study: SELECT was a phase III, double-blind, placebo-controlled 4-arm study of selenium, vitamin E, selenium and vitamin E together, and placebo designed to assess the effect of these supplements on the incidence of prostate cancer. Funded by the National Cancer Institute and conducted by SWOG, the study opened in August 2001 and quickly exceeded its accrual goal of 35,533 men.In the fall of 2008, the trial's Data Safety and Monitoring Committee recommended that participants discontinue taking study supplements due to convincing evidence (planned interim futility analysis) that neither vitamin E nor selenium supplements were associated with the prevention of prostate cancer. A subsequent analysis in 2011 showed a significant 17% increase in prostate cancer incidence in participants who were on the vitamin E only arm. Approximately 17,000 participants from the original trial recently completed an additional four years of centralized follow-up. This follow-up ended on May 31, 2014 and SELECT is now closed. PCPT study: The Prostate Cancer Prevention Trial (PCPT) was a SWOG Cancer Research Network-coordinated study designed to test whether the drug finasteride (Proscar®) would prevent prostate cancer in men ages 55 and older. This study was closed on June 24, 2003 because the study objective had been reached. The results of the study, which did find a preventive benefit for the drug, were published as "The Influence of Finasteride on the Development of Prostate Cancer," in the New England Journal of Medicine on July 17, 2003.

  Study phs003382

• Environmental Chemical Body Burden and Prospective Breast Cancer Risk in the Cancer Prevention Study-3 Cohort - CIDR

  This study is focused on chemical body burden of per- and poly-fluoroalkyl substances (PFAS), and concomitant risk of developing invasive breast cancer during the menopausal transition. We hypothesized that elevated body-burden levels of these endocrine-disrupting chemicals (EDCs) will increase the risk of developing breast cancer, and that alterations of the methylome will link these chemical exposures and breast cancer. In Specific Aim 1, using samples and data from a prospective study of women in the American Cancer Society (ACS) Cancer Prevention Study 3 (CPS-3), we are assessing the association between body burden of PFAS during the menopausal transition and subsequent development of invasive breast cancer. The California Environmental Chemistry lab is determining PFAS levels in plasma samples collected 1 to 7 years prior to a diagnosis of invasive breast cancer from 998 ACS CPS-3 participants and 998 matched, cancer-free CPS-3 participants. All subjects were between 40 and 57 years of age when the blood sample was taken. In Specific Aim 2, studying the same participants, DNA methylation (DNAm) using Infinium MethylationEPIC BeadChips was conducted at Center for Inherited Disease Research (CIDR). We are conducting an epigenome-wide association study (EWAS) to identify DNAm changes associated with levels of PFAS in the cancer-free participants. We then will determine the association between the PFAS-associated DNAm changes and risk of developing breast cancer. The design is a nested case control study within the ACS CPS-3 cohort. Available data include the DNAm data and phenotypic data on case or control status, age at diagnosis of breast cancer, age at blood draw for cases and controls, and self-reported race/ethnicity.

  Study phs003494

• Comprehensive Genomic Characterization of Translocation Renal Cell Carcinoma

  Xp11 translocation renal cell carcinoma (tRCC) is a rare, female-predominant cancer driven by a fusion between the TFE3 gene on chromosome Xp11.2 and a partner gene on either chrX or an autosome. It remains unknown what types of rearrangements underlie TFE3 fusions, whether fusions can arise from both the active (chrXa) and inactive X (chrXi) chromosomes, and whether TFE3 fusions from chrXi translocations account for the female predominance of tRCC. To address these questions, we performed haplotype-specific analyses of chrX rearrangements in tRCC whole genomes. We show that TFE3 fusions universally arise as reciprocal translocations and that oncogenic TFE3 fusions can arise from chrXi:autosomal translocations. Female-specific chrXi:autosomal translocations result in a 2:1 female-to-male ratio of TFE3 fusions involving autosomal partner genes and account for the female predominance of tRCC. Our results highlight how X chromosome genetics uniquely constrains somatic chrX alterations and underlies cancer sex differences.This version of the dbGaP study provides a comprehensive set of whole genome data and tables with clinical information collected for the 16 patients (15 pateints as tRCC and 1 patient as ccRCC) in the study cohort. The data also contains 12 RNA-seq samples used in the study and analyses. We anticipate that this data will considerably advance our molecular and genetic understanding of oncogenic translocations in TFE3-tRCC involving inactive chromosome X and its role in cancer sex bias.

  Study phs003008

• DNA-Sequencing of Baseline and Progression Plasma from the Phase III Alliance A031201 Trial

  Circulating tumor DNA (ctDNA) in plasma cell free DNA (cfDNA) of cancer patients is associated with poor prognosis, but is challenging to detect from low plasma volumes. In metastatic castration-resistant prostate cancer (mCRPC), ctDNA assays are needed to prognosticate outcomes of patients treated with androgen receptor (AR) inhibitors. We developed a custom targeted cfDNA sequencing assay, named AR-ctDETECT, to detect ctDNA in limiting plasma cfDNA available from mCRPC patients in the Alliance A031201 randomized phase 3 trial of enzalutamide with or without abiraterone. For the AR ctDETECT assay, DNA-seq libraries were constructed from cfDNA using Takara ThruPLEX Tag-Seq or Plasma-Seq kits, and subjected to hybridization enrichment using a custom-designed Agilent SureSelect bait panel. Post-capture DNA-seq libraries were pooled and sequenced on an Illumina HiSeq 2500 or an Illumina NovaSeq 6000 SP using 2x150 bp settings. ctDNA positivity was defined by samples harboring high ctDNA aneuploidy as measured by a modified ichorCNA algorithm, or samples harboring low ctDNA aneuploidy but displaying AR gain or genomic structural rearrangement (AR-GSR), MYC/MYCN gain, or a pathogenic mutation. We used the AR-ctDETECT assay to analyze plasma collected at baseline from 776 patients, and found that 59% were ctDNA-positive. Patients who were ctDNA-positive at baseline had significantly worse median overall survival than patients who were ctDNA-negative at baseline. We also used the AR-ctDETECT assay to analyze plasma collected at progression from 431 patients. Relative to baseline cfDNA, progression cfDNA exhibited enrichment of features associated with poor prognosis, including elevated cfDNA concentrations and increased ctDNA positivity. AR alterations were enriched at progression relative to baseline, primarily driven by AR-GSRs, including those predicted to truncate the AR ligand binding domain and originate from AR amplification on extrachromosomal DNA. Stratification by radiographic progression-free survival revealed that patients with rapid progression were enriched for non-AR gene alterations, while patients with initially durable responses showed selective enrichment of AR alterations. These results indicate that non-AR genetic alterations in ctDNA are associated with primary resistance to AR pathway inhibitors in first-line mCRPC, while AR alterations are associated with secondary resistance, even in patients who initially respond. .

  Study phs003325

• Personalized DNA and Peptide Vaccines Elicit Neoantigen-Driven T-Cell Responses in Pancreatic Cancer

  This study provides data from two phase I clinical trials (NCT03122106, NCT03956056) that evaluated the safety and immunogenicity of DNA-based and synthetic long peptide personalized cancer vaccines. Exome and RNA sequence data were used to identify somatic mutations, predict neoantigens, and design personalized cancer vaccines. Immune monitoring was performed on each patient to assess neoantigen specific T-cell responses.

  Study phs004463

• Blood and Marrow Clinical Trials Network (BMT CTN) Comparing Peripheral Blood Stem Cell Transplantation versus Bone Marrow Transplantation in Individuals With Hematologic Cancers (0201) (BMT-CTN-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. ObjectivesTo compare survival rates of patients with hematologic cancers that received transplantation of granulocyte colony stimulating factor (G-CSF) mobilized peripheral blood stem cells (PBSC) versus marrow from HLA-compatible unrelated donors.BackgroundMany studies of allogeneic marrow transplantation have shown that a higher dose of marrow cells correlates with a stronger hematopoietic engraftment and lower mortality from infectious complications. Peripheral blood stem cells (PBSC) collected after mobilization with granulocyte colony stimulating factor (G-CSF) contain a large number of CD34-positive progenitors and total cells than bone marrow. These observations led to the hypothesis that transplantation of PBSC would lead to lower mortality compared to transplantation of marrow. However, some studies have also shown increased risk of acute and chronic graft-versus-host disease (GVHD), as compared to bone marrow.Participants Between March 2004 and September 2009, 551 subjects were enrolled at 48 centers. Eligible subjects were less than 66 years of age and were planning to undergo transplantation for acute leukemia, myelodysplasia, chronic myeloid or myelomonocytic leukemia, or myelofibrosis. Design Subjects were randomly assigned in a 1:1 ratio to peripheral-blood stem-cell or bone marrow transplantation, stratified according to transplantation center and disease risk. Donors and recipients were DNA typed to ensure matching for 5 or 6 of the HLA-A, B, and DRB1 antigens. Peripheral-blood stem-cell donors were prescribed filgrastim or lenograstim at a dose of 10 μg per kilogram per day for 5 days and underwent apheresis. Recipients received one of four conditioning regimens and one of two GVHD prophylaxis regimens that were specified prior to randomization. Supportive care and treatment for GVHD were provided according to institutional standards. Subjects were followed in the study for 3 years. The primary end point was 2-year survival as assessed by means of an intention-to-treat analysis. Secondary end points included post-transplantation incidences of neutrophil and platelet engraftment, graft failure, acute and chronic GVHD, relapse, and infections. Conclusions There was no detected significant survival differences between peripheral-blood stem-cell and bone marrow transplantation from unrelated donors. Further analysis indicated that peripheral-blood stem cells may reduce the risk of graft failure, whereas bone marrow may reduce the risk of chronic GVHD (Anasetti, C. et al., N Engl J Med. 2012).

  Study phs004601

• Somatic Mutation in Normal Bladder Study

  Adult human somatic tissues are landscapes of mutant clones, but little is known about how these landscapes are shaped by known cancer risk factors. The goal of this study was to determine how the main bladder cancer risk factors (sex and smoking) change the mutational landscape of the normal urothelium. We collected normal urothelium from 45 donors at autopsy by brushing ~2cm² of the surface epithelium in the upper part (dome) and lower part (trigone) of the bladder (79 samples total). To identify mutations with high sensitivity we employed ultradeep (~5000x) DNA error-correcting duplex-sequencing on a panel of 15 protein coding genes and the TERT promoter, previously described to be under positive selection in normal urothelium or relevant to bladder cancer. We identified thousands of clonal driver mutations, which demonstrate pervasive positive selection in the normal urothelium. Males showed a significantly higher number of driver truncating mutations in RBM10, CDKN1A and ARID1A, despite similar rates of non-coding mutations, indicating stronger positive selection and clonal expansion in the male urothelium. We also discovered clonal expansions driven by activating TERT promoter mutations in the normal bladder, which were strongly associated with age and smoking. These results demonstrate that sex and smoking shape the clonal landscape of the normal bladder and indicate that the high mutational content of normal tissues might be leveraged to study the effect of mutations in vivo (i.e. natural saturation mutagenesis). We will deposit in dbGaP de-identified relevant clinical information from the 45 donors and the fastq files derived from duplex sequencing of the 79 samples in the study. We will also deposit fastq files derived from duplex sequencing of 3 control cord blood samples.

  Study phs004105

• BTC GBM TeamLab Trial 1: Longitudinal Tissue Profiling of Recurrent Malignant Glioma During Repeat Dosing of Oncolytic Viral Immunotherapy (NCT03152318)

  The data in this repository is generated from the work of the GBM TeamLab as part of Break Through Cancer (BTC) (https://breakthroughcancer.org/). The TeamLab's goal is to evaluate the feasibility, safety, and value of performing serial brain biopsies to obtain biological readouts during the assessment of novel glibolastoma (GBM) therapeutics. The first investigational agent studied by the TeamLab is a novel oncolytic viral immunotherapy (agent: CAN-3110, also known as rQNestin34.5v.2) which was delivered via repeated intratumoral delivery at up to 6 timepoints over a 4-month period in recurrent IDH-wild type GBM patients. Biopsy tissues, blood, and CSF were collected and subjected to multi-omic profiling at each surgical timepoint. This work is being conducted as one of the trial arms for NCT03152318. Controlled access omic data from this study will be deposited here as the results are published.

  Study phs004189

• Transcriptomic Profiling of Peripheral Immune Cells in a Trial of Ruxolitinib with Nivolumab for Anti-PD1 Non-Responsive cHL

  Treatment with checkpoint inhibitors is effective in multiple cancer types. However, even in cancers with high response rates such as Hodgkin lymphoma, some patients fail to respond or relapse following an initial response to checkpoint inhibitors. In this study, we examined patients enrolled in a clinical trial of ruxolitinib with nivolumab in relapsed or refractory Hodgkin lymphoma (NCT03681561). Patients relapsed or refractory to anti-PD1 therapy received ruxolitinib for 8 days followed by nivolumab every 4 weeks and continued ruxolitinib twice daily. For this transcriptomic study, peripheral blood mononuclear cells (PBMCs) were collected at baseline and 8 days of ruxolitinib therapy and analyzed by single-cell and bulk RNA-sequencing.

  Study phs003601

• Epigenetic Control of Topoisomerase 1 by MacroH2A1.1

  DNA transactions introduce torsional constraints that pose an inherent risk to genome integrity. While topoisomerase 1 (TOP1) activity is essential for removing DNA supercoiling, aberrant stabilization of TOP1:DNA cleavage complexes (TOP1ccs) can result in cytotoxic single-stranded DNA lesions (SSLs). What protects the genome from aberrant TOP1 activity remains unknown. Using a combination of CUT&RUN and TOP1 Covalent Adduct Detection (CAD) Seq in MDA-MB-231 breast cancer cells (American Type Culture Collection, ATCC), we identified chromatin context as an essential means to ensure TOP1cc resolution at TOP1 hot spots. Through its ability to bind poly(ADP-ribose) (PAR), a protein modification required for TOP1cc repair, the histone variant macroH2A1.1 establishes a TOP1-permissive chromatin environment, while the alternatively spliced macroH2A1.2 isoform is unable to bind PAR or protect from TOP1ccs. MacroH2A1 isoform-specific analyses were based on reconstitution of macroH2A1.1 knockout cells with wild-type or PAR binding-deficient FLAG-tagged macroH2A1.1 in human breast cancer cells. Mechanistically, we find that macroH2A1.1 facilitates the recruitment of the TOP1cc repair factor XRCC1 in response to both endogenous and drug-induced topological stress. Impaired macroH2A1.1 splicing, a frequent cancer feature, was predictive of increased sensitivity to TOP1 poisons in a pharmaco-genomic screen in breast cancer cells, and macroH2A1.1 inactivation mirrored this effect in breast and ovarian cancer cells. Consistent with this, low macroH2A1.1 expression correlated with improved survival in cancer patients treated with TOP1 inhibitors (TOP1i). We propose that macroH2A1 alternative splicing serves as an epigenetic modulator of TOP1-associated genome maintenance and a potential cancer vulnerability.

  Study phs003729

• Women's Health Initiative Clinical Trial and Observational Study - Imaging

  Objectives: The clinical trial assessed the safety and efficacy of three interventions. Specifically, it evaluated (1) the major health benefits and risks of estrogen plus progestin and estrogen alone, (2) the effects of a low-fat eating pattern on risk of colorectal cancer, and (3) the efficacy of calcium with vitamin D supplementation for preventing hip and other fractures. The objective of the memory study was to determine whether estrogen plus progestin therapy protects global cognitive function, and evaluate the therapy's effect on the incidence of dementia and mild cognitive impairment.The observational study is examining the relationship between lifestyle, socioeconomic, health, and other risk factors with cardiovascular, breast cancer, colorectal cancer and osteoporotic fracture outcomes. Secondary objectives include providing more reliable estimates of the extent to which known risk factors predict disease, more precise estimates of new occurrences of disease, and to provide a future resource for the identification of new or novel risk factors especially factors found in blood. Background: The Women's Health Initiative (WHI) is a long-term national health study that has focused on strategies for preventing the major causes of death, disability, and frailty in postmenopausal women, specifically heart disease, cancer, and osteoporotic fractures. The WHI is primarily composed of an observational study (OS), as well a clinical trial (CT) with three components: Hormone Replacement Therapy (HT), Dietary Modification, (DM) and Calcium/Vitamin D supplementation (CaD).Prior to the WHI, observational studies suggested that postmenopausal hormone therapy was associated with a decreased risk of coronary heart disease (CHD). Potential cardioprotection was based on generally supportive data on lipid levels in intermediate outcome clinical trials, trials in nonhuman primates, and a large body of observational studies suggesting a 40% to 50% reduction in risk among users of either estrogen alone or, less frequently, combined estrogen and progestin. Observational studies primarily examining unopposed estrogen preparations have suggested a 30% to 50% reduction in coronary events, and an 8% to 30% increase in breast cancer with extended use. Other research findings indicated that hormone therapy was also associated with a decreased risk of osteoporosis and increased bone density. The WHI HT trials were designed to test the effects of postmenopausal hormone therapy on risk for coronary heart disease and assess overall risks and benefits in predominantly healthy women. The Women's Health Initiative Memory Program (WHIMS) consists of a suite of studies which include cohorts of women who participated in the WHI HT trials. Postmenopausal women have a greater risk than men of developing Alzheimer's disease, but studies of the effects of estrogen therapy on Alzheimer's disease have been inconsistent. Additionally, observational studies have suggested that postmenopausal hormone treatment may improve cognitive function, but data from randomized clinical trials have been sparse and inconclusive. International comparisons and migration studies have suggested that countries with 50% lower fat intake than the US population had approximately one third the risk of colorectal cancer. Additionally, fairly consistent evidence existed for an effect of dietary fat, vegetables and fruits, and grains on colorectal cancer risk from within-country observational studies, although the protective effect of lower fat intake was no longer clear after adjusting for energy intake. The WHI DM trial was the first randomized trial to directly address the health effects of a low-fat eating pattern in predominantly healthy postmenopausal women from diverse racial/ethnic, geographic, and socioeconomic backgrounds. Osteoporosis is a major cause of injury, loss of independence, and death, and contributes to hip fractures. Observational evidence and data from previous randomized clinical trials suggest that calcium and/or vitamin D supplements may slow bone loss and reduce the risk of falls in postmenopausal and elderly women. However, evidence from trials, observational studies, and meta-analyses of calcium and vitamin D supplementation with respect to hip and other fractures was limited at the time the WHI was initiated. In two prior randomized trials, calcium plus vitamin D supplements did not reduce the risk of nonvertebral fractures among older women. When the WHI CaD trial was designed, guidelines recommended daily intakes of 800 to 1200 mg of calcium with 400 IU of vitamin D for the prevention of osteoporosis, which was not met by many American women. Therefore, the WHI CaD trial was designed to test the primary hypothesis that postmenopausal women randomly assigned to calcium plus vitamin D supplementation would have a lower risk of hip fracture and, secondarily, of all fractures than women assigned to placebo. Subjects: Postmenopausal women ages 50 to 79 were eligible to participate. A woman was considered postmenopausal if she had experienced no vaginal bleeding for 6 months (12 months for women under 55 years of age), had had a hysterectomy, or had ever used postmenopausal hormones. Recruitment was carried out in 40 US clinical centers in 1993-1998. The clinical trial components had additional specific inclusion or exclusion criteria.A total of 68,132 women were randomized into at least one component of the clinical trial. 27,347 women were enrolled in the hormone therapy component with 16,608 in the estrogen plus progestin trial and 10,739 in the unopposed estrogen trial, 48,835 women were enrolled in the diet modification component, and 36,282 women were enrolled in the calcium/vitamin D component. 7,479 women 65 years of age and older at baseline and that participated in the HT trial component were enrolled in the ancillary memory study. Women who were either ineligible or unwilling to participate in the clinical trial component were enrolled in the observational study. For example, many potential participants to the clinical trial component of the study were already undertaking a low fat diet or were using hormone replacement therapy. The effect of the selection process was that women enrolled in the observational study tended to have healthier lifestyles compared to those enrolled in the clinical trial. In total, 93,676 subjects were enrolled in WHI OS, with over 16% being members of a racial/ethnic minority group. The first WHI Extension Study enrolled 115,407 consenting participants from all components of the original WHI study for an additional five years of follow-up, from 2005 to 2010. In 2010, 93,567 women consented to continued follow-up. Design: The clinical trial component of the WHI included three randomized comparisons: hormone therapy, dietary modification, and calcium/vitamin D supplementation. Women could have been randomized into one, two or all three trials.The hormone therapy trial enrolled women to one of two double-blinded trials: estrogen (0.625 mg of conjugated equine estrogens daily) plus progestin (2.5 mg of medroxyprogesterone acetate daily) or estrogen alone. Women with a prior hysterectomy were eligible for the trial of unopposed estrogen. Women with an intact uterus at screening were initially also eligible for unopposed estrogen, but were reassigned to the trial of combined postmenopausal hormones beginning in 1995. Both trials randomized participants 1:1 to either hormone therapy or placebo. A 3-month washout period was required before baseline evaluation of women using postmenopausal hormones at initial screening. Study participants were contacted by telephone 6 weeks after randomization to assess symptoms and reinforce adherence. Follow-up contacts by telephone or clinic visit occurred every 6 months, with clinic visits required annually. The estrogen plus progestin trial was halted in July 2002 after a mean 5.2 years of follow-up because health risks, including increased risk of breast cancer and cardiovascular disease, exceeded benefits. The estrogen alone trial was stopped early in March 2004, because an increased risk of stroke was found with no benefit for coronary heart disease. The primary outcome was coronary heart disease (CHD) (nonfatal myocardial infarction and CHD death), with invasive breast cancer as the primary adverse outcome. The dietary modification trial evaluated the effect of a low-fat, high fruit, vegetable, and grain diet on preventing cardiovascular disease and cancer. Participants were randomly assigned to an intervention or a comparison group in the ratio of 2:3 for cost-efficiency. The intervention was an intensive behavioral modification program, using 18 group sessions in the first year and quarterly sessions thereafter, led by specially trained and certified nutritionists. The program was designed to promote dietary change with the goals of reducing total fat to 20% of energy intake, increasing vegetables and fruits to at least 5 servings daily and grains to at least 6 servings daily. The intervention did not include total energy reduction or weight loss goals. Comparison group participants received a copy of the US Department of Health and Human Services' Dietary Guidelines for Americans and other health-related materials but were not asked to make dietary changes. Dietary intake was monitored using the WHI food frequency questionnaire at 1 year and in a rotating one-third subsample every year thereafter. Women completed a medical update questionnaire every 6 months, and medical records were sought for all women reporting colorectal cancer. The primary outcome was invasive colorectal cancer incidence. Participants in the calcium/vitamin D trial were randomized 1:1 to either supplements or placebo. Active tablets contained 500 mg of elemental calcium (as calcium carbonate) and 200 IU of vitamin D3, to be taken twice daily with meals. The presence and severity of symptoms, safety concerns, and outcomes were ascertained at annual clinic visits and telephone or clinic visits at intervening six-month intervals. Risk factors for fracture were assessed by questionnaire, interview, and clinical examination. The primary outcome was incidence of hip fracture. Participants in the observational study attended a baseline examination and were re-examined three years later. Participants completed annual updates of exposures and clinical outcomes by mail. Final data were collected by mail during the close-out period in April 2004 to March 2005. The major clinical outcomes of interest were coronary heart disease, stroke, breast cancer, colorectal cancer, endometrial cancer, ovarian cancer, osteoporotic fractures, diabetes, and total mortality. Most outcomes were initially ascertained by self-report on an annual questionnaire and documented by hospital and related records. Charts with potential cardiovascular, cancer, and fracture outcomes were sent to the local physician adjudicator for evaluation and classification. Staff at the Clinical Coordinating Center coded and adjudicated all cancers of major interest in the study using standardized SEER guidelines. In 2005, WHI participants were invited to join the Extension Study for an additional five years of follow-up in order to collect long-term outcomes. Participants completed annual data collection forms primarily by mail, similar to the OS follow-up. Women reporting study outcomes were contacted by WHI field center staff to obtain additional details and medical records, which were evaluated by physician adjudicators. In 2010, the woman remaining were invited to join the next Extension Study. In the second extension, women were divided into two groups, one of which would have outcomes documented with medical records (the Medical Records Cohort, MRC), and the other would just be followed by self-report (the Self-Report Cohort, SRC). The MRC consists of women who were in the hormone therapy trials, and all African-American and Hispanic women. In 2012-2013, a subset of the MRC was identified for a potential in-home visit to collect blood and several objective measures of physical functioning. Conclusions: Overall health risks exceeded benefits from use of combined estrogen plus progestin after an average 5.2 year follow-up among healthy postmenopausal US women (Rossouw et al., 2002, PMID:12117397). Among postmenopausal women aged 65 years or older, estrogen plus progestin did not improve cognitive function when compared with placebo (Rapp et al., 2003, PMID: 12771113), increased the risk for probable dementia, and did not prevent mild cognitive impairment (Shumaker, et al., 2003, PMID: 12771112). The use of conjugated equine estrogen increased the risk of stroke, decreased the risk of hip fracture, and did not affect CHD incidence in postmenopausal women with prior hysterectomy after an average of 6.8 years of follow-up (Anderson et al., 2004, PMID: 15082697). Over approximately 8 years of follow-up, a low-fat dietary pattern did not reduce the risk of colorectal cancer (Beresford, et al., PMID: 16467233). Calcium with vitamin D supplementation resulted in a small but significant improvement in hip bone density; however, no significant difference was observed in hip fractures (Jackson, et al., 2006, PMID: 16481635). A recent review summarizes the conclusions from the WHI clinical trials with a focus on clinical practice (Manson, et al., 2024, PMID: 38691368).Description of ECG Imaging Data: Electric cardiograms (ECGs) were given to all clinical trial participants at baseline and in years 3, 6, and 9 of the original WHI study.EKG data consist of 12 lead 10 seconds ECGS sampled at 500Hz via GE ECG machines and process via GE MUSE system. The ECG waveform were directly exported from GE MUSE using MUSE export function in XML format, which include EKG waveform data as well as other ECG characteristics. Waveform data is in base64 encoded format, when it is decoded, it is a binary data that can be used to draw waveform graph. Many programming languages and data tools have built in functions to decode base64 strings. All the other necessary information is included in the LeadData section, total byte size, total sample size etc. (usually 1 sample is 2 bytes). See example below: encoded-data (base64 encoded string) JwAoAC0AKAAiACIAJAAkACQAIwAiACIAHgAcABwAGwAZABgAGAAYABcAEwAQABAAEAAL^/AAsADAAM... decoded-binary-data (1 sample is 2 bytes) 270028002D002800220022002400240024002300220022001E001C001C001B00 1900180018001800170013001000100010000B000B000C000C000D000D000D00 0A000A000A0009000600040004000700070005000500020... These binary values are integers (Y axis data of the graph), hence it is a straightforward process to draw the waveform graph. Acquisition dates have been redacted from this ECG data to comply with WHI policy. All acquisition dates within files and in file names have been set to January 1, 1900 (19000101) to comply with this policy.

  Study phs003824

• Immediate Postoperative Minimal Residual Disease Detection with MAESTRO Predicts Recurrence and Survival in Head and Neck Cancer Patients Treated with Surgery

  We selected 24 patients with locally advanced head and neck squamous cell carcinoma (HNSCC) who were surgically treated. MAESTRO, our ultrasensitive, tumor-informed, mutation enrichment sequencing assay, was applied in a pooled format (MAESTRO-Pool) to plasma samples collected from these patients at baseline (pre-op) and postoperatively. We show that detection of circulating tumor DNA (ctDNA) 1 to 9 days after surgery is associated with significantly worse survival. Many plasma samples also had tumor fractions detected below 100 parts-per-million, the detection limit for first-generation commercial assays, highlighting the need for more sensitive ctDNA assays. Here we provide whole genome sequencing of matched tumor biopsy and normal germline DNA from 24 patients that were used to identify somatic single nucleotide variants (SNVs) to be tracked using our MAESTRO-Pool assay.

  Study phs003981

• NCTN: A Randomized Phase III Trial of CC-5013 (Lenalidomide) and Low Dose Dexamethasone (LLD) versus Bortezomib, Lenalidomide and Low Dose Dexamethasone (BLLD) for Induction, in Patients with Previously Untreated Multiple Myeloma (S0777)

  Study ID: S0777NCT Number: NCT00644228 SWOG Cancer Research NetworkSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Phase III Trial of CC-5013 (Lenalidomide) and Low Dose Dexamethasone (LLD) versus Bortezomib, Lenalidomide and Low Dose Dexamethasone (BLLD) for Induction, in Patients with Previously Untreated Multiple Myeloma (S0777)Trial Description: This randomized phase III trial studies lenalidomide, dexamethasone, and bortezomib to see how well it works compared to dexamethasone and lenalidomide alone in treating patients with previously untreated multiple myeloma. Biological therapies, such as lenalidomide, may stimulate the immune system in different ways and stop cancer cells from growing. Drugs used in chemotherapy, such as dexamethasone, work in different ways to stop the growth of cancer cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Bortezomib may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth or by blocking blood flow to the cancer. It is not yet known whether lenalidomide and dexamethasone is more effective with or without bortezomib in treating multiple myeloma. Data presented in the following publication(s): PMID 28017406Disease type(s): Hematopoietic Neoplasm/Myeloma - MyelomaClinical Dataset(s) included:NCT00644228-D1 (PMID 28017406): There are two datasets for S0777's primary publication 28017406 (-D1 and -D2). This dataset, NCT00644228_D1.txt, contains data included in the aforementioned publication, which included primary and secondary efficacy results evaluating the addition of bortezomib to lenalidomide and low dose dexamethasone induction therapy for the treatment of patients with newly diagnosed multiple myeloma in the SWOG phase III trial, S0777. The dataset includes baseline characteristics, treatment discontinuation reasons, stratification factors, survival, outcome, second primary cancer, and FISH data.NCT00644228-D2 (PMID 28017406): There are two datasets for S0777's primary publication 28017406 (-D1 and -D2). This dataset, NCT00644228_D2.txt, contains data for the safety analyses included in the aforementioned publication, which compared toxicity between bortezomib, lenalidomide and low dose dexamethasone versus lenalidomide and low dose dexamethasone induction therapy for the treatment of patients with newly diagnosed multiple myeloma in the SWOG phase III trial, S0777.You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004247

• Genomic Characterization CS-MATCH-0007 Arm P

  The CS-MATCH-0007 protocol is part of a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing and RNA sequencing using pre-and post-treatment tumor biopsy specimens from patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to specific genomic alterations found in their cancers. Arm P is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with PTEN loss by IHC are treated with the drug GSK2636771. This subprotocol is one of the treatment arms included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood.

  Study phs002152

• The Oral Microbiome and Head and Neck Cancer

  Oral microbiota may influence head and neck squamous cell carcinoma (HNSCC) development, potentially related to carcinogen metabolism. The human oral cavity hosts a diverse microbiota, including bacteria and fungi. We performed shotgun sequencing and ITS1 sequencing on 236 HNSCC case participants who developed HNSCC during a mean follow-up of 5.1 years and 458 matched controls who remained HNSCC-free. Oral samples were obtained from a prospective nested case-control study within three epidemiological cohorts: the American Cancer Society Cancer Prevention Study II Nutrition Cohort (ACS CPS-II), the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO), and the Southern Community Cohort Study (SCCS). Control participants were selected using 2:1 frequency matching based on cohort, age, sex, race and ethnicity, and time since oral sample collection.

  Study phs004018

• NCTN: A Randomized Trial of Axillary Node Dissection in Women With Clinical T1-2 N0-1 M0 Breast Cancer Who Have a Positive Sentinel Node (ACOSOG-Z0011)

  Study ID: ACOSOG-Z0011NCT Number: NCT00003855 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: A Randomized Trial of Axillary Node Dissection in Women with Clinical T1-2 N0-1 M0 Breast Cancer Who Have a Positive Sentinel Node (ACOSOG-Z0011)Trial Description: RATIONALE: Surgery to remove lymph nodes in the armpit may remove cancer cells that have spread from tumors in the breast.PURPOSE: Randomized phase III trial to determine the effectiveness of removing lymph nodes in the armpit in treating women who have stage I or stage IIA breast cancer.Clinical data presented in the following publication(s):PMID 21304082 Disease type(s): Breast Neoplasm - Breast Neoplasm, MiscellaneousClinical dataset(s) included:NCT00003855-D1 (PMID 21304082): There is one dataset associated with the primary analysis publication (PubMed ID: 21304082) for study NCT00003855. This dataset contains baseline characteristics, treatment arm, lymph node surgery information, estrogen and progesterone receptor status, and recurrence and survival data.You are encouraged to view the PDF data dictionaries found in the "Documents" tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004234

• Center for Cancer Genomics (CCG) Cancers of Unknown Primary Project (CUPP)

  The Cancers of Unknown Primary Project (CUPP) aims to characterize difficult tumor types with the goal of determining future best treatment practices. NCI will utilize whole exome sequencing, copy-number variation, DNA methylation in conjunction with transcriptome sequencing to provide a comprehensive genomic landscape of Cancers of Unknown Primary (CUP). The samples will be processed and submitted for genomic characterization using pipelines and procedures established within the Center for Cancer Genomics (CCG).

  Study phs001801

• Derivation of Doxorubicin Mutational Signatures in Cancer

  Study design and aims: This study utilizes doxorubicin exposed cell lines to derive doxorubicin mutational signatures. To validate the methodology used (bulk whole-genome sequencing of cells exposed to drug with a pulsed dose-escalation approach), cisplatin mutational signatures are first derived and compared to previously published data (single constant dose of drug and whole-genome sequencing of single-cell clones). The primary aim of the study was to characterize the impact of doxorubicin mutagenesis on the genome. Furthermore, to assess the presence of derived doxorubicin signatures in patient samples treated with a doxorubicin-containing regimen. Population information: The study utilizes atypical teratoid rhabdoid tumor (ATRT) (n=2) and renal medullary carcinoma (RMC) (n=2) cell lines. To acquire cisplatin and doxorubicin exposed cells, parental cells were treated with escalating doses of cisplatin and doxorubicin in a pulsed manner for between 2-12 months. This study also contains 2 cell lines derived from one patient with metastatic disease, treated with a doxorubicin-containing regimen. Molecular technologies: Whole-genome sequencing of the bulk cell population.Principal findings: Cisplatin mutational signatures were consistent with previously published data. This study identified two related single-base substitution (SBS) doxorubicin mutational signatures. While the two resulting signatures had some similarities, they differed in their frequencies of C > A (SBS-Doxorubicin-1) and T > C (SBS-Doxorubicin-2) substitutions. A double-base substitution (DBS) signature was also observed in association with SBS-Doxorubicin-2. This DBS signature harbored peaks at TG > CA, TG > GT, and TT > CC substitutions. Next, two INDEL signatures were derived. The first consisted of 1bp insertions and deletions at T homopolymers, >=2bp insertions at repetitive DNA, and microhomology deletions. The second consisted of >=2bp insertions at non-repetitive regions. Finally, both SBS-Doxorubicin signatures were found to be significantly present in patient samples exposed to a doxorubicin-containing regimen. Data Available through dbGaP: This dataset contains paired-end whole genome sequencing of parental (n=4), cisplatin exposed (n=2), and doxorubicin exposed (n=4) SMARCB1-deficient cell lines, as well as cell lines derived from one patient with metastatic disease (n=2), where the patient was treated with a doxorubicin-containing regimen.

  Study phs004740

• NCTN: A Phase III Randomized Study of Nivolumab Plus Ipilimumab versus Nivolumab for Previously Treated Patients with Stage IV Squamous Cell Lung Cancer and No Matching Biomarker (Lung-Map Sub-Study) (S1400I)

  Study ID: S1400INCT Number: NCT02785952SWOG Cancer Research NetworkSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Phase III Randomized Study of Nivolumab plus Ipilimumab versus Nivolumab for Previously Treated Patients with Stage IV Squamous Cell Lung Cancer and No Matching Biomarker (Lung-Map Sub-Study) (S1400I)Trial Description: This randomized phase III trial compares nivolumab with ipilimumab and nivolumab alone in treating patients with stage IV squamous cell lung cancer that has come back after previous treatment. This is a "non-match" sub-study that includes all screened patients not eligible for a biomarker-driven sub-study. Monoclonal antibodies, such as nivolumab and ipilimumab, may be able to shrink tumors. It is not yet known whether nivolumab works better with or without ipilimumab in treating patients with squamous cell lung cancer. Clinical data presented in the following publication(s):PMID 34264316 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung CancerClinical Dataset(s) included:NCT02785952-D1 (PMID 34264316): There are three datasets (-D1 through -D3) for PMID 34264316, a primary publication for S1400I. This clinical dataset, NCT02785952-D1, contains patient-level data (one row per patient), including baseline, demographic, metastatic sites, and treatment information. It also contains assessment, survival, reasons for going off treatment, tumor mutational burden, PDL1 expression, and patient-reported outcome data.NCT02785952-D2 (PMID 34264316): There are three datasets (-D1 through -D3) for PMID 34264316, a primary publication for S1400I. This toxicity dataset, NCT02785952-D2, contains event-level data (one row per patient per adverse event experienced on trial).NCT02785952-D3 (PMID 34264316): There are three datasets (-D1 through -D3) for PMID 34264316, a primary publication for S1400I. This dataset, NCT02785952-D3, contains biomarker data (one row per patient per gene alteration).You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004242

• DNA Methylation in Prostate Tumor and Paired Benign Tissue for African and European Ancestry Men

  We recruited prostate cancer (PCa) patients undergoing robotic-assisted laparoscopic radical prostatectomy at the University of Chicago Medical Center Urology Clinic between 2011 and 2017. Our study includes 76 African American (AA) and 75 European American (EA) men with PCa of Gleason Score (GS) ≥7, recruited by the Epidemiology Research Recruitment Core at the University of Chicago. All patients consented to the collection of questionnaire data, prostate tissue, and medical records. The study was approved by the Institutional Review Board of the University of Chicago. Following prostatectomy, prostate tissue was sent to the Human Tissue Research Center (HTRC) at the University of Chicago. Each sample underwent histological examination and Gleason scoring by University of Chicago genitourinary pathologists. The presence of adenocarcinoma was confirmed by overexpression of alpha-methylacyl-coenzyme-A racemase (AMACR) and areas for DNA extraction were marked. Tissue samples used for DNA extraction were obtained using with either a 1mm biopunch or laser microdissection of a 100 µm2 area of tissue. Genome-wide DNA methylation profiles were generated using Illumina's Infinium MethylationEPIC BeadChip array kit. Genome-wide SNP data was generated (from benign tissue DNA) using the Illumina Infinium Multi-Ethnic Global-8 v1.0 array at the University of Chicago Genomics Core Facility. We performed imputation using the Haplotype Reference Consortium (HRC, Version r1.1 2016) panel, which includes all samples from the 1,000 Genomes Project (Phase 3), using the Michigan Imputation Server. The imputed SNP data for mQTL analysis was imputed based on genotype SNP data which was all from benign tissue DNA and the methylation data was identified in both tumor and benign tissue, both AA and EA men, and identified QTLs co-occuring with prostate cancer susceptibility loci.Data including SNP genotypes, DNA methylation, tissue type, and participant characteristics will be available in dbGaP.

  Study phs003516

• NCTN: Dexamethasone Compared with Prednisone During Induction Therapy and Methotrexate with or without Leucovorin During Maintenance Therapy in Treating Patients with Newly Diagnosed High-Risk Acute Lymphoblastic Leukemia (AALL0232)

  Study ID: AALL0232NCT Number: NCT00075725 Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: Dexamethasone Compared with Prednisone during Induction Therapy and Methotrexate with or without Leucovorin during Maintenance Therapy in Treating Patients with Newly Diagnosed High-Risk Acute Lymphoblastic Leukemia (AALL0232)Trial Description: This randomized phase III trial is studying dexamethasone to see how well it works compared to prednisone during induction therapy. This trial is also studying methotrexate and leucovorin calcium to see how well they work compared to methotrexate alone during maintenance therapy in treating patients with newly diagnosed acute lymphoblastic leukemia (ALL). Drugs used in chemotherapy, such as dexamethasone, prednisone, methotrexate, and leucovorin calcium, work in different ways to stop cancer cells from dividing so they stop growing or die. Giving more than one drug may kill more cancer cells. It is not yet known which combination chemotherapy regimen is more effective in treating acute lymphoblastic leukemia. Clinical data presented in the following publication(s):PMID 27114587Disease type(s): Hematopoietic Neoplasm/Leukemia - Acute Lymphoblastic LeukemiaClinical Dataset(s) included:NCT00075725-D1 (PMID 27114587): There are three datasets associated with this publication (NCT00075725-D1, NCT00075725-D2, and NCT00075725-D3): NCT00075725-D1 includes all patients enrolled on the study. This dataset contains baseline characteristics, BCR-ABL fusion status, MLL rearrangement, bone marrow status at end of induction, and survival data.NCT00075725-D2 (PMID 27114587): There are 3 datasets associated with this publication (NCT00075725-D1, NCT00075725-D2, and NCT00075725-D3). NCT00075725-D2 is the subset of patients included in the randomized comparison between Capizzi and High-dose Methotrexate. The dataset includes baseline characteristics, BCR-ABL fusion status, MLL rearrangement, bone marrow status at end of induction, and survival data. Outcomes (EFS time, EFS indicator) in this dataset are different from the outcomes in NCT00075725-D1. The outcome of those assigned to Capizzi who subsequently received High-dose Methotrexate was censored at time of therapy crossover, since in AALL0232, therapy changes were recommended to provide HD-MTX to all participants who had not yet completed maintenance course 1 or received cranial irradiation.NCT00075725-D3 (PMID 27114587): There are three datasets associated with this publication (NCT00075725-D1, NCT00075725-D2, and NCT00075725-D3). NCT00075725-D3 is the toxicity data observed in the randomized cohorts (steroid and methotrexate).Additional whole genome genotyping data for this trial is available under phs001350.You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004039

• Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. ObjectivesHypertension Study: To determine whether treatment with a calcium channel blocker or an angiotensin-converting enzyme inhibitor lowers the incidence of coronary heart disease (CHD) or other cardiovascular disease (CVD) events vs treatment with a diuretic.Lipid Study: To determine whether pravastatin compared with usual care reduces all-cause mortality in older, moderately hypercholesterolemic, hypertensive participants with at least an additional CHD risk factor. BackgroundHypertension Study: Antihypertensive therapy is well established to reduce hypertension-related morbidity and mortality, but the optimal first-step therapy is unknown.Lipid Study: Studies have demonstrated that statins administered to individuals with risk factors for coronary heart disease (CHD) reduce CHD events. However, many of these studies were too small to assess all-cause mortality or outcomes in important subgroups.ParticipantsHypertension Study: A total of 33,357 participants. Lipid Study: A total of 10,355 participants. Baseline mean total cholesterol was 224 mg/dL; LDL-C, 146 mg/dL; high-density lipoprotein cholesterol, 48 mg/dL; and triglycerides, 152 mg/dL. Mean age was 66 years; 49% were women, 38% black and 23% Hispanic, 14% had a history of CHD, and 35% had type 2 diabetes. DesignHypertension Study: A randomized, double-blind, active-controlled clinical trial conducted from February 1994 through March 2002. Participants were randomly assigned to receive chlorthalidone, 12.5 to 25 mg/d (n = 15,255); amlodipine, 2.5 to 10 mg/d (n = 9048); or lisinopril, 10 to 40 mg/d (n = 9054) for planned follow-up of approximately 4 to 8 years. The primary outcome was combined fatal CHD or nonfatal myocardial infarction, analyzed by intent-to-treat. Secondary outcomes were all-cause mortality, stroke, combined CHD (primary outcome, coronary revascularization, or angina with hospitalization), and combined CVD (combined CHD, stroke, treated angina without hospitalization, heart failure (HF), and peripheral arterial disease).Lipid Study: Multicenter (513 primarily community-based North American clinical centers), randomized, non-blinded trial conducted from 1994 through March 2002 in a subset of participants from the Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT). The interventions in the trial were pravastatin, 40 mg/d, vs usual care. The primary outcome was all-cause mortality, with follow-up for up to 8 years. Secondary outcomes included non-fatal myocardial infarction or fatal CHD (CHD events) combined, cause-specific mortality, and cancer.ConclusionsHypertension Study: Thiazide-type diuretics are superior in preventing one or more major forms of CVD and are less expensive. They should be preferred for first-step antihypertensive therapy.Lipid Study: Pravastatin did not reduce either all-cause mortality or CHD significantly when compared with usual care in older participants with well-controlled hypertension and moderately elevated LDL-C. The results may be due to the modest differential in total cholesterol (9.6%) and LDL-C (16.7%) between pravastatin and usual care compared with prior statin trials supporting cardiovascular disease prevention.

  Study phs004021

• Pre-Existing Skin-Resident CD8 and γδ T Cell Circuits Mediate Immune Response in Merkel Cell Carcinoma and Predict Immunotherapy Efficacy

  Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer with a ~50% response rate to immunotherapy. Here, we attempted to identify novel predictive biomarkers of response through extensive and deep multi-omics interrogation of 186 samples from 116 patients. We collectively integrated bulk RNAseq, single-cell RNAseq, multiplex immunofluorescence, and spatial transcriptomics. Importantly, we were also able to study 14 matched pairs of tissue samples from pre- and post-immunotherapy. In non-responders, tumors show evidence of increased tumor cell cycling, expression of neuronal stem cell markers, and IL-1α/β. Responders have evidence of increased type I/II interferon signatures and evidence of pre-existing tissue resident (Trm) CD8 or Vδ1 γδ T cells that functionally converge with overlapping antigen-specific transcriptional programs and clonal expansion of multiple T cell receptors. Spatial transcriptomics demonstrated higher co-localization of T cells with B and dendritic cells in responders, with evidence of expression of chemokines important for co-stimulation. Finally, immunotherapy increased clonal expansion or recruitment of Trm and Vδ1 cells in tumors in responders, further underscoring their therapeutic importance. These data identify potential novel actionable biomarkers and therapeutic targets for MCC.

  Study phs003629

• Analyzing Somatic Mutagenesis in Systemic Sclerosis

  The study was undertaken with the aim of estimating differences in the mutational burden in lung tissues from healthy vs systemic sclerosis (SSc) patients. SSc is an auto-immune disease, with patients often developing cancer. However, the etiology of this phenomenon is poorly understood. As such we sought to uncover potential molecular mechanisms prevalent within SSc tissues that might be potentiating cancer. Samples were randomly collected from individuals from two broad ethnic groups, European (EA) and African American (AA). In total, samples were obtained from 7 individuals belonging to the EA group and 4 individuals from the AA group. For this study, ethnicity was not included as a confounding variable, given that the data set has roughly comparable number of individuals from both ethnicities for the healthy and SSc cohorts. Study participants ranged in age from 37-63 years old. Median age (52 years old) of healthy individuals was comparable to the SSc cohort (~48 years old). Participants were self-described as current/former smokers or non-smokers. Lung tissues were obtained under a protocol approved by the University of Pittsburgh Institutional Review Board. Written informed consent statements were provided to the University of Pittsburgh IRB by the study participants/patients. Sample sizes were determined by the ability of bulk lung fibroblast tissues to stably propagate in culture until single cell clones could be obtained. Samples for which sufficient cell density could not be achieved for downstream high-depth sequencing analysis were excluded from the study and are not reported. Five or greater than 5 samples are collected from each cohort including healthy and SSc patients. Subjects were allocated to two basic cohorts based on diagnosis at the time of explant. Participants with no reported lung anomalies were allocated to the "healthy" cohort, whereas individuals with reported lung abnormalities, primarily SSc with pulmonary fibrosis and/or hypertension were allocated to the "SSc" cohort. All tissue samples were cultured, propagated and processed in identical fashion without requiring individual-specific protocols. Additionally, equivalent amounts of DNA were used for preparing sequencing libraries from both cohorts, and all samples were sequenced using Illumina whole genome sequencing (WGS) and analyzed using identical computational pipelines. Our study primarily discovered that there is a significantly higher burden of somatic mutations in SSc samples, compared to healthy samples. We observed an overall increase in a range of mutations in genomes of SSc patients, including single base substitutions, indels, structural variants and copy number alterations. Additionally, we uncovered a novel mutation signature associated with SSc samples, hinting at the activity of POLH in these samples, and highlighting the potential nexus between inflammation, DNA damage, and cancer.

  Study phs003700

• CSER: Exome Sequencing in Diverse Populations in Colorado and Oregon/CHARM Cancer Health Assessments Reaching Many

  The CHARM (Cancer Health Assessment Reaching Many) study, part of the Clinical Sequencing Evidence-Generating Research (CS.ER2) effort, aimed to assess the utility of clinical exome sequencing and how it affects care in diverse populations. The study population included adults at risk for hereditary cancer syndromes. The primary objective was the implementation of a hereditary cancer risk assessment program in healthy 18-49 year-olds in primary care settings within a vertically integrated health delivery system (Kaiser Permanente) and a federal qualified health center (Denver Health). The investigators aimed to assess clinical exome sequencing implementation and interpretation, as well as tailored interactions for low health literacy including a contextualized consent process, and a modified approach to results disclosure and genetic counseling. The investigators were also assessing the clinical utility (healthcare utilization and adherence to recommended care) and personal utility of primary and additional results from clinical exome sequencing, and evaluate the ethical and policy implications of considering personal utility of genomic information decisions for health care coverage.Sequencing and analysis for CHARM was conducted at the Northwest Clinical Genomics Laboratory, University of Washington, Seattle (https://nwgc.gs.washington.edu/).

  Study phs002111

• HINTS Geo-Coded Data 2014 (HINTS 4 Cycle 4)

  The Health Information National Trends Survey (HINTS) is a nationally representative survey which has been administered every few years by the National Cancer Institute since 2003. HINTS 4 includes four mail-mode data collection cycles over the course of three years. Cycle 4 was conducted from August 19 through November 17, 2014. Cycle 4 was conducted by mail using a protocol similar to that used in Cycles 1, 2, and 3 with a goal of obtaining 3,500 completed questionnaires, with a final respondent sample of 3,677.

  Study phs004209

• Global Health Centers of Excellence-New Delhi (GHCoE New Delhi-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. ObjectivesProtocol 1 To develop a model surveillance system for cardio-metabolic diseases (CMD) and their risk factors which can be adopted for continuing surveillance by other countries in South East Asia. To measure the incidence of CMD risk factors and disease events, as well as the associated morbidity and mortality. Protocol 2 To test whether an intensive and comprehensive health care intervention to reduce cardiovascular disease (CVD) risk among type 2 diabetes patients in South Asia is more effective and sustainable compared to existing care.Protocol 3 To develop a model surveillance system for cardio-metabolic diseases (CMD) and their risk factors in rural India. To measure the incidence of CMD risk factors and disease events, as well as the associated morbidity and mortality.Background Although animal and ecologic studies have suggested a link between dietary fat and the incidence of breast cancer, previous observational studies have not yielded definitive results. In the Women's Health Initiative dietary trial, breast cancer incidence was not significantly different between the low-fat diet group and the control group. However, findings from previous studies in humans on the association between adolescent diet and breast cancer are inconsistent and self-reports of childhood diets may yield biased results. The DISC06 follow-up study explored the hypothesis that diet during adolescence may play a greater role in breast cancer risk than diet during adulthood by evaluating the longer-term effects of the DISC intervention during childhood and adolescence on subsequent biomarkers that have been associated with breast cancer risk in adults. Background Cardio-metabolic diseases (CMDs) include diabetes mellitus, cardiovascular disease, kidney disease and common risk factors that underlie these conditions such as central obesity, insulin resistance, glucose intolerance, dyslipidemia, and hypertension. CMDs are a growing global public health problem, with high mortality rates particularly in low- and middle-income countries. However, CMDs have the advantage of being predictable through identification of risk factors and also preventable through changes in lifestyle, particularly through healthy eating habits and regular physical activity. The greatest gains in prevention have been seen when early and target-driven interventions address multiple risk factors. However, achieving control of individual risk factors is poor, globally. Quality improvement schemes have shown promise in high-income countries, but were untested in South Asia at the time of these studies. In people of South Asian origin, diabetes, and CMD risk factors and events occur at younger ages and lower body mass indices when compared to other ethnic groups, and are rapidly increasing with socioeconomic and nutrition transitions. CVD is currently the leading cause of death in both urban and rural India. Prior to these studies, the major source of population level estimates of CMD risk factors, morbidity and mortality in India was ad hoc surveys. Such methods are limited by problems of sample design, lack of standardization, frequent measurement errors and incomplete reporting of results. A surveillance model of study would allow for more extensive comprehension of the distribution and trends of determinants and disease, dynamic integration of information from multiple sources, and aid in the development of safe, effective prevention and care models. Participants Protocol 1 Households within each study site were randomly selected. Any non-pregnant individuals permanently residing in the household and at least 20 years of age were eligible for enrollment. 4,943 participants from Chennai, 4,425 participants from New Delhi, and 4,016 participants from Karachi were enrolled in the first surveillance cohort. The study aimed to recruit 6,500 new participants at each of the three sites for the second cohort. Protocol 2 Eligible patients were at least 35 years of age with a diagnosis of diabetes, poor glycemic control (HbA1c ≥ 8.0%), and one or both of: dyslipidemia (LDL ≥ 130 mg/dl) or systolic hypertension (SBP ≥ 140 mmHg), irrespective of medication use. The study enrolled a total of 1,146 patients from ten clinical sites, with 575 randomized to the intervention group and 571 randomized to the usual care group. Protocol 3 Participants were recruited from 38 sub-centers in the Solan district located in the Indian state of Himachal Pradesh. All community members, aged 20 years or older and permanently residing in well-defined rural communities in the selected geographical areas, were eligible to participate. Design Protocols 1/3 The Solan Surveillance study was the rural counterpart of CARRS Surveillance study, and therefore they used similar methodology. The CARRS surveillance study was conducted in three sites: two in India (Chennai and New Delhi) and one in Pakistan (Karachi). The Solan Surveillance study was conducted in the Solan District of Himachal Pradesh, India. Recruitment occurred and data were collected via household surveys. While the primary study design for the surveillance model was cross-sectional, a cohort study design was used to follow-up the participants for three to four years subsequent to the initial cross-sectional study. Baseline surveys gathered information on demographic and socio-economic characteristics, presence of CMDs and risk factors, previous or existing target organ damage, female reproductive history, quality of life, disability, health care utilization, and quality and cost of care. Additional clinical measurements included blood pressure, pulse rate, mid-arm circumference, waist circumference, hip circumference, skinfold thickness, height, and body composition. Each surveillance study implemented a second independent cross-sectional survey several years after the first in order to estimate the trend in prevalence of CMDs and their risk factors. Outcomes of interest included anthropometric changes; incidence of new intermediate risk factors or changes in pre-existing risk factors such as dyslipidemia, hypertension, and diabetes; and morbidity and mortality associated with CMDs. Protocol 2 The CARRS Translational trial was a multi-site, individually randomized, controlled parallel group study that tested a comprehensive, multi-factorial CVD risk reduction intervention in type 2 diabetes patients attending established out-patient clinics in South Asia. The intervention strategies followed internationally accepted evidence-based CVD risk management algorithm-guidelines for individuals with diabetes, with adaptations to increase relevance to the South Asian population. The intervention utilized two major health care management strategies: (1) a web-enhanced decision-support software to store patient health records, provide automated decision-support prompts for patient management, and remind providers and participants of the guideline-recommended care processes, and (2) a non-physician care coordinator to facilitate care according to the CVD risk factor management guidelines, provide individualized follow-up according to baseline risk and compliance, empower and encourage patients to achieve management targets, and coordinate guidance from a multi-disciplinary team. The control group received the existing standard care existing at the clinical site. Potential participants were invited for two pre-randomization screening visits to assess history, anthropometry, blood pressure, heart rate, and to collect a fasting venous blood sample for glucose, HbA1c, lipid profile, creatinine, potassium, sodium, and ALT measurements. At the baseline/randomization visit, all participants underwent further assessments including a detailed history and physical examination, questionnaires (self-management, quality of life, treatment satisfaction, and cost of care), and preventive exams including urine analysis, electrocardiogram, and foot and eye examinations. Participants in the intervention group were scheduled for follow-up every three months, and participants in the control group were scheduled for yearly follow-up. Median follow-up was 28 months. The primary outcome was a sustained relative difference in those achieving multiple risk factor targets (glycemic and BP or lipid control, or both) in the intervention group, compared to the control group. Conclusions Protocol 1 Not available Protocol 2 Compared with usual care, intervention participants achieved larger reductions in HbA1c level and reported higher health related quality of life and treatment satisfaction. The multicomponent care management strategy improved achievement of diabetes care goals. Protocol 3 Not available

  Study phs004776

• NCTN: A Randomized Phase III Study of Ibrutinib (PCI-32765)-Based Therapy vs Standard Fludarabine, Cyclophosphamide, and Rituximab (FCR) Chemoimmunotherapy in Untreated Younger Patients With Chronic Lymphocytic Leukemia (CLL) (E1912)

  Study ID: E1912NCT Number: NCT02048813 ECOG-ACRIN Cancer Research GroupSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Phase III Study of Ibrutinib (PCI-32765)-Based Therapy vs Standard Fludarabine, Cyclophosphamide, and Rituximab (FCR) Chemoimmunotherapy in Untreated Younger Patients with Chronic Lymphocytic Leukemia (CLL) (E1912)Trial Description: This phase III trial studies ibrutinib and rituximab to see how well they work compared to fludarabine phosphate, cyclophosphamide, and rituximab in treating patients with untreated chronic lymphocytic leukemia or small lymphocytic lymphoma. Ibrutinib may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth. Chemotherapy drugs, such as fludarabine phosphate and cyclophosphamide, work in different ways to stop the growth of cancer cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Rituximab is a monoclonal antibody. It binds to a protein called CD20, which is found on B cells (a type of white blood cell) and some types of cancer cells. This may help the immune system kill cancer cells. It is not yet known whether fludarabine phosphate, cyclophosphamide, and rituximab may work better than ibrutinib and rituximab in treating patients with untreated chronic lymphocytic leukemia or small lymphocytic lymphoma. Clinical data presented in the following publication(s):PMID 31365801 PMID 34407545Disease type(s): Hematopoietic Neoplasm/Leukemia - Chronic Lymphoid LeukemiaClinical dataset(s) included:NCT02048813-D1 (PMID 31365801): There are three different datasets (-D1 through -D3) for ECOG-ACRIN trial E1912's primary publication, PMID 31365801. This dataset, NCT02048813-D1, contains baseline characteristics, stratification factors, IGHV mutation status, treatment, second primary cancer, and efficacy data. NCT02048813-D2 (PMID 31365801): There are three different datasets (-D1 through -D3) for ECOG-ACRIN trial E1912's primary publication, PMID 31365801. This dataset, NCT02048813-D2, contains grade 3 and above toxicity data as shown in Table 2 of the paper. NCT02048813-D3 (PMID 31365801): There are three different datasets (-D1 through -D3) for ECOG-ACRIN trial E1912's primary publication, PMID 31365801. This dataset NCT02048813-D3 contains worst grade, treatment-related toxicity data as shown in supplemental Table S7 of the paper. NCT02048813-D4 (PMID 34407545): There are two different datasets (-D4 and -D5) for ECOG-ACRIN trial E1912's publication, PMID 34407545, reporting on measurable residual disease and progression-free survival. This dataset, NCT02048813-D4, contains baseline characteristics, baseline leukocytes, thymidine kinase, and survival data for patients with MRD data that were not already included in NCT02048813-D1.NCT02048813-D5 (PMID 34407545): There are two different datasets (-D4 and -D5) for ECOG-ACRIN trial E1912's publication, PMID 34407545, reporting on measurable residual disease and progression-free survival. This dataset, NCT02048813-D5, contains longitudinal measurable residual disease data.You are encouraged to view the PDF data dictionaries found in the "Documents" tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004233

• Women's Health Initiative Clinical Trial and Observational Study-BioLINCC (WHI-BioLINCC )

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Related Studies: This accession includes only deidentified phenotypic data. Related accessions for WHI include: WHI Cohort (dbGaP phs000200, and Women's Health Initiative Clinical Trial and Observational Study – Imaging (dbGaP phs003824), and Women's Health Initiative - Life and Longevity After Cancer (dbGaP phs004174).Available Data: Data are available from the following: the multi-component clinical trial (CT), the observational study (OS), the extension studies (ES), and the ancillary memory study (MS). Includes outcome data through 3/31/2018.Objectives: The clinical trial assessed the safety and efficacy of three interventions. Specifically, it evaluated (1) the major health benefits and risks of estrogen plus progestin and estrogen alone, (2) the effects of a low-fat eating pattern on risk of colorectal cancer, and (3) the efficacy of calcium with vitamin D supplementation for preventing hip and other fractures. The objective of the memory study was to determine whether estrogen plus progestin therapy protects global cognitive function, and evaluate the therapy's effect on the incidence of dementia and mild cognitive impairment.The observational study is examining the relationship between lifestyle, socioeconomic, health, and other risk factors with cardiovascular, breast cancer, colorectal cancer and osteoporotic fracture outcomes. Secondary objectives include providing more reliable estimates of the extent to which known risk factors predict disease, more precise estimates of new occurrences of disease, and to provide a future resource for the identification of new or novel risk factors especially factors found in blood. Background: The Women's Health Initiative (WHI) is a long-term national health study that has focused on strategies for preventing the major causes of death, disability, and frailty in postmenopausal women, specifically heart disease, cancer, and osteoporotic fractures. The WHI is primarily composed of an observational study (OS), as well a clinical trial (CT) with three components: Hormone Replacement Therapy (HT), Dietary Modification, (DM) and Calcium/Vitamin D supplementation (CaD).Prior to the WHI, observational studies suggested that postmenopausal hormone therapy was associated with a decreased risk of coronary heart disease (CHD). Potential cardioprotection was based on generally supportive data on lipid levels in intermediate outcome clinical trials, trials in nonhuman primates, and a large body of observational studies suggesting a 40% to 50% reduction in risk among users of either estrogen alone or, less frequently, combined estrogen and progestin. Observational studies primarily examining unopposed estrogen preparations have suggested a 30% to 50% reduction in coronary events, and an 8% to 30% increase in breast cancer with extended use. Other research findings indicated that hormone therapy was also associated with a decreased risk of osteoporosis and increased bone density. The WHI HT trials were designed to test the effects of postmenopausal hormone therapy on risk for coronary heart disease and assess overall risks and benefits in predominantly healthy women.The Women's Health Initiative Memory Program (WHIMS) consists of a suite of studies which include cohorts of women who participated in the WHI HT trials. Postmenopausal women have a greater risk than men of developing Alzheimer's disease, but studies of the effects of estrogen therapy on Alzheimer's disease have been inconsistent. Additionally, observational studies have suggested that postmenopausal hormone treatment may improve cognitive function, but data from randomized clinical trials have been sparse and inconclusive.International comparisons and migration studies have suggested that countries with 50% lower fat intake than the US population had approximately one third the risk of colorectal cancer. Additionally, fairly consistent evidence existed for an effect of dietary fat, vegetables and fruits, and grains on colorectal cancer risk from within-country observational studies, although the protective effect of lower fat intake was no longer clear after adjusting for energy intake. The WHI DM trial was the first randomized trial to directly address the health effects of a low-fat eating pattern in predominantly healthy postmenopausal women from diverse racial/ethnic, geographic, and socioeconomic backgrounds.Osteoporosis is a major cause of injury, loss of independence, and death, and contributes to hip fractures. Observational evidence and data from previous randomized clinical trials suggest that calcium and/or vitamin D supplements may slow bone loss and reduce the risk of falls in postmenopausal and elderly women. However, evidence from trials, observational studies, and meta-analyses of calcium and vitamin D supplementation with respect to hip and other fractures was limited at the time the WHI was initiated. In two prior randomized trials, calcium plus vitamin D supplements did not reduce the risk of nonvertebral fractures among older women. When the WHI CaD trial was designed, guidelines recommended daily intakes of 800 to 1200 mg of calcium with 400 IU of vitamin D for the prevention of osteoporosis, which was not met by many American women. Therefore, the WHI CaD trial was designed to test the primary hypothesis that postmenopausal women randomly assigned to calcium plus vitamin D supplementation would have a lower risk of hip fracture and, secondarily, of all fractures than women assigned to placebo. Participants: A total of 68,132 women were randomized into at least one component of the clinical trial. 27,347 women were enrolled in the hormone therapy component with 16,608 in the estrogen plus progestin trial and 10,739 in the unopposed estrogen trial, 48,835 women were enrolled in the diet modification component, and 36,282 women were enrolled in the calcium/vitamin D component. 7,479 women 65 years of age and older at baseline and that participated in the HT trial component were enrolled in the ancillary memory study.Women who were either ineligible or unwilling to participate in the clinical trial component were enrolled in the observational study. For example, many potential participants to the clinical trial component of the study were already undertaking a low fat diet or were using hormone replacement therapy. The effect of the selection process was that women enrolled in the observational study tended to have healthier lifestyles compared to those enrolled in the clinical trial. In total, 93,676 subjects were enrolled in WHI OS, with over 16% being members of a racial/ethnic minority group.The first WHI Extension Study enrolled 115,407 consenting participants from all components of the original WHI study for an additional five years of follow-up, from 2005 to 2010. In 2010, 93,567 women consented to continued follow-up. Design: The clinical trial component of the WHI included three randomized comparisons: hormone therapy, dietary modification, and calcium/vitamin D supplementation. Women could have been randomized into one, two or all three trials.The hormone therapy trial enrolled women to one of two double-blinded trials: estrogen (0.625 mg of conjugated equine estrogens daily) plus progestin (2.5 mg of medroxyprogesterone acetate daily) or estrogen alone. Women with a prior hysterectomy were eligible for the trial of unopposed estrogen. Women with an intact uterus at screening were initially also eligible for unopposed estrogen, but were reassigned to the trial of combined postmenopausal hormones beginning in 1995. Both trials randomized participants 1:1 to either hormone therapy or placebo. A 3-month washout period was required before baseline evaluation of women using postmenopausal hormones at initial screening. Study participants were contacted by telephone 6 weeks after randomization to assess symptoms and reinforce adherence. Follow-up contacts by telephone or clinic visit occurred every 6 months, with clinic visits required annually.The estrogen plus progestin trial was halted in July 2002 after a mean 5.2 years of follow-up because health risks, including increased risk of breast cancer and cardiovascular disease, exceeded benefits. The estrogen alone trial was stopped early in March 2004, because an increased risk of stroke was found with no benefit for coronary heart disease. The primary outcome was coronary heart disease (CHD) (nonfatal myocardial infarction and CHD death), with invasive breast cancer as the primary adverse outcome.The dietary modification trial evaluated the effect of a low-fat, high fruit, vegetable, and grain diet on preventing cardiovascular disease and cancer. Participants were randomly assigned to an intervention or a comparison group in the ratio of 2:3 for cost-efficiency. The intervention was an intensive behavioral modification program, using 18 group sessions in the first year and quarterly sessions thereafter, led by specially trained and certified nutritionists. The program was designed to promote dietary change with the goals of reducing total fat to 20% of energy intake, increasing vegetables and fruits to at least 5 servings daily and grains to at least 6 servings daily. The intervention did not include total energy reduction or weight loss goals. Comparison group participants received a copy of the US Department of Health and Human Services' Dietary Guidelines for Americans and other health-related materials but were not asked to make dietary changes. Dietary intake was monitored using the WHI food frequency questionnaire at 1 year and in a rotating one-third subsample every year thereafter. Women completed a medical update questionnaire every 6 months, and medical records were sought for all women reporting colorectal cancer. The primary outcome was invasive colorectal cancer incidence.Participants in the calcium/vitamin D trial were randomized 1:1 to either supplements or placebo. Active tablets contained 500 mg of elemental calcium (as calcium carbonate) and 200 IU of vitamin D3, to be taken twice daily with meals. The presence and severity of symptoms, safety concerns, and outcomes were ascertained at annual clinic visits and telephone or clinic visits at intervening six-month intervals. Risk factors for fracture were assessed by questionnaire, interview, and clinical examination. The primary outcome was incidence of hip fracture.Participants in the observational study attended a baseline examination and were re-examined three years later. Participants completed annual updates of exposures and clinical outcomes by mail. Final data were collected by mail during the close-out period in April 2004 to March 2005. The major clinical outcomes of interest were coronary heart disease, stroke, breast cancer, colorectal cancer, endometrial cancer, ovarian cancer, osteoporotic fractures, diabetes, and total mortality. Most outcomes were initially ascertained by self-report on an annual questionnaire and documented by hospital and related records. Charts with potential cardiovascular, cancer, and fracture outcomes were sent to the local physician adjudicator for evaluation and classification. Staff at the Clinical Coordinating Center coded and adjudicated all cancers of major interest in the study using standardized SEER guidelines.In 2005, WHI participants were invited to join the Extension Study for an additional five years of follow-up in order to collect long-term outcomes. Participants completed annual data collection forms primarily by mail, similar to the OS follow-up. Women reporting study outcomes were contacted by WHI field center staff to obtain additional details and medical records, which were evaluated by physician adjudicators. In 2010, the woman remaining were invited to join the next Extension Study. In the second extension, women were divided into two groups, one of which would have outcomes documented with medical records (the Medical Records Cohort, MRC), and the other would just be followed by self-report (the Self-Report Cohort, SRC). The MRC consists of women who were in the hormone therapy trials, and all African-American and Hispanic women. In 2012-2013, a subset of the MRC was identified for a potential in-home visit to collect blood and several objective measures of physical functioning.Conclusions: Overall health risks exceeded benefits from use of combined estrogen plus progestin after an average 5.2 year follow-up among healthy postmenopausal US women (Rossouw et al., 2002, PMID: 12117397). Among postmenopausal women aged 65 years or older, estrogen plus progestin did not improve cognitive function when compared with placebo (Rapp et al., 2003, PMID: 12771113), increased the risk for probable dementia, and did not prevent mild cognitive impairment (Shumaker et al., 2003, PMID: 12771112). The use of conjugated equine estrogen increased the risk of stroke, decreased the risk of hip fracture, and did not affect CHD incidence in postmenopausal women with prior hysterectomy after an average of 6.8 years of follow-up (Anderson, et al., 2004, PMID: 15082697). Over approximately 8 years of follow-up, a low-fat dietary pattern did not reduce the risk of colorectal cancer (JAMA 2006;295:643-654). Calcium with vitamin D supplementation resulted in a small but significant improvement in hip bone density; however, no significant difference was observed in hip fractures (Jackson, et al., 2006, PMID: 16481635).

  Study phs004266

• NCI COVID-19 in Cancer Patients Study (NCCAPS): A Longitudinal Natural History Study

  NCCAPS is a longitudinal prospective cohort study designed to assess patient, disease and treatment factors associated with short- and long-term outcomes in patients with cancer who develop COVID-19. We also aimed to describe COVID-19 symptoms and treatments, and to describe disruptions in cancer treatment due to COVID-19. The study enrolled patients with cancer on active treatment or with a history of stem cell transplant or CAR-T cell therapy with new, active COVID-19, defined as being within 14 days of their first positive SARS-CoV-2 test. The study found that receipt of chemotherapy and baseline history of stroke, atrial fibrillation or pulmonary embolism were associated with a higher risk of hospitalization for COVID-19. Vaccination for SARS-CoV-2 was associated with a lower risk of hospitalization. Death due to COVID-19 was highest in patients with lymphoma, intermediate in those with acute leukemia and lung cancer, and lowest in those with other solid tumors and other hematologic cancers. Disruptions of cancer treatment were frequent in the first 30 days after SARS-CoV-2 infection.

  Study phs004178

• Uncovering Colorectal Cancer Etiology and Biology by Integrating Proteomics with Other Omics Data

  This study included the expression profiling of approximately 10,000 proteins generated in normal colon tissue samples collected from 323 participants of European descent, paired with genome-wide genotype data obtained from blood samples. Using these proteomics and genotype datasets, we developed genetically prediction models for protein expression and conducted a proteome-wide association study (PWAS) of colorectal cancer (CRC) in European populations to identify proteins associated with CRC risk.

  Study phs004089

• The Somatic Mutational Landscape of Thyroid Cancer in Patients with Germline PTEN Mutations

  PTEN hamartoma tumor syndrome (PHTS) is associated with a high rate of thyroid cancer and benign thyroid disease, yet nothing is known of the genomic landscape of PHTS-associated thyroid tumors. In this study, exome sequencing was performed on 58 thyroid tumors (28 cancers, 30 benign nodules) from 19 patients with PHTS, sequenced in tumor-normal pairs. Somatic variant calling was utilized to determine the somatic mutational landscape of thyroid tumors in this population. This was then compared to the known mutational landscape of sporadic thyroid cancer in the general population using sequencing data from The Cancer Genome Atlas. The primary finding of the study was that PHTS-associated thyroid tumors had a unique genomic landscape, including a high frequency of second-hit somatic PTEN alterations compared to the sporadic thyroid tumors. Additionally, PHTS-associated thyroid cancers were found to have somatic alterations in BRAF, RAS family members, and genes associated with DNA double stranded break repair. Data available through dbGAP will include tumor BAM files for each tumor, normal BAM files for each patient, and MAF files for PHTS-associated thyroid cancer and PHTS associated benign thyroid nodules.

  Study phs003640

• Chromatin Accessibility Profiling Identifies a Stem Cell-Like Subtype of Small Cell Lung Cancer with Poor Prognosis

  Eight-week-old male or female NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ; #005557, Jackson Laboratory) were subcutaneously implanted with fresh patient needle biopsies. Mice were monitored daily, with caliper measurements and body weights performed twice weekly. Once tumors reached the size limit (2000 mm³) or mice became moribund, the mouse was euthanized, and a 3x3 mm³ tumor fragment was transplanted into a new mouse (P2). This process was repeated to achieve a minimum of passage three (P3) for each patient-derived origin. ATAC sequencing on PDX samples was conducted using the high-throughput Illumina HiSeq 4000 system. The same biopsy samples used for ATAC-seq were utilized for RNA-seq library preparation and sequencing, following the Illumina HiSeq protocol (NCI CCR Sequencing Facility). The study identified the stem cell subtype within Small Cell Lung Cancer (SCLC) cases and identified the gene signature associated with stemness behavior., which were validated in independent limited and extensive stage patients dataset.

  Study phs003983

• Kids First: Genomics of Isolated Cleft Lip

  Isolated Cleft Lip (CL, Human Phenotype Ontology # HP0100335) is a subtype within Orofacial Clefts (OFC, HP0000202) birth defects. OFCs can involve gaps in the lip, alveolus and/or the hard or soft palate. Developmental origins of the affected structures, epidemiology, and familial patterns of CL versus other OFCs suggest some common risk factors, but emerging evidence emphasizes that these subtypes also have unique risk factors. Isolated CL has seldom been investigated separately in genetic studies. Early studies using microsatellite markers prior to the availability of SNP chips found differences in CL families versus other cleft subtypes, notably reporting increased association with certain IRF6 variants in CL families versus other cleft types. With the advent of SNP chips, some studies addressed CL, e.g. genome-wide association of CL was seen with TPM1 and NOG and 9q21.32. We have performed some of the only genome-wide association studies (GWAS) to compare and contrast CL and Cleft Lip with Cleft Palate (CLP). We find evidence that CL and CLP have some distinct genetic risk factors, differences in strength or direction of effects between CL and CLP, and modifying loci that predispose specifically for CL over CLP. Some loci are most-significant in families where all affected members had CL. Modifiers of cleft lip laterality and side of the cleft were more successful in CL than in CLP and the loci identified in CL had no detectable effect in CLP, reinforcing the idea that CL and CLP have distinct risk factors. An overall conclusion from these studies is that CL appears more genetically homogeneous than does CLP, thus highlighting the importance of subtype and family type inclusion in studies of OFCs. Importantly, the homogeneity of CL makes it more amenable to gene discovery in the moderate sample sizes available with whole genome sequencing (WGS). The current project builds upon the GWAS and WGS analyses by our group and others. The WGS data generated will be used to discover new loci for CL, to replicate/prioritize previously published loci, and to aid in determining CL-specific causal genes/alleles. Short Read WGS data available for 1903 individuals include 629 affected probands: 553 CL and 40 CLP (with CL relatives) complete trios, 29 CL and 1 CLP dyads, and 5 CL and 1 CLP singletons. Of the 1903 total individuals, 554 are of European descent, 381 Central/South American descent, 857 of Asian descent, 7 of African descent, and 104 are race other/unknown. With our phenotypic data plus the WGS, we will be able to find new loci, gain better understanding of how risk related to those loci differs across populations, create the knowledge needed to choose loci for follow-up functional studies, build the knowledge needed for accurate risk predictions, and ultimately set the stage for translation into clinical practice. Study Population: The individuals and families utilized in this project were recruited through the Pittsburgh Orofacial Cleft study (POFC) involved research collaborations world-wide coordinated by the Center for Craniofacial and Dental Genetics of the University of Pittsburgh (CCDG). Extensive information is available for many of these trios, including sex, self-reported race and ethnicity, birth date and age at enrollment, phenotypes for affected cases (i.e. extensive detail on the OFC defect in terms of type, laterality, completeness), phenotypes for all affected and unaffected family members (including facial measurements, lip morphology, dental characteristics and many more), vital status and age at last known vital status, clinical information (e.g. surgical and medical history for all affected cases, some limited systems review for unaffected family members), and family medical history (e.g., family history of cancer and birth defects).Molecular Technology: Short Read WGSData Available: Demographics (site, age, sex, race, ethnicity) Cleft details Family level cleft details (i.e. multiplex, clefting maternal side, clefting paternal side, or both) Height/Weight Pregnancy Exposures data (birth height, birth weight, smoking, vitamins, alcohol, epilepsy, gestational diabetes) for 3 months prior to first trimester and first trimester. Subject_IDs from other sequencing studies Data use limitations from the consents The remaining phenotypic/medical/image data for this study are available through FaceBase (facebase.org): DOI: 10.25550/5A-FJBJ and DOI: 10.25550/56-ES6P.

  Study phs003893

• Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor

  Immune checkpoint inhibitors (ICIs) are widely used in anti-cancer therapies, but they can cause morbid and potentially fatal immune-related adverse events (irAEs), such as ICI-related myocarditis (irMyocarditis). The pathogenesis of irMyocarditis and its relationship to anti-tumor immunity remain poorly understood. We sought to define immune responses in heart, tumor, and blood in irMyocarditis patients and controls by leveraging single‐cell RNA sequencing (scRNA‐seq) coupled with T-cell Receptor Sequencing (TCR-Seq). Our analysis demonstrated increased frequencies of cytotoxic T cells, inflammatory mononuclear phagocytes (MNPs), conventional dendritic cells (cDCs), and inflammatory fibroblasts in irMyocarditis heart tissue. Additionally, we revealed decreased frequencies of plasmacytoid dendritic cells, cDCs, and B lineage cells but an increased frequency of MNPs in the blood of irMyocarditis patients. Raw data for heart and blood can be found in dbGaP. All processed data and raw TCRseq data from heart tissue and tumor samples for this study can be found in GEO (Accession number GSE228597).Subject IDs with the prefix "SIC" were collected by the Severe Immunotherapy Complications (SIC) service at MGH due to suspicion of immune-related adverse events. Subject IDs with the prefix "donor" were collected by the MGH Melanoma Biobank at scheduled timepoints; this biobank systematically collects samples from patients at MGH at clinically relevant timepoints.

  Study phs003413

• Detroit Research on Cancer Survivors (ROCS) and Disparities and Cancer Epidemiology - Colorectal Cancer (DANCE)

  The goals for this study were as follows:1. Enroll a total of 5,060 African Americans newly diagnosed with cancer into the Detroit Research on Cancer Survivors (Detroit ROCS) Cohort. These population-based cases will be ascertained through the Detroit Metropolitan Detroit Cancer Surveillance System (MDCSS), a founding member of the NCI SEER Program. Participation at baseline will include a written, web-based, or telephone interview, saliva and/or blood collection, and tumor block retrieval, with detailed cancer-related information coming from the MDCSS registry and medical records.2. Enroll a subgroup of colorectal cancer patients identified through the Louisiana Tumor Registry (LTR). An additional 500 colorectal cancer patients, approximately half non-Hispanic white and half African American, will be identified through the LTR and enrolled into the ROCS protocol. The survey is the same survey administered to the ROCS cohort. The Louisiana (“DANCE-CRC”) cohort will not be followed beyond baseline, and blood will not be collected (tumor tissue, however, will be collected, deidentified, and sent for processing through Dr. Rozek's laboratory at Georgetown University).The proposed cohorts will provide for a broad research agenda evaluating cancer outcomes in African Americans across a variety of factors from individual, provider, health care system and community perspectives. These factors include tumor characteristics driving individualized treatment planning, quality of life after a diagnosis and recurrence. Utilizing the MDCSS registry, we will enroll a large population-based sample of African-American cases with lung, breast, colorectal, and prostate cancers and their caregivers resulting in a cohort that will provide substantial benefit to the cancer research community. KCI has a strong history of research in the African-American community and the faculty represents a breadth of experience that includes clinical oncology, genetic epidemiology, environmental exposures, quality of life, treatment decision making, racism/discrimination, and health behaviors. Drs. Schwartz and Beebe-Dimmer have been and will continue to be generous collaborators with other institutions to ensure that this resource will be extensively utilized. The proposed overall cohort will be the only one of its kind, to our knowledge, filling a substantial gap in our understanding of the determinants driving cancer outcomes in African Americans. In addition to registry data detailing cancer specifics, yearly surveys have collected information about individualized treatment experiences, heath histories, family histories, quality of life after a diagnosis, recurrence and caregiving. Population: Adult cancer survivors (see inclusion criteria in next section) Molecular Technologies: Genotyping: Infinium Expanded Multi-Ethnic Genotyping Array (MEGAEX) DNA Sequencing: Illumina NovaSeq X Plus using XLEAP-SBS (sequencing by synthesis) Whole genome sequencingPrincipal Findings: The preliminary data collected reinforces differences by race in factors affecting cancer outcomes. Variants in DNA damage repair genes and HOXB13 may be important cancer risk factors for Black men diagnosed with prostate cancer, and are more frequently observed in men with a family history of cancer. ROCS participants reported high rates of a family history of cancer. The high rate of eligibility for Cancer genetic counseling among ROCS participants supports the need for interventions to increase referrals and uptake of genetic counseling among African Americans 60% of ROCS participants reported participating in regular physical activity (PA), with 24% reporting ≥150 min/wk. There were no differences by sex, but prostate cancer survivors were the most likely to report participating in regular PA, whereas lung cancer survivors were the least likely. Survivors who reported participating in regular PA reported higher health-related quality of life and lower depression. More African American than White survivors reported financial hardship and limiting care. More White than African American survivors reported utilizing assets, while more African American survivors reported cancer-related debt. Data available in dbGaP: Individual phenotype data Individual genotype data Individual sequencing dataSample types: Germline DNA

  Study phs003116

• An Ultrasensitive Method for Detection of Cell-Free RNA

  Our study describes the development of a novel method for cell free RNA (cfRNA) analysis called RARE-Seq (Random priming & Affinity capture of cell-free RNA fragments for Enrichment analysis by Sequencing). We find RARE-Seq improves the limit of detection for tumor-naïve cancer detection while maintaining high specificity. We explore the potential utility of RARE-Seq in diverse clinical applications, including non-invasive ctRNA genotyping, treatment resistance monitoring, and molecular characterization of non-malignant conditions.

  Study phs004091

• Interdisciplinary Approaches for Understanding how Arsenic and Micronutrients Affect the Epigenome to Influence Spina Bifida Risk

  This hospital-based case-control study was conducted in Bangladesh between December 2016 and December 2022 to investigate the association between environmental arsenic exposure and the risk of spina bifida. The study enrolled children with spina bifida (cases) and unaffected children (controls), along with their biological parents. Cases included infants under one year of age with clinically confirmed diagnoses of myelomeningocele or meningocele at the National Institute of Neurosciences & Hospital (NINS). Controls were frequency-matched on age and recruited from the same catchment area through NINS and Dhaka Shishu Hospital. Children with conditions potentially related to arsenic exposure, such as keratosis or cancer, were excluded from the control group. A small subset of case families were reclassified as controls following surgical reevaluation and a revised diagnosis of lipomeningocele, then later removed from the control group. They are no longer assigned to either the case or control category in the datasets. Saliva samples were collected from children and parents using Oragene® kits and stored at room temperature before shipment to Boston, MA, USA. DNA extraction was carried out with the Maxwell® RSC Buccal Swab DNA kit. A total of 749 saliva DNA samples, representing 713 unique individuals and 36 replicates, were shipped to the Broad Institute for analysis. Samples were randomized across Illumina Global Screening Array (GSA) chips to minimize batch effects. The primary molecular technology employed in this study was the Illumina Global Screening Array (GSAMD-24v1-0), which includes approximately 688,000 genetic markers. Data generated include raw and processed genotype files as well as a comprehensive quality control report. The genotyping dataset available through dbGaP will consist of genotype calls from spina bifida cases, controls, and their parents, along with associated demographic, clinical, and exposure metadata, enabling future analyses of gene-environment interactions in the context of neural tube defect risk.

  Study phs003733

• Real-Time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine

  Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole exome sequencing (WES) and RNA-sequencing (RNA-Seq) for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data. Twenty-six patients had germline and/or somatic alterations in DNA-damage repair genes, and 5 additional patients had mutational signatures of homologous recombination deficiency but no identified causal genomic alteration. Two patients had oncogenic in-frame BRAF deletions, and we report the first clinical evidence that this alteration confers sensitivity to MAP-kinase pathway inhibition. Moreover, we identified tumor/stroma gene expression signatures with clinical relevance. Collectively, these data demonstrate the feasibility and value of real-time genomic characterization of advanced PDAC.

  Study phs001652

• APOBEC Mutagenesis, Kataegis, Chromothripsis in EGFR-Mutant Osimertinib-Resistant Lung Adenocarcinomas

  Expanding on studies investigating apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) mutagenesis in histological transformation of epidermal growth factor receptor (EGFR)-mutant lung cancers, it has been hypothesized that mutational signature analysis may help better understand acquired resistance to targeted therapies. Using mutational signature analysis in Receptor Tyrosine Kinase (RTK) driven lung adenocarcinomas, more specifically EGFR mutant lung cancer, APOBEC dominant mutational signatures were noted more frequently in subclonal post Tyrosine Kinase Inhibitor (TKI) treatment biospecimen samples and in the presence of large-scale genomic rearrangements. This is hypothesized to be due to the pressure of treatment with TKIs; a fact that should be further explored and can be potentially manipulated in order to overcome drug resistance.

  Study phs003812

• scRNA-seq of Multiple Myeloma and Tumor Microenvironment Cells from Bone Marrow During CAR T-Cell Therapy

  Multiple myeloma (MM) is a treatable, yet incurable, plasma cell malignancy for which molecular mechanisms driving the development of therapy resistance remain largely elusive. To better characterize tumor intrinsic and immune tumor microenvironment (iTME) factors associated with CAR T-cell efficacy, scRNAseq (10x Genomics V3.1) was performed on purified MM cells (CD138+) and associated iTME cells (CD138- mononuclear cells) from fresh bone marrow aspirates harvested prior to therapy in 13 patients treated at Moffitt Cancer Center. After biopsy, 7 of these patients were treated with ABECMA (idecabtagene vicleucel or ide-cel) and 6 were treated with ciltacabtagene autoleucel (cilta-cel or CARVYKTI®). Bone marrow biopsies were collected between 2021 and 2023. In addition to the molecular data, demographic information for the samples is provided. These data allow for the assessment of transcriptional signatures at the single-cell level in both the tumor and its bone marrow iTME, associated with CAR T-cell therapy in MM patients.

  Study phs004878

• Genome Sequencing of Individuals with PTEN Hamartoma Tumor Syndrome

  This study investigated genomic modifiers of cancer and neurodevelopmental outcomes among individuals with PTEN hamartoma tumor syndrome (PHTS), a rare hereditary disorder caused by germline PTEN variants and associated with broad clinical variability, including cancer predisposition, autism spectrum disorder, developmental delay, and intellectual disability. The primary aim was to determine whether additional inherited genomic variation beyond PTEN contributes to divergent clinical manifestations, particularly the development of cancer versus neurodevelopmental disorders.The main analytic cohort consisted of 543 probands with germline PTEN variants, including participants with cancer, neurodevelopmental disorders, both cancer and neurodevelopmental disorders, or neither phenotype at the time of consent.Molecular data were generated from germline DNA extracted from peripheral blood leukocytes using PCR-free whole-genome sequencing at approximately 30× coverage. Sequence reads were aligned to the hg38 human reference genome, followed by standard variant calling, quality control, annotation, and downstream genomic analyses. The study evaluated pathogenic or likely pathogenic variants in established cancer predisposition genes and neurodevelopmental disorder genes, and also performed genome-wide common-variant and rare-variant association analyses to identify candidate modifier loci.Principal findings showed that a subset of individuals with PHTS carried additional germline variants in known cancer- or neurodevelopment-related genes. Specifically, additional cancer-associated variants were identified in 37 of 543 probands, most commonly involving MITF, DICER1, and BRCA2, while neurodevelopment-associated variants were identified in 43 of 543 probands, including variants in DHCR7, POLG, ARSA, and other genes. Genome-wide analyses further identified candidate modifier loci with potential biological relevance to PTEN signaling and phenotype divergence, including ZNF713, TPTE2P1, and PDPK1. These findings support the hypothesis that PHTS clinical outcomes are influenced not only by germline PTEN variation, but also by additional inherited genomic modifiers.Data to be made available through dbGaP will include de-identified individual-level germline whole-genome sequencing data and associated phenotype information relevant to PHTS, cancer status, neurodevelopmental status, demographic variables, and PTEN variant classification, consistent with participant consent and institutional certification. The individual-level data are intended for controlled access.

  Study phs004787

• A Personalized Neoantigen Vaccine Generates Anti-Tumor Immunity in High-Risk Renal Cell Carcinoma

  Personalized cancer vaccines (PCVs) can generate circulating immune responses against predicted neoantigens. However, whether such responses can target cancer driver mutations, lead to immune recognition of a patient's tumor, and result in clinical activity are largely unknown, particularly in patients with lower mutation burden tumors. We conducted a phase I trial testing a neoantigen-targeting PCV in patients with high-risk, fully resected clear cell renal cell carcinoma (RCC; stage III or IV), with or without ipilimumab administered adjacent to the vaccine. At a median follow-up of 40.2 months from surgery, none of the 9 initial participants experienced a recurrence of RCC. No dose-limiting toxicities were observed. All patients generated T cell immune responses against PCV antigens, including RCC driver mutations in VHL, PBRM1, BAP1, KDM5C, and PIK3CA. Following vaccination, there was a durable expansion of peripheral T cell clones, and T cell reactivity against autologous tumor was detected in 7 of the 9 patients. Our results demonstrate that neoantigen-targeting PCVs in high-risk RCC are highly immunogenic, capable of targeting key driver mutations, and induce anti-tumor immunity. These observations, in conjunction with the absence of recurrence in all 9 vaccinated patients, highlights the promise of PCV as effective adjuvant therapy in RCC. We are submitting whole exome sequencing (WES) data from whole blood samples and tumor FFPE samples, and RNA-Seq data from tumor FFPE samples. We are also submitting RNA-Seq data from purified tumor samples. Single-cell RNA sequencing (scRNA-seq) data will be submitted for skin samples (vaccine site biopsies at weeks 0, 4, and 13), tumor samples (including resected metastatic tumor samples for two patients), and normal kidney samples. Bulk T-cell receptor sequencing (TCR-seq) data will be submitted for blood samples.

  Study phs003710

• Single-Cell RNA-Sequencing of Human Prostatectomy Tissue

  The tissue microenvironment in prostate cancer is profoundly altered. How prostate cancer cells and their precursors mediate those changes is unclear, in part due to the inability to longitudinally study the disease evolution in human tissues. To overcome this limitation, we performed extensive single-cell RNA-sequencing (scRNA-seq) to assess the transcriptional profiles of the tissue microenvironment in prostate tissues from prostatectomies from men diagnosed with prostate cancer. For each subject, benign-enriched and tumor-enriched tissues were collected from the peripheral zone of the prostate. Additionally, to understand zone-specific differences of the prostate, benign tissues were also collected from the transition and central zones.

  Study phs003480

• Genomic Alterations and Transcriptional Phenotypes in Circulating Tumor DNA and Matched Metastatic Tumor

  We analyzed a prospective cohort of 49 plasma samples obtained before, during, and after treatment from 20 patients with recurrent small cell lung cancer. We conducted cfDNA low-pass whole genome sequencing (0.1X coverage) and exome sequencing (130X coverage) in comparison with time-point matched tumor characterized using whole-exome (130X) and transcriptome sequencing. A direct comparison of cfDNA and tumor biopsy revealed that cfDNA not only mirrors the mutation and copy number landscape of the corresponding tumor, but also identifies clinically relevant resistance mechanisms and cancer driver alterations not detected in matched tumor biopsies. Longitudinal cfDNA analysis reliably tracks tumor response, progression, and clonal evolution. Sequencing coverage of plasma DNA fragments around transcription start sites showed distinct treatment-related changes and captured the expression of key transcription factors n the corresponding SCLC tumors.

  Study phs003689

• Women's Health Initiative (WHI) - Life and Longevity After Cancer (LILAC) (WHI-LILAC-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: The LILAC substudy was initiated to collect information on cancer treatment and long-term outcomes in women diagnosed with eight selected cancers during their participation in WHI.Background: Improvements in early detection and treatment have led to a surge in the number of cancer survivors in the United States creating a demand for a better understanding of their health concerns. Cancer survivor health concerns are diverse and complex due to the heterogeneity among individuals, cancer type, and treatment variability. To effectively examine these concerns, new resources need to be developed, including a much more comprehensive assessment on a large sample with longer-term follow-up than is typically available in cancer clinical trials. The WHI cohort, which is a large study with long-term follow-up, continues to be a good resource to study issues related to aging and health. The LILAC substudy was initiated with WHI participants who had been diagnosed with cancer to examine cancer survivorship among older women.Participants: Participants with no cancer (other than non-melanoma skin cancer) prior to enrollment in WHI and a confirmed invasive cancer diagnosis during WHI follow-up of one of the eight selected cancers were eligible for LILAC.A total of 9934 WHI participants living with cancer were eligible. Of those, 7751 consented and returned the baseline survey. This included 821 participants with melanoma, 781 participants with colorectal cancer, 648 participants with endometrial cancer, 397 participants with lung cancer, 4173 participants with breast cancer, 442 participants with non-Hodgkin lymphoma, 181 participants with leukemia, and 208 participants with EOC (which includes ovarian, fallopian tube and primary peritoneal cancers). Design: Participants still in active WHI follow-up who were eligible for the LILAC substudy were sent an invitational mailing that included a baseline survey. Baseline surveys collected data on initial cancer treatment, symptoms after treatment completion, and quality of life. WHI participants who consented to the LILAC substudy were subsequently sent annual surveys. Annual surveys collected any updates on treatment, as well as other topics related to cancer survivorship such as social support. Additional treatment information was obtained from Medicare claims and medical records.Conclusions: The LILAC substudy provides a resource for studying cancer survivorship among older women diagnosed with eight selected cancers.

  Study phs004174

• Effector CD4 T Cells Convert Transient Responses to KRAS-Targeted Therapy into Long-Term Durable Remissions in Pancreatic Cancer

  Pancreatic ductal adenocarcinoma (PDAC) is refractory to most therapies, including immunotherapies in which reinvigoration of CD8 T cells is insufficient to induce durable long-term remissions. Direct KRAS inhibitors are clinically promising; however, acquired resistance is common. Using AI-assisted computational design, we developed a de novo IL-21 mimic, 21h10, with enhanced stability and high signaling potency in both humans and mice. Using an orthotopic PDAC mouse model, we evaluated responses and relapse following KRAS inhibitor treatment and demonstrated that, unlike combinations with chemotherapy or checkpoint blockade, the combination of 21h10 and KRAS inhibition is curative. Single-cell transcriptional profiling with TCR-seq revealed oligoclonal expansion of effector Th1-polarized CD4 T cells and depletion of Tregs. To evaluate the efficacy of 21h10 in human samples, we performed single-cell RNA-seq analyses on treatment-naive specimens following short-term ex vivo treatment with 21h10. This dataset consists of Illumina NovaSeq sequencing output (FASTQ files) generated from tumor libraries prepared using the 10x Genomics Single Cell 5′ Immune Profiling platform. FASTQ files are provided for gene expression (GEX), TCR, and, for multiplexed samples, HTO libraries.

  Study phs004509

• NCTN_NCORP: Phase III Trial of LHRH Analog Administration During Chemotherapy to Reduce Ovarian Failure Following Chemotherapy in Early Stage, Hormone-Receptor Negative Breast Cancer (S0230)

  Study ID: S0230NCT Number: NCT00068601 SWOG Cancer Research NetworkSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN_NCORP: Phase III Trial of LHRH Analog Administration during Chemotherapy to Reduce Ovarian Failure following Chemotherapy in Early Stage, Hormone-Receptor Negative Breast Cancer (S0230)Trial Description: RATIONALE: Goserelin blocks hormone production in the ovaries. It is not yet known whether ovarian suppression using goserelin will prevent ovarian failure (early menopause) in women receiving chemotherapy for breast cancer.PURPOSE: This randomized phase III trial is studying how well giving goserelin together with chemotherapy works compared with chemotherapy alone in preventing early menopause in women with stage I, stage II, or stage IIIA breast cancer. Clinical data presented in the following publication(s):PMID 25738668Disease type(s): Breast Neoplasm - Breast Cancer - InvasiveClinical Dataset(s) included:NCT00068601-D1 (PMID 25738668): There is one dataset for S0230's primary publication 25738668. This dataset contains baseline characteristics, planned chemotherapy regimen, hormone receptor status, premature ovarian failure, fertility, survival, ovarian failure, and adverse event data.You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004261

• Botensilimab, an Fc-enhanced Anti-CTLA-4 Antibody, is Effective Against Tumors Poorly Responsive to Conventional Immunotherapy

  This study explores the genomic landscape associated with a novel Fc-engineered anti-CTLA-4 antibody (botensilimab) in advanced solid tumors. We seek to understand if enhancing the Fc-region affinity of anti-CTLA-4 antibodies can improve anti-tumor efficacy and expand clinical benefit to tumors poorly responsive to conventional immunotherapy. As part of an ongoing open-label, Phase 1, multicenter study, we conducted an exploratory sub-analysis of genomics data. The primary study evaluates the safety, tolerability, pharmacokinetics, and pharmacodynamics of botensilimab monotherapy and in combination with an anti-PD-1 antibody (balstilimab) in participants with advanced solid tumors. RNA from formalin-fixed paraffin-embedded (FFPE) tumor biopsies and matched normal blood samples were isolated and subjected to RNA-sequencing using the Personalis ImmunoID NeXT Platform. We demonstrated that anti-CTLA-4 engineered for enhanced FcγR affinity leverages FcγR-dependent mechanisms to potentiate T cell responsiveness, reduce intratumoral Tregs, and enhance antigen presenting cell activation. This genomic analysis contributes to our understanding of the molecular mechanisms underlying patient responses to Fc-engineered anti-CTLA-4 therapy and may inform future strategies to expand the clinical benefit of immune checkpoint blockade in cancer immunotherapy.

  Study phs003704

• Open-Label, Phase I study of NeoVax with Nivolumab in Patients with Ovarian Cancer

  Personalized neoantigen-targeting cancer vaccines (PCV) in the adjuvant setting are of increasing interest across malignancies. Herein, we report the results of a first-in-disease phase I clinical trial testing the feasibility and safety of PCV for high-grade epithelial ovarian cancer (HGOC). ‘NeoVax' consisted of pools of synthetic long peptides targeting patient-specific neoantigens admixed with the immunostimulant poly-ICLC, was combined with delayed administration of anti-PD-1 antibody, and was tested in 10 patients (one newly diagnosed patient (Cohort A) and 9 patients at first recurrence (Cohort B)) with platinum-sensitive OC following standard-of-care (SOC) platinum doublet chemotherapy. Nine of 12 evaluable Cohort B patients were vaccinated (75%, 90% CI 47-93%) and 1 of 9 Cohort A patients (11%, 90% CI 0.6 – 43%). No unexpected safety signals were encountered, and no patients discontinued treatment due to toxicity. Across patients, >70% selected targets remained detectable by non-invasive cell-free DNA analysis despite a median of 6.5 months from the time of diagnostic biopsy to vaccine administration, during which patients received SOC chemotherapy. Biomarker analysis was suggestive of biologic activity of the vaccine in 6 of 10 patients and this was associated with broader tumor and vaccine-specific immune responses in blood and tumor following vaccination. Resistant tumor clones reflected diverse mechanisms affecting antigen presentation, indicative of immune-selective pressure exerted by vaccination. Overall, the interplay between the repertoire of antigens presented by the tumor and the breadth of induced immunity appeared to dictate clinical efficacy following vaccination.We are submitting:WES and WGS data from whole blood samples and tumor FFPE samplesRNA-seq data from tumor FFPE samplesscRNA-seq and scTCR-seq data from tumor biopsiesBulk TCR-seq data from CD3+ PBMC from blood samplesWGS and RNA-seq data from organoids

  Study phs004380

• BPH Tissues for Cell Culture and Analysis - A Patient-Derived Xenograft Model Using Benign Prostatic Tissues

  Our goal was to establish and characterize a patient-derived xenograft model for benign prostatic hyperplasia (BPH) using human benign prostatic tissues. Characterization of the model was done by histology, immunohistochemistry, proteomics, and transcriptome analysis (RNAseq). The RNAseq data will be deposited in dbGaP. Subjects were undergoing prostatectomy for prostate or bladder cancer, with concurrent BPH, and consented to the use of surplus tissue for research studies. The RNAseq studies included 6 patients. Phenotypic data include patient age, sex, prostate size, serum prostate-specific antigen (PSA) level, and international prostate symptom score (IPSS). Sequencing was done on an Illumina NovaSeq 6000, and data were analyzed using Kallisto. Data are submitted as raw sequencing (fastq) files.

  Study phs003692

• A Phase 1-2 Study of the Combination of Olaparib and Tremelimumab in BRCA1 and BRCA2 Mutation Carriers with Recurrent Ovarian Cancer (NCT02571725)

  INST1419: A phase 1-2 study of the combination of olaparib and tremelimumab in BRCA1 and BRCA2 mutation carriers with recurrent ovarian cancer (NCT02571725) was designed to evaluate the safety and efficacy of combined treatment with the PARP inhibitor olaparib and the CTLA4 immune checkpoint inhibitor tremelimumab in women with recurrent ovarian cancer and a germline BRCA1 or BRCA2 mutation. This was a multi-site single-arm open-label study that enrolled 50 subjects with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer between 2016 and 2020. Treatment efficacy was assessed using best overall response by modified WHO (mWHO) criteria, and secondary endpoints included disease control rate, duration of response, and progression-free and overall survival. The median age was 56 (range 39-78). All patients had measurable disease and pathogenic germline mutations in BRCA1 (72%) or BRCA2 (28%). Subjects received 300mg of olaparib by mouth, twice daily, and tremelimumab at 10mg/kg IV every four weeks for 6 doses, and then every 12 weeks for up to 24 months. Following an interim data safety monitoring review in 2018, the protocol was modified to reduce the frequency of tremelimumab infusions to 10mg/kg IV every four weeks for 4 doses, followed by infusions every 12 weeks. Exploratory biomarker assessments were performed using archived formalin-fixed paraffin-embedded (FFPE) tumor samples collected at the time of initial cytoreductive surgery from 33 subjects. Clinical characteristics and outcomes for the biomarker cohort were similar to the overall and response cohorts. Candidate biomarkers were identified based on differential gene expression in samples from patients with clinical benefit from treatment, defined as disease control for at least 12 weeks, versus those with progressive disease. For RNAseq, sample integrity was assessed using Agilent Tapestation, to ensure the DV200 was greater than or equal to 30. Sequencing was done on the Illumina NovaSeq instrument by Personalis. Gene expression used in this analysis was the normalized measure defined as transcripts per million (TPM) total RNA molecules. Welch's t-test was used to assess whether there was a difference in gene expression based on clinical benefit. The area under the receiver operating characteristic curve (AUC) was also computed for TPM gene expression based on clinical benefit. The AUC, as determined by the trapezoidal rule, was estimated by the concordance index (SAS 9.4 LOGISTIC procedure). DNA quality was confirmed if the DNA integrity number was greater than or equal to 3. Exome enrichment was performed using the Accuracy and Content Enhanced (ACE) version 4 (ACE ImmunoID NeXT) enrichment platform of Personalis. Briefly, DNA from tumor and cryopreserved PBMC samples were used to construct whole-exome capture libraries, and additional custom probes and optimized chemistry improved uniformity of coverage in sequence regions of high G-C content across the exome using ACE technology. Sequencing was performed at 20 Gigabase (G) sequencing depth for normal samples and 35G sequencing depth for tumor samples. All DNA and RNA reads were aligned to the hs37d5 reference genome built in accordance with the Personalis ACE Cancer Exome Analysis Pipeline, duplicate reads were removed, and the Genome Analysis toolkit was used to correct base quality scores and improve sequence alignment. Mutational burdens were generated using tumor-specific genomic events (SNVs, indels and fusions) of at least 5% allelic fraction that were verified using transcriptomic data. All potential neoepitopes were created for each mutation and tested for presentation, and considered putative neoepitopes if they were predicted to bind to any patient-specific alleles. The Xenium platform was used for spatial transcriptomic analyses using Xenium slides and sample prep reagents (10x Genomics). The immune panel was augmented with custom-ordered genes. Initial preprocessing included quality control, normalization, batch correction, and clustering. Cells with fewer than 20 detected features were excluded as low-quality. High-quality cell-by-gene count matrices were processed using Seurat 5.3.0, with normalization performed using SCTransform. Batch correction was carried out using Harmony integration, following standard preprocessing: individual dataset normalization, merging, PCA (RunPCA), and integration via RunHarmony. Clustering was performed on the Harmony-corrected embeddings using FindNeighbors and FindClusters (resolution = 0.03), and visualized with UMAP (RunUMAP). Cell types were initially assigned using SingleR with the HPCA reference dataset. To resolve cellular heterogeneity, subclustering was performed on select clusters using the FindSubCluster function in Seurat. Canonical marker genes used for cell type identification included CD3E for T cells, MS4A1 for B cells and EPCAM for epithelial and DCN for fibroblasts. Results from this trial demonstrated grade 3 or 4 non-hematologic toxicity in 57% of subjects. The overall response rate was 32.7% (95% CI 19.5-45.8%), with a disease control rate of 47.7% (95% CI 33.0-62.5%). In exploratory biomarker analyses, low VSTM5 or IFIT1B expression predicted treatment benefit and progression-free survival (pData available through dbGaP include RNAseq, whole exome sequencing, and Xenium spatial transcriptomic data.

  Study phs004512

• Epigenomics of Prostate Cancer from Cell Free Plasma

  We sought to perform epigenomic characterization of prostate cancers by profiling circulating nucleosomes isolated from patient plasma using cell free chromatin immunoprecipitation followed by sequencing (cfChIP-seq). Our major findings include identification of prostate-cancer specific regulatory elements using a novel statistical method accounting for variable tumor DNA fraction in plasma, inferring transcription factor activity based on binding motif enrichment within regulatory elements, and epigenetically phenotyping patients based on clinical and genomic features. Data available in dbGaP will include cfChIP-seq and targeted sequencing from approximately 50 patients with a known diagnosis of cancer and healthy patient controls.

  Study phs003482

• HINTS Geo-Coded Data 2017 (HINTS 5 Cycle 1)

  The Health Information National Trends Survey (HINTS) is a nationally representative survey which has been administered every few years by the National Cancer Institute since 2003. HINTS 5 includes four data collection cycles over the course of four years. The first round of data collection for HINTS 5 (Cycle 1) was conducted from January 25 through May 5, 2017 with a goal of obtaining 3,500 completed questionnaires, with a final sample including 3,285 respondents.

  Study phs004210

• WGS of Five Pancreatic Cancer Patients-Tumor and Normal

  We performed whole genome sequence on tumor-derived and normal cell lines from patients who had terminal pancreatic cancer and consented for rapid autopsy upon their death. The 5 samples are from Dr. Christine Iacobuzio-Donahue's rapid autopsy program as reported in Boland et al. (PLOSOne, 2024, In Press, PMID 38352348).

  Study phs003775

• Luminal Androgen Receptor-Enriched Triple Negative Breast Cancer

  This is a study to determine the efficacy of androgen receptor (AR) inhibitors in LAR (luminal androgen receptor)-enriched triple-negative breast cancer (TNBC) in the neoadjuvant setting. Twenty-four patients were treated with neoadjuvant AR inhibitor enzalutamide and paclitaxel for 12 weeks. Whole exome sequencing and RNA-sequencing was performed prior to treatment. The data for only two patients are consented for release through dbGaP. The remaining data are available under a Materials Transfer Agreement with the University of Texas MD Anderson Cancer Center.

  Study phs003586

• Field Effect-Informed Urine Liquid Biopsy Analysis for Assessment of Adjuvant BCG Response in Non-Muscle Invasive Bladder Cancer

  The goal of this study was to develop a urine tumor DNA-based minimal residual disease liquid biopsy assay for bladder cancer that improves specificity by considering field effect mutations. We performed targeted cell free DNA sequencing on tumor, adjacent normal, and urine cell free DNA (cfDNA) from non-muscle invasive bladder cancer patients and urine cfDNA from healthy controls. We developed a method called RePhyNERX and used it to identify three molecular response classes: complete responders to surgery, responders to adjuvant Bacillus Calmette-Guérin immunotherapy, and non-responders. These molecular classifications correlated with patient outcome. We also performed RNA sequencing on tumor tissues to identify expression differences between the response classes.

  Study phs004110

• The Discovery and Validation of AML Prognostic Biomarkers

  This study includes RNA-Seq and targeted DNA sequencing from a large collection of unsorted mononuclear cells (MNCs) and enriched viable leukemic blasts (VLBs) from bone marrow (BM) and peripheral blood (PBL) specimens collected at diagnosis from adult patients with acute myeloid leukemia (AML). Viable leukemic blasts were isolated using forward by side scatter, DAPI staining and fluorescently-labeled antibodies to CD45, CD34, CD38, and CD117. DNA and RNA were extracted using Qiagen AllPrep DNA/RNA Extraction kits. Transcriptome libraries were generated using KAPA Stranded RNA-Seq Library Preparation Kit after ribosomal RNA depletion with Roche RiboErase. Paired-end 75 bp reads were sequenced on either Illumina HiSeq 2500 (HiSeq) or NovaSeq 6000 (NovaSeq) instruments. RNA-Seq data were analyzed by the Fred Hutch Cancer Center Bioinformatics Shared Resource. STAR 2.7.1, with 2-pass mapping, was used to align reads to human reference genome GRCh37/hg19. Internal tandem duplication in FLT3 (FLT3-ITD) were identified via fragment analyses. DNA was sequenced using Illumina TruSight™ Myeloid Sequencing Panel and supplemented with in-house targeted MiSeq assays for CEBPA and NRAS exon 3 loci inadequately covered by TruSight™ platform on Illumina MiSeq instrument. Paired-end reads were first aligned to the human genome reference assembly (GRCh37/hg19) using Burrows-Wheeler Aligner (BWA, v0.7.12) and then, the resulting alignment data were processed according to the best practice of Genome Analysis Toolkit (GATK, v3.5).

  Study phs002805

• Southern Community Cohort Study - the Gut Microbiome Project

  The Southern Community Cohort Study (SCCS) is an ongoing prospective cohort study, with the aim to investigate risk factors of cancer and other chronic diseases across 12 southeastern U.S. states: Alabama, Arkansas, Florida, Georgia, Kentucky, Louisiana, Mississippi, North Carolina, South Carolina, Tennessee, Virginia, and West Virginia. Approximately 86,000 adults, two-thirds Black people, between 40 and 79 years of age were enrolled from 2002 to 2009. Approximately 86% of the participants were recruited from community health centers (CHCs) and institutions providing basic health care and preventative services in underserved areas, so the cohort encompassed a substantial number of individuals characterized by low income, low education, and lack of insurance. The remaining 14% of cohort participants were recruited through mail-based general population sampling. Sociodemographic characteristics, lifestyle factors including tobacco exposure and alcohol consumption, and personal medical history were collected at cohort enrollment. Data collection methods varied by recruitment source: CHC participants completed standardized computer-assisted personal interviews, while individuals from the general population responded to self-administered mailed questionnaires. The SCCS Biospecimen Repository includes blood samples from ~40,000, mouth cells from 39,000, urines from 24,000, stool specimens from 8,000 participants, and tumor blocks from incident cancer cases. This microbiome study nested within SCCS included 594 Black participants whose stool samples were analyzed using shotgun metagenomic sequencing. We investigated associations between the gut microbiome and several physical activity measures.

  Study phs004716

• Childhood Cancer Data Initiative (CCDI): NCI-COG Pediatric MATCH Precision Medicine Clinical Trial

  The National Cancer Institute-Children's Oncology Group (NCI-COG) Pediatric Molecular Analysis for Therapy Choice (MATCH) trial provides a framework for biomarker-driven early phase trials of targeted therapies in pediatric and young adult cancer patients across the United States. Pediatric MATCH enrolled more than 1,300 patients with treatment-refractory cancers, offering access to molecular screening and investigational targeted therapies. To further advance this, matched diagnostic, refractory tumor, and normal samples from Pediatric MATCH cases were molecularly characterized, creating one of the largest comprehensive data sets available for childhood cancers. This analysis has the potential to provide novel insights into the genetics of refractory pediatric, adolescent, and young adult cancers, as well as inform potential therapeutic strategies. The following molecular characterization assays were performed: Tumor whole exome sequencing (WES) Tumor whole genome sequencing (WGS) Tumor RNA sequencing (RNA-seq) Blood whole exome sequencing (WES) Blood whole genome sequencing (WGS)

  Study phs002883

• Childhood Cancer Data Initiative (CCDI): CCDI Pediatric In Vivo Testing Program - Leukemia

  The goal of this study is to molecularly characterize a large panel of pediatric acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) previously established in immune-deficient mice. These PDXs are utilized as part of the NCI-funded Pediatric Preclinical In vivo Testing (PIVOT) program to identify novel agents and combinations. Biospecimen data include next-generation sequencing (RNAseq, whole exome sequencing, DNA copy number variation), whole-genome analysis of cytogenetic abnormalities, and DNA fingerprint for quality control.

  Study phs003164

• APOLLO-OV: Applied Proteogenomics of High Grade Serous Ovarian Carcinoma

  APOLLO is a proteogenomic study seeking to describe the major genome, transcriptome, proteome and phosphoproteome alterations, subtypes, and molecular predictors of patient outcomes. This study includes 70 high grade serous ovarian carcinoma tissues from the Gynecologic Cancer Center of Excellence (https://medschool.usuhs.edu/gso/research/gyn-cancer-center-of-excellence). Bulk and laser microdissection enriched tumor tissues were profiled by whole genome sequencing, transcriptome sequencing, MS-based proteomics and reverse phase protein arrays. Clinical and sample data include survival times, patient features, and tumor characteristics.

  Study phs003488

• NCTN: A Randomized Phase III Comparison of Standard-Dose (60 Gy) versus High-Dose (74 Gy) Conformal Radiotherapy with Concurrent and Consolidation Carboplatin/Paclitaxel +/- Cetuximab in Patients with Stage IIIA/IIIB Non-Small Cell Lung Cancer (RTOG-0617)

  Study ID: RTOG-0617 NCT Number: NCT00533949 NRG Oncology Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: A Randomized Phase III Comparison of Standard-Dose (60 Gy) versus High-Dose (74 Gy) Conformal Radiotherapy with Concurrent and Consolidation Carboplatin/Paclitaxel +/- Cetuximab in Patients with Stage IIIA/IIIB Non-Small Cell Lung Cancer (RTOG-0617) Trial Description: RATIONALE: Radiation therapy uses high-energy x-rays to kill tumor cells. Drugs used in chemotherapy, such as paclitaxel, carboplatin work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Monoclonal antibodies, such as cetuximab can block tumor growth in different ways. Some block the ability of tumor cells to grow and spread. Others find tumor cells and help kill them or carry tumor-killing substances to them. It is not yet known whether high-dose radiation therapy is more effective than standard-dose radiation therapy when given together with combination chemotherapy with or without cetuximab in treating patients with non-small cell lung cancer. PURPOSE: This randomized phase III trial is studying high-dose or standard-dose radiation therapy given together with chemotherapy with or without cetuximab to see how well they work in treating patients with newly diagnosed stage III non-small cell lung cancer that cannot be removed by surgery. Clinical data presented in the following publication(s): • PMID 25601342 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung Cancer Clinical Dataset(s) included: • NCT00533949-D1 (PMID 25601342): There are three datasets for RTOG-0617's primary publication 25601342 (-D1 through -D3). This dataset, NCT00533949-D1, contains treatment arm, baseline characteristics, radiotherapy technique used, EGFR H-score, radiation treatment details, select toxicity data, and survival data. • NCT00533949-D2 (PMID 25601342): There are three datasets for RTOG-0617's primary publication 25601342 (-D1 through -D3). This dataset, NCT00533949-D2, contains adverse events reported in Appendix 10. • NCT00533949-D3 (PMID 25601342): There are three datasets for RTOG-0617's primary publication 25601342 (-D1 through -D3). This dataset, NCT00533949-D3, contains the most frequently reported adverse events reported in Tables 3 and 4. You are encouraged to view the PDF data dictionaries found in the "Documents" tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004191

• Reduction of Lethal Prostate Cancer Disparities in Underserved Hispanic/Latino Populations

  This pilot study investigated the genomic underpinnings of prostate cancer in Puerto Rican Hispanic/Latino men, a group disproportionately affected by this disease, in terms of incidence, mortality and aggressiveness. By examining tumors from 35 patients for specific genetic mutations and gene expression patterns using cutting-edge genomic sequencing, we aimed to identify distinct genetic profiles that could influence the course of the disease and its treatment. Our initial findings suggest the presence of unique genomic characteristics in this population, offering a promising avenue for developing personalized treatments that could reduce the health disparities observed in these men. This study underscores the importance of including diverse ethnic groups in genomic studies to ensure that the published data required for personalized cancer care are available.

  Study phs004487

• Blood and Marrow Clinical Trials Network - Allogeneic Hematopoietic Cell Transplant for Hematological Cancers and Myelodysplastic Syndromes in HIV-Infected Individuals (BMT CTN-0903-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To evaluate the safety and effectiveness of allogeneic hematopoietic cell transplantation for patients with hematologic malignancies or myelodysplastic syndromes and coincident-HIV infection.Background: Allogeneic hematopoietic cell transplantation (alloHCT) has been a safe and curative option for many patients with hematologic malignancies but was not well studied in the HIV+ population despite the interest in the HIV research community of the curative potential of alloHCT. Hematologic malignancies in people with HIV infection (HIV+) have been associated with poor outcomes due to opportunistic infections, but the development of antiretroviral therapy (ART) has increased the possibility of these patients achieving clinical outcomes comparable to those of the general population following stem cell transplant. The BMT CTN 0903 trial was designed to evaluate the safety and effectiveness of alloHCT for patients with HIV infection and hematologic malignancies.Participants: Patients had documented HIV infection, were a minimum of 15 years of age and had acute myeloid leukemia (AML) or acute lymphocytic leukemia (ALL) in first or second complete remission (CR); Int-2 or high-risk myelodysplastic syndromes (MDS) with CCR5delta32. AlloHCT using cord blood units or T-cell depletion was not allowed. Patients with history of prior alloHCT were excluded. Patients had to meet adequate organ function. Karnofsky/Lansky performance status ≥ 70% and could not have active central nervous system disease, HIV infection resistant to all antiretroviral therapy, or opportunistic infection unresponsive to treatment.There were seventeen HIV-infected patients with acute leukemia, myelodysplasia (MDS), NHL or classical HL who were enrolled in the trial.Design: Patients with HIV infection and hematological malignancies or myelodysplastic syndromes (MDS) were treated with either reduced-intensity conditioning (RIC) or myeloablative conditioning (MAC) followed by alloHCT. RIC or MAC was at the discretion of investigator. Where feasible, an attempt was made to identify hematopoietic cell donors who were homozygotes for the CCR5delta32 polymorphism. Graft-versus-host disease (GVHD) was treated per institutional standards.Four regimens were permitted for conditioning. RIC regimens were: fludarabine and busulfan (Flu/Bu), and fludarabine and melphalan (Flu/Mel). MAC regimens were busulfan and fludarabine (Bu/Flu), or cyclophosphamide and total body irradiation (Cy/TBI). GVHD prophylaxis regimens included tacrolimus/methotrexate, tacrolimus/sirolimus, and post-transplant cyclophosphamide with tacrolimus/mycophenolate. Patients receiving busulfan-containing preparative regimens were not eligible to receive tacrolimus/sirolimus. A committee reviewed individual patient's HIV treatment history and ART options before initiation of the transplant conditioning regimen and advised changes to minimize potential drug interactions. It was recommended that ART be continued except ritonavir-containing regimens during MAC.The goal of the study was to assess the 100-day non-relapse mortality. Secondary endpoints included 100-day disease status, percentage donor chimerism, hematologic function, infections, six-month overall survival (OS), incidence of acute and chronic GVHD, immunologic reconstitution, and impact of alloHCT upon measures of HIV persistence in blood including peripheral blood mononuclear (PBMC)-associated HIV DNA and infectious virus from resting CD4+T-cells using a quantitative virus outgrowth assay.Follow-up visits occurred weekly through 8 weeks post-transplant, at 100 days, 6 months, 1 year, and 2 years.Conclusions: There was no non-relapse mortality (NRM) at 100 days, or at 6 months, and therefore no evidence to suggest that NRM is prohibitive or more than that seen in non-HIV-infected patients. The cumulative incidence of grades II-IV acute GVHD was 41%. After year one, overall survival was 59%. In patients who achieved complete chimerism, cell-associated HIV DNA and inducible infectious virus in the blood were not detectable.

  Study phs004697

• Niraparib in Pancreatic Cancer

  Pancreatic cancer patients with pathogenic variants in DNA repair genes may benefit from PARP inhibitor therapy, but efficacy beyond germline BRCA1/2 mutations remains uncertain. This multicenter phase II trial (NCT03601923) enrolled 32 patients with advanced pancreatic cancer harboring germline or somatic pathogenic variants in BRCA1, BRCA2, PALB2, ATM, or CHEK2 who had not progressed on prior platinum-based chemotherapy. Patients received niraparib 200-300 mg daily. Here we deposit the whole exome samples of six patients from the study (N=13 total samples). Patients P02, P03, P06, and P21 have matched tumor-normal blood pairs; patient P22 has a single tumor sample; and patient P30 has four tumor samples collected at different timepoints for longitudinal analysis.

  Study phs004405

• The Cancer Dependency Map (DepMap)

  The Cancer Dependency Map (DepMap) aims to accelerate precision cancer medicine by creating a comprehensive map of tumor vulnerabilities. The DepMap project genomically profiles a wide range of cancer models and characterizes them for their sensitivity to genetic and compound perturbations. The data is computationally analyzed to create a systematic overview of the genetic dependencies and compound sensitivities of cancer types and the predictive biomarkers that point to patient populations most likely to benefit from targeting of these vulnerabilities. The DepMap public portal has become a comprehensive resource to identify cancer vulnerabilities by providing datasets at scale, cutting-edge computational tools, and sophisticated visualization tools that together have accelerated the discovery of novel targets and biomarkers. Please visit Depmap.org to access the public portal.

  Study phs003444

• KDM6A Loss Triggers an Epigenetic Switch that Disrupts Urothelial Identity and Drives Cell Proliferation in Bladder Cancer

  Disruption of KDM6A, a histone lysine demethylase, is one of the most common somatic alternations in bladder cancer. How mutations of this chromatin modifier impact the epigenetic landscape to promote carcinogenesis is poorly understood. Here, we demonstrate that KDM6A loss triggers an epigenomic switch that disrupts urothelial identity and induces a neoplastic state characterized by increased cell proliferation. In bladder cancer cells with intact KDM6A, FOXA1 binds KDM6A at enhancers to activate genes instructing urothelial differentiation. In KDM6A-deficient cells, we observed simultaneous loss of FOXA1 target binding and genome-wide redistribution of the bZIP transcription factor ATF3, which in turn represses FOXA1 target genes and activates cell-cycle progression genes. Importantly, ATF3 depletion reverses the cell proliferation phenotype. These data establish that KDM6A loss creates an epigenetic state that drives tumor growth in an ATF3-dependent manner, forging a molecular vulnerability that can be targeted by novel therapeutic strategies.

  Study phs002801

• Inherited Genetic Susceptibility in Langerhans Cell Histiocytosis

  We recruited cases of Langerhans cell histiocytosis (LCH) who were recruited to the Children's Oncology Group Childhood Cancer Research Network, Project:EveryChild projects, or to a local patient biobank to conduct an expanded genome-wide association study for risk variants and to perform post-GWAS analysis of a previous hit in the SMAD6 gene. Publicly available control data were used for our analyses; however, here we provide the SNP array data and targeted SMAD6 sequence data for the LCH cases and some non-LCH cases included in the analysis.

  Study phs004547

• MP2PRT: Evaluation of an Inflammation Polygenic Risk Score (iPRS) to Predict Cancer Related Cognitive Impairment and Fatigue in Patients Receiving Chemotherapy for Non-Metastatic Breast Cancer in URCC0701 and URCC10055

  This study is a secondary analysis of cancer related cognitive impairment (CRCI) and cancer related fatigue (CRF) among participants in URCC0701 and URCC10055 from the University of Rochester NCI Community Oncology Research Program (NCORP) Research Base. CRCI and CRF are common, troublesome, and dose-limiting toxicities reported by patients undergoing breast cancer chemotherapy that have an etiologic basis linked to low-grade systemic inflammation. Chronic, low-grade systemic inflammation is, in part, genetically determined with common single nucleotide polymorphisms (SNPs) capturing variation across individuals. This study aimed to 1) determine whether an inflammation polygenic risk score (iPRS) is associated with CRCI or CRF, 2) determine whether the relationship between the iPRS and CRCI or CRF is modified by exercise at the time of cancer treatment, 3) identify SNPs associated with serum cytokines measured at the time of cancer treatment, and 4) identify novel CRCI- and CRF-associated risk SNPs via genome-wide association analyses. We found that there was a significant inverse correlation between the iPRS and change in fatigue score from pre-chemotherapy to post-chemotherapy while there was no statistically significant association between the iPRS and cognitive impairment score. The inverse relationship between the iPRS and fatigue may be explained in part by the finding that the iPRS was also significantly associated with greater pre-chemotherapy fatigue, suggesting that women with a genetic predisposition to low-grade systemic inflammation (i.e., high iPRS) have more fatigue at the time of breast cancer diagnosis and, therefore, are less likely to worsen over the course of treatment. In contrast, women with a low iPRS had significantly less fatigue pre-chemotherapy and a significant worsening of fatigue from pre- to post-chemotherapy. The relationship between the iPRS and fatigue remained after adjustment for patient and cancer treatment covariates and was most pronounced in women who reported regularly exercising for at least 6 months prior to starting their cancer treatment. Exploratory genome-wide analysis identified a novel risk locus on chromosome chr6q27, tagged by rs9365961, associated with CRCI. This locus is upstream of TBXT, which encodes an embryonic nuclear transcription factor previously associated with susceptibility to neural tube defects. The genome-wide SNP data, patient-reported CRCI and CRF outcome measures, and covariate data used in this analysis are available through dbGaP.

  Study phs003688

• Metabolic Biomarkers in Thoracic Cancers

  Here we present RNA sequencing (RNA-Seq) of non-small cell lung cancer (NSCLC) and adjacent lung tissue. These samples were acquired from primarily untreated, surgically resected primary tumors. The first analysis published with this data was to determine the metabolic signatures between primary tumors and adjacent lung tissue.The associated clinical trial (NCT02095808) includes patients with many kinds of thoracic cancers, including NSCLC and other diseases, such as thymoma and esophageal adenocarcinoma. However, the current dbGaP data is focused on the NSCLCs described in the associated paper.

  Study phs003880

• Healthy Communities Study (HCS-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: To examine the relationships between characteristics of community programs and policies that are designed to prevent childhood obesity and are focused on Body Mass Index, diet, and physical activity in children.Background: Childhood obesity is a major public health issue in the U.S. with 18.5% of children aged 2-19 having obesity (Hales, Caroll, Fryer, and Ogden, 2017). Children who have obesity are more likely to have cardiovascular risk factors (Freedman, Mei, Srinivasan, Berenson, & Dietz, 2007; Koskinen et al., 2018), type 2 diabetes (Goran, Ball, & Cruz, 2003) and are at increased risk for morbidity and mortality as adults (Reilly & Kelly, 2011) including increased risk of developing several types of cancer (World Cancer Research Fund/American Institute for Cancer Research, 2007).Community programs and policies targeting childhood obesity are being implemented across the country, but their approaches have not been systematically studied. There is natural variation in many aspects of community programs and policies, including intensity level, duration, funding, target population, and how they are implemented. However, no previous studies have examined these variations and how such aspects of community programs and policies are related to childhood obesity outcomes. The Healthy Communities Study (HCS) was initiated to address the need for a study of community programs and policies and their relationship with childhood obesity.The three aims of HCS are to: 1) determine the associations between characteristics of community programs and policies and obesity outcomes in children; 2) identify factors that modify or mediate the associations; and 3) examine the association between characteristics of program and policies and obesity outcomes in communities that have a high proportion of African American or Hispanic residents. This study was not designed to evaluate any one specific program, policy or community, but was designed to systematically assess if components or characteristics of programs/policies in communities across the country are related to BMI, diet, and physical activity in children.Design: Community selection: For the purposes of HCS, a community was defined as a high school catchment area, and child participants were students at public elementary and middle schools (kindergarten through eighth grade) within the catchment areas. Communities were selected using a hybrid sampling approach. Some of the communities were “certainty” communities, which had implemented promising program and policies targeting childhood obesity. Other communities were sampled using a stratified national probability-based sample, using weights proportional to the number of children aged 4-15 in each Census Tract.Participant recruitment At the school level, children were recruited from two public elementary and two public middle schools in each community. Materials were distributed to children in these schools and families who completed the forms were contacted by the study.The HCS employed a complex study design that included a diverse sample of communities across the country and combines current/cross-sectional and retrospective data. Data were collected at multiple levels including at the child/household, schools, and community levels.Cross-sectional component: Interviews conducted in households along with community and school assessments were the primary data collection activities for HCS. Cross-sectional data were collected on a) children and their families, b) schools, and c) communities:a. Children and households: All children participated in the Standard Protocol measure consisting of: medical history, height, weight, and waist circumference measurements of the child; height and weight measurements (or self-reported measurements) of the two parent(s)/caregiver(s); general demographic and background questions; brief nutrition and physical activity behavior questionnaires; and a modified Windshield Survey of the home. A subset of children (approximately 14% of the children in the 130 communities) received an Enhanced Protocol, which included: all of the Standard Protocol measures listed previously plus (2) 24-hour dietary recalls during both of the home visits, the use of an accelerometer for a one-week period between the first and second home visit, and a previous day physical activity assessment questionnaire at the end of the second visit.b. Schools: School assessments were comprised of web-based surveys and observations of the 4 participating schools. Observations in the 2 elementary and 2 middle schools included lunchroom observations, an interview of the physical education instructor, and a Physical Activity Resource Assessment (PARA) was administered to observe the school's outdoor physical activity resources. Web-based surveys were administered to the district food service administrator/manager and a staff member from each school. The school staff completed a survey on school policies and practices related to physical activity and nutrition, whereas, the district –level personnel completed a food environment questionnaire for each of the recruited schools that were in their district.c. Communities: In each community, interviews were conducted with key informants (10-14 persons per community) to review and gather characteristics on current community policies and programs and for communities programs and policies for up to 10 years prior.Retrospective component:a. Among children, medical records were abstracted for going back up to 10 years in approximately 65-70% the sample to develop longitudinal BMI trajectories.b. Communities: Data were collected from key informants in each community on characteristics of programs and polices going back up to 10 years to assess how programs and policies unfolded over time in each community.Demographics:Communities: A total of 130 diverse communities participated in the HCS. Communities were diverse with respect to low income (38.5%), urbanicity (38.5% urban, 38.5% suburban, 23.1% rural), and geographic region (42.3% South, 22.3% West, 20% Midwest, 15.4% Northeast). Communities with a high proportion of race-ethnic groups also were oversampled (32.3% Hispanic, 26.2% African American, 41.5% other). Data were collected in a total of 436 schools; 227 elementary (52%), 53 elementary/middle (12%), and 158 middle schools (36%).There were 1,421 key informants interviewed across the 130 communities. Through the key informant interviews and document abstraction, 9,681 community programs and policies (CPPs) over the ten year retrospective study period were identified and characterized.Participants: A total of 5,138 children and their parent(s)/caregiver(s) from 130 diverse communities across the country were recruited for the HCS study. Child participants were evenly distributed across ages 4–15 years and gender; 21.5% were African American and 43.5% were Hispanic. Nearly a third of households reported an annual income below $20,000.

  Study phs004494

• Childhood Cancer Data Initiative (CCDI): A Cohort of Hispanic Children with Acute Lymphoblastic Leukemia; Bloom Syndrome in a Mexican American Family with Rhabdomyosarcoma

  Retrospective case-control genetic study of Hispanic children with acute lymphoblastic leukemia (ALL) treated 1994-2013, comparing 14 treatment-related pancreatitis (TRP) cases to 46 treatment-matched controls without pancreatitis. Targeted sequencing of 23 genes (pancreatitis-related and asparagine-metabolism genes) was performed from post-remission blood DNA; select HLA types were inferred from whole-exome data in cases. CFTR and ASNS variants were enriched in TRP (notably CFTR V470M, OR 4.27, p=0.025).

  Study phs002823

• Impact of HLA Aberrations on Tumor Neoepitope Presentation

  TP53 mutations may encode tumor-specific truncal neoantigens for targeting cytotoxic T lymphocyte (CTL). Using mass spectrometry followed by X-ray crystallographic analysis of HLA-bound p53 neoantigens, clinical tumor database analyses, and functional studies of neoantigen-directed T cell receptors (TCRs), we have built a comprehensive p53 immunopeptidome. As a component of this study, we noted that tumors with neoantigens displayable on HLA-A*02:01 or HLA-B*07:02, and structurally divergent from p53 wild-type peptide-HLA complexes, may exploit an allele's absence for growth in patients. The data deposited highlights that in brain metastasis of an ovarian cancer, that a damaged HLA-A*02:01 allele resulted in inability to present the p53 I195F neoepitope (GLAPPQHLFRV). Conversely, a simultaneously processed glioblastoma sample, sequenced as a control (and bearing a p53 R248W mutation on an A*24:02/A*32:01 background), revealed full exome genomic reads and transcript reads of the HLA-A locus. This indicated that biallelic HLA-A loss in the 10-417-1023 tumor was not a technical issue but represented damage to the 5' encoding exons of HLA-A.

  Study phs004529

• Childhood Cancer Data Initiative (CCDI): Metastatic Osteosarcoma snMultiome Profiling

  Metastatic osteosarcoma is an aggressive bone malignancy affecting pediatric, adolescent, and young adults. While recent research has increasingly focused on understanding the complex biology of the osteosarcoma microenvironment, the tumor vasculature is understudied, especially in the context of metastatic disease. To address this, we performed single-nuclei multi-ome (RNA+ATAC) sequencing on a cohort of 24 human metastatic osteosarcoma specimens. Our data shows that endothelial cells universally exhibit a hybrid endothelial–mesenchymal state consistent with endothelial-to-mesenchymal transition (EndMT). Additionally, we uncovered that a subset of diploid endothelial cells adopts an osteoblastic cell fate as evidenced by gene expression and gene regulatory network (GRN) analysis. Joint copy-number analysis of our dataset identified a subset of osteosarcoma cells with endothelial transcriptional programs and GRNs, indicative of vascular mimicry. In vitro assays and in vivo lineage tracing experiments using syngeneic murine models validated both vascular mimicry and endothelial to-osteoblastic transdifferentiation. Collectively, these findings highlight the remarkable plasticity and lineage infidelity of both endothelial and osteosarcoma cells in patient specimens and a metastatic syngeneic murine model, provide novel insights into the functional role of endothelial cells in the metastatic osteosarcoma microenvironment, and challenge current understanding of osteosarcoma biology.

  Study phs004490

• Childhood Cancer Data Initiative (CCDI): Frameshift Mutation Profiling of Constitutional Mismatch Repair Deficiency Syndrome Patients

  Samples from patients with Constitutional Mismatch Repair Deficiency Syndrome (CMMRD) were sequenced using the Archer NextSeq platform to detect frameshift mutations in cell-free DNA (cfDNA), matched tumor samples, and other tissue types. The goal of the study is to evaluate whether a frameshift mutation biomarker panel can be used for disease monitoring. Limited treatment information is included when available. The listed genes represent those in which recurrent frameshift mutations were identified and evaluated as candidate biomarkers for disease monitoring in CMMRD.

  Study phs004017

• Blood and Marrow Transplant Clinical Trials Network - Randomized Multicenter Trial Comparing Sirolimus Plus Prednisone and Sirolimus/Calcineurin Inhibitor Plus Prednisone for the Treatment of Chronic Graft-versus-Host Disease (BMT-CTN-0801-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. ObjectivesFor the phase II component, to compare the responses of patients with graft-versus-host disease who received sirolimus/calcineurin inhibitor plus prednisone versus sirolimus plus prednisone after 6 months of therapy. For the phase III component, to compare the proportion of subjects with complete resolution of all reversible manifestations at 24 months after starting therapy.BackgroundChronic graft-versus-host disease (cGVHD) is the major treatment-related complication among patients who survive after allogeneic hematopoietic cell transplantation (HCT). Standard immunosuppressive therapy (IST) with prednisone ± a calcineurin inhibitor (CNI) has not changed for three decades, but most patients respond inadequately with slow and most often incomplete control of their disease. Renewed understanding of regulatory T cells (Tregs) led to the hypothesis that experimental therapies permissive of Treg expansion would better abrogate GVHD than CNI-containing (control) IST. Sirolimus and extracorporeal photopheresis (ECP) are permissive of Treg expansion. Because of their acceptance in clinical practice, sirolimus and ECP were considered good candidates for adding to prednisone in clinical trials in cGVHD.ParticipantsAdult and pediatric allogeneic HCT recipients were eligible if they had classic cGVHD ± acute GVHD (overlap subtype) that met 2005 NIH diagnostic consensus criteria. This included newly diagnosed patients, defined as individuals who had received One hundred patients were evaluated for the phase II primary endpoint after all had completed 6 months of follow-up. All 151 enrolled subjects were followed for phase III endpoints. 77 patients were randomized to the prednisone/sirolimus arm and 74 patients to the prednisone/sirolimus/CNI arm.DesignThe trial was designed as an adaptive phase II/III randomized, open-label, prospective study of three treatments for chronic GVHD. Phase II was to include two parallel, 100-patient, randomized trials, comparing prednisone/sirolimus or prednisone/sirolimus/ECP versus identical (prednisone/sirolimus/CNI) comparator arms, where centers selected only one trial in which to participate. However, the prednisone/sirolimus/ECP arm was closed prematurely due to poor accrual. Comparison of complete/partial response rates did not support proceeding to phase III and further accrual was suspended.The starting dose of prednisone (or prednisone-equivalent) was 1 mg/kg once daily, unless contraindicated, in which case the prednisone dose began at 0.5–1 mg/kg once daily. It was recommended that the dose of prednisone was tapered down, over 4–8 weeks to reach a dose of 0.5–1 mg/kg every other day, with the tapering starting within 2 weeks after the first evidence of GVHD improvement. Once an every-other-day prednisone (or equivalent) regimen was achieved, this dose remained constant for 10–12 weeks until all reversible chronic GVHD manifestations resolved. The sirolimus therapy began at a dose of 2 mg orally once daily (1 mg/m2 per day if the patient weighed Health-related quality of life was measured by self-report instruments, including the Functional Assessment of Cancer Therapy Bone Marrow Transplantation (FACT-BMT), Short Form-36 (SF-36).For phase II, the primary outcome was complete or partial response after 6 months of therapy. For phase III, the primary outcome was complete response at 24 months.ConclusionsInitial therapy of chronic GVHD with prednisone/sirolimus is an acceptable alternative and better tolerated than therapy with prednisone/sirolimus/CNI.Carpenter PA, Logan BR, Lee SJ, et al. A phase II/III randomized, multicenter trial of prednisone/sirolimus versus prednisone/ sirolimus/calcineurin inhibitor for the treatment of chronic graft-versus-host disease: BMT CTN 0801 (Carpenter PA et al. Haematologica, 2018).

  Study phs004641

• RNA Sequencing Analysis of Patient-Derived Xenograft Tissue PIM-084 Treated with L-NMMA+Alpelisib vs Vehicle Control

  This dataset contains RNA-seq analysis of vehicle control compared to L-NMMA+alpelisib treated metaplastic breast cancer PDX PIM084 tumors (RNA sequencing and analysis performed by Novogene). The submitted data contains the gene ID, gene name, normalized read counts from all samples from control group and combination treatment group, log2-fold change derived from DESeq2 R/EdgeR package, p-value, adjusted p-value, read counts from each group, and gene FPKM from the each sample in the group. Due to patient privacy, we are submitting only the processed and desensitized RNA sequencing analysis to this repository.

  Study phs003814

• The Study of Somatic LINE1 Activity in Cancers

  This study focuses exclusively on the quantification of LINE1 mobilization. We analyzed a recent whole genome sequencing data release from multiple Cancer Genome Atlas (TCGA) sub-projects. In addition to the somatic LINE1 insertions (present in tumor and having no support in the matched normal) there are "pseudo-germline" non-reference LINE1 elements identified in tumor tissue and having some support in the matched normal. This dataset reports such "pseudo-germline" LINE1 retrotranspositions. Individual level data for TCGA can be accessed by requesting access to phs000178.

  Study phs003888

• NCI's Collection of Studies for General Cancer Research

  This collection contains all of NCIs authorized individual-level genomic datasets currently in dbGaP that are approved for Cancer Research (DS-CA) use only and limitations outlined in the model Data Use Certification Agreement. Access to this study will include any additional authorized individual-level DS-CA datasets that become available. Renewal of this study is required annually. To request access to this study collection, select phs003967.v1.p1 in the dbGaP Authorized Access System.

  Study phs003967

• Involvement of the FGF8/FGF Receptor Signaling Pathway in the Maintenance and Progression of Fusion-Positive Rhabdomyosarcoma

  In our previous work, we used a myoblast model of fusion-positive rhabdomyosarcoma (FP-RMS) to demonstrate that FGF8, a target of the PAX3-FOXO1 (P3F) transcription factor, is essential for tumorigenicity driven by P3F. When aberrantly expressed, FGF8 can also sustain tumorigenicity in recurrent tumors that are independent of P3F. In this study, we report that FGF8, along with its receptors FGFR1 and FGFR4, is often highly expressed in FP-RMS tumors. We found that high levels of FGF8 expression in FP-RMS cells correlate with increased sensitivity to an FGFR4 inhibitor and a pan-FGFR inhibitor. Conversely, downregulating FGF8 led to a loss of sensitivity to these inhibitors. Interestingly, when FGF8 was upregulated in myoblasts, it resulted in decreased FGFR4 expression and sensitized the cells to an FGFR1 inhibitor and a pan-FGFR inhibitor. The downregulation of FGFR4 expression mediated by FGF8 could be reversed by inhibiting FGFR1, MEK, or ERK, thereby defining a signaling pathway through which FGF8 exerts its regulatory effects. Additionally, we discovered that high FGF8 expression in P3F-independent recurrent tumors is due to a rearrangement of viral long terminal repeat (LTR) sequences into the 3' untranslated region (UTR) of FGF8, leading to increased stability of FGF8 mRNA. These findings indicate that FGF8 plays an oncogenic role in FP-RMS through FGFR4 and may also exert oncogenic effects in P3F-independent relapses via FGFR1. Our study highlights the functional significance of FGF8 in FP-RMS and supports the rationale for preclinical investigations of FGFR inhibitors in treating this type of cancer.

  Study phs004009

• Human Cancer-Targeted Immunity via Transgenic Hematopoietic Stem Cell Progeny

  Analysis of a patient biopsy from the clinical trial (NCT03240861), a first-in-human study of transgenic NY-ESO-1 TCR- T cells and NY-ESO-1 TCR+ sr39tk autologous hematopoietic stem cells tandem therapy for solid tumors after myeloablative conditioning chemotherapy with busulfan and fludarabine. Single-cell RNAseq and single-cell ATACseq analysis from peripheral blood mononuclear cells obtained from subject NYSCT-03.

  Study phs003898

• CDK2 Inhibition Demonstrates RB-Independent Efficacy in CDK4/6 Inhibitor-Resistant HR-Positive/HER2-Negative Breast Cancer

  Preliminary clinical data from hormone receptor (HR)-positive, human epidermal growth factor receptor-2 (HER2)-negative metastatic breast cancer (MBC) patients with resistance to CDK4/6 inhibitors treated with the CDK2 inhibitor PF-07104091 as monotherapy indicate that therapeutic efficacy correlates with TP53 status, but not with RB expression or phosphorylation. Using a panel of HR+/HER2- MBC patient-derived (PD) cell lines, including both CDK4/6 inhibitor-naïve and resistant models, we found that CDK2, unlike CDK4/6, is dispensable for RB phosphorylation. Notably, in models derived from tumors that had progressed on CDK4/6 inhibitor therapy, as well as in models with acquired in vitro resistance, CDK2 inhibition reduced DNA replication rate, induced DNA damage, and inhibited mitotic entry in an RB-independent manner. Data available through this dbGaP submission include whole-exome sequencing (WES) from four CDK4/6 inhibitor-naïve HR+/HER2- MBC PD cell lines (MGH10035.1, MGH10035.2, MGH358.1, and MGH358.2), their corresponding isogenic derivatives with acquired in vitro resistance to the CDK4/6 inhibitor palbociclib, and one PD cell line (MGH321.4) derived from a letrozole/ribociclib-resistant HR+/HER2- MBC tumor. MGH10035.1 and MGH10035.2 were derived from the same patient at different stages of treatment, as were MGH358.1 and MGH358.2.

  Study phs004466

• NCTN: Phase III Trial of Tamoxifen Alone vs. Tamoxifen Plus Radiation Therapy for Good Risk Duct Carcinoma In-Situ (DCIS) of the Female Breast (RTOG-98-04)

  Study ID: RTOG-98-04 NCT Number: NCT00003857 NRG Oncology Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: Phase III Trial of Tamoxifen Alone vs. Tamoxifen plus Radiation Therapy for Good Risk Duct Carcinoma In-Situ (DCIS) of the Female Breast (RTOG-98-04) Trial Description: RATIONALE: Radiation therapy uses high-energy x-rays to damage tumor cells. Estrogen can stimulate the growth of breast cancer cells. Hormone therapy using tamoxifen may fight breast cancer by blocking the uptake of estrogen by the tumor cells. It is not yet known if radiation therapy is more effective than observation, with or without tamoxifen, in treating ductal carcinoma in situ. PURPOSE: Randomized phase III trial to compare the effectiveness of radiation therapy with that of observation, with or without tamoxifen, in treating women who have ductal carcinoma in situ.Clinical data presented in the following publication(s): • PMID 25605856 Disease type(s): Breast Neoplasm - Breast Neoplasm, Miscellaneous Clinical Dataset(s) included: • NCT00003857-D1 (PMID 25605856): This dataset is for RTOG-98-04's primary publication 25605856. The dataset contains reasons for exclusion, baseline characteristics, survival, local failure, distant metastasis, salvage mastectomy, and toxicity data. You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004264

• Blood and Marrow Clinical Trials Network (BMT CTN) A Phase III Randomized, Multicenter Trial Comparing Sirolimus/Tacrolimus With Tacrolimus/Methotrexate as Graft-versus-Host Disease Prophylaxis After HLA-Matched, Related Peripheral Blood Stem Cell Transplantation (BMT-CTN-0402-BioLINCC)

  ObjectivesThe primary objective was to determine if the combination of tacrolimus and sirolimus (Tac/Sir) was more effective than tacrolimus and methotrexate (Tac/Mtx) in preventing acute graft-versus-host disease and early mortality after allogeneic related donor hematopoietic cell transplantation.BackgroundStem cell transplantation is a standard therapy for leukemia and myelodysplastic disorders. Recipients of human leukocyte antigen (HLA)-matched, related donor (MRD) stem cell transplants are at risk for a number of infections and complications. One of these complications is a condition known as acute graft-versus-host disease (GVHD). Recipients of HLA-MRD stem cell transplants for the treatment of myelodysplastic disorders and leukemia experience a 35% incidence of GVHD. Furthermore, GVHD contributes significantly to 1-year early treatment-related mortality (TRM) estimates of approximately 20%.The standard prophylaxis regimen for GVHD is a calcineurin inhibitor combined with methotrexate. Calcineurin inhibitors block calcineurin, a protein phosphatase that catalyzes some of the intracellular processes associated with T-lymphocyte activation. Inhibition is achieved by binding to immunophilins. The result is reduced production of interleukin-2 and reduced proliferation of T-cells. Methotrexate, an antineoplastic antimetabolite, has immunosuppressant properties that prevents the synthesis of tetrahydrofolate. Tetrahydrofolate is necessary for synthesis of thymidylate, an essential component of DNA. Of particular clinical concern is the theory that the injury caused by methotrexate to tissues could play a contributory role in initiation of the cytokine cascade associated with GVHD.The standard prophylaxis regimen for GVHD was established in the mid-1980s. Minor alterations to the standard regimen have shown limited effect on TRM outcomes in spite of the improvements that have been made to allogeneic hematopoietic cell transplantation (HCT) outcomes. Sirolimus, a rapamycin inhibitor, has been suggested as an alternative for methotrexate. Previous studies have suggested that sirolimus use results in decreased incidence of acute GVHD and treatment-related toxicity after HLA-MRD and unrelated donor transplantation, at the expense of higher rates of endothelial injury syndromes. Sirolimus has additional immunomodulatory properties that include effects on antigen-presenting cells, the thymus, and preservation of regulatory T-cell subsets after transplantation. The purpose of this study was to determine if sirolimus, in place of methotrexate, would produce improved outcomes in GVHD and TRM.ParticipantsEligible participants were 2 to 60 years of age, of either gender, and were undergoing transplantation for one of the following conditions: acute leukemia in remission, myelodysplastic disorder, or chronic myeloid leukemia in chronic or accelerated phase. All participants were required to have a 6/6 Class I HLA-A and B and molecular Class II DRB1 matched sibling donor medically able and willing to donate peripheral blood stem cells that also met institutional criteria for stem cell donation.Participants were excluded from participating in the trial for the following: prior allogenic or autologous transplant, HIV or another uncontrolled active infection, pregnant or breast-feeding, known allergy to sirolimus, requiring voriconazole at time of study entry, currently receiving another investigational drug (unless cleared by protocol officer or chair), or participants with a history of cancer.Participants were excluded from continuation for the following laboratory criteria if measured within 4 weeks of study entry: measured creatinine clearance 500mg/dL; forced vital capacity (FVC) or forced expiratory volume (FEV1) 45% in adults or A total of 304 participants were enrolled in the study. 151 participants were randomized to the tacrolimus/sirolimus (Tac/Sir) treatment, which 149 completed and 2 did not undergo transplantation. 153 participants were randomized to the tacrolimus/methotrexate (Tac/Mtx) treatment, which 152 completed and 1 did not undergo transplantation.DesignBMT 0402 was an interventional study with the purpose of determining the best combination of medications for the prevention of GVHD after HLA-MRD peripheral blood stem cell transplantation. Two GVHD prophylaxis conditioning regimens were tested: tacrolimus/sirolimus (Tac/Sir) and tacrolimus/methotrexate (Tac/Mtx). The study was Phase III, and designed to be multicenter, randomized, open label, and with parallel assignment treatment arms. Randomization occurred within 7 days of initiation of pretransplantation conditioning therapy, and was performed in a 1:1 ratio with the use of random block sites, stratified by transplantation center. The transplant physician selection of treatment occurred prior to participant's assignment to the study. All parties involved in the trial knew the treatment arm assigned to each participant.Participants received pretransplantation myeloablative conditioning with total body irradiation in combination with either cyclophosphamide or etoposide. Initially, a conditioning regimen comprised of myeloablative doses of busulfan with CY was permitted, however this was removed due to excess toxicity and veno-occulusive disease of the liver. The participants that received busulfan-based conditioning were not included in the primary outcome analyses. PBSC donors received filgrastim and underwent large volume apheresis with a goal of collecting 2 to 10 × 106/kg CD34+ stem cells. No graft manipulation was allowed prior to the infusion of the stem-cell product.For GVHD prophylaxis, tacrolimus was begun on day −3 for all participants at a dose of 0.02 mg/kg/day by continuous IV infusion, adjusted to maintain a serum concentration of 5 to 10 ng/mL. For participants in the Tac/Sir group, sirolimus was started on day −3 with a 12 mg oral loading dose, followed by daily oral doses of 4 mg, adjusted to maintain a serum trough concentration of 3 to 12 ng/mL. For participants in the Tac/Mtx group, methotrexate was IV administered on day +1 (15 mg/m2), +3, +6, and +11 (10 mg/m2 each day).The primary endpoint of grades II-IV acute GVHD-free survival was assessed 114 days from the time of randomization based on intention-to-treat. The study had 80% power to detect a 15% difference between the 2 prophylaxis strategies based on the standardized difference in Kaplan-Meier estimates with a 2-sided α of 5%. A committee of investigators blinded to GVHD prophylaxis assignment reviewed all case records, focusing on the incidence of acute and chronic GVHD, relapse, toxicity, and causes of death. Participants were followed for two years after transplantation for evaluation of secondary endpoints, which included cumulative incidence of acute GVHD, time to neutrophil and platelet engraftment, mucositis severity, rate of veno-occlusive disease, thrombotic microangiopathy infection, cytomegalovirus reactivation, treatment-related mortality, malignant disease relapse, all infections, overall survival, and time to discharge after transplant.ConclusionsParticipants who received Tac/Sir engrafted significantly earlier and had significantly less severe oropharyngeal mucositis after transplantation; however, no difference was observed in the primary end point of GVHD-free survival at 114 days post randomization between participants treated with Tac/Sir and Tac/Mtx (Cutler C. et al., Blood 2014).

  Study phs004629

• NCTN: A Phase III Trial Evaluating the Addition of Trastuzumab to Trimodality Treatment of HER2-Overexpressing Esophageal Adenocarcinoma (RTOG-1010)

  Study ID: RTOG-1010NCT Number: NCT01196390 NRG OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Phase III Trial Evaluating the Addition of Trastuzumab to Trimodality Treatment of HER2-Overexpressing Esophageal Adenocarcinoma (RTOG-1010)Trial Description: This randomized phase III trial studies how well radiation therapy, paclitaxel, and carboplatin with or without trastuzumab work in treating patients with esophageal cancer. Radiation therapy uses high-energy x-rays to kill tumor cells. Drugs used in chemotherapy, such as paclitaxel and carboplatin, work in different ways to stop the growth of tumor cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Monoclonal antibodies, such as trastuzumab, may interfere with the ability of tumor cells to grow and spread. It is not yet known whether giving radiation therapy and combination chemotherapy together with or without trastuzumab is more effective in treating esophageal cancer. Clinical data presented in the following publication(s):PMID 35038433Disease type(s): Gastrointestinal Neoplasm - Gastroesophageal CancerClinical Dataset(s) included:NCT01196390-D1 (PMID 35038433): There are three datasets for RTOG-1010's primary publication 35038433 (-D1 through -D3). This dataset, NCT01196390-D1, contains the baseline characteristics, treatment, reasons for treatment discontinuation, surgery information, survival, and toxicity data. NCT01196390-D2 (PMID 35038433): There are three datasets for RTOG-1010's primary publication 35038433 (-D1 through -D3). This dataset, NCT01196390-D2, contains the treatment-related adverse event data. NCT01196390-D3 (PMID 35038433): There are three datasets for RTOG-1010's primary publication 35038433 (-D1 through -D3). This dataset, NCT01196390-D3, contains the treatment-related serious adverse event data. You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004237

• Ongoing Replication Stress Tolerance and Clonal T Cell Responses Distinguish Liver and Lung Recurrence and Patient Outcomes in Pancreatic Ductal Adenocarcinoma

  Patients with metastatic pancreatic ductal adenocarcinoma (PDAC) survive longer when disease spreads to the lung but not to the liver. We generated overlapping, multi-omic datasets to identify molecular and cellular features that distinguish patients whose disease develops liver metastasis (liver cohort) from those whose disease progression results in lung metastasis without liver metastases (lung cohort). Lung cohort patients generally survived longer than liver cohort patients, independent of tumor subtype. We developed a pORG gene signature that distinguishes primary tumors in the liver and lung cohorts. We identified ongoing replication stress (RS) response pathways in high pORG/liver cohort tumors, while low pORG/lung cohort tumors had greater densities of lymphocytes and shared T cell clonal responses. Our study demonstrates that liver-avid PDAC is associated with tolerance to ongoing RS, limited tumor immunity, and less favorable outcomes; whereas low RS, lung-avid/liver-averse tumors are associated with active tumor immunity that may account for favorable outcomes. As expected, we found high frequencies of KRAS, TP53, CDKN2A, and SMAD4 gene alterations in our tumor samples. High pORG activity (GSVA scores) in our primary tumors appear to be positively correlated with alteration frequencies in both TP53 and CDKN2A. We did not see a correlation with alterations in KRAS as almost all the tumor samples have KRAS alterations. From a de-identified dataset of 1,873 patients diagnosed with and/or treated for PDAC at our institution between 2004 and 2020, we identified 422 patients for which we had specimens with sequencing data (N=374) and/or specific evidence of disease metastasis site(s) from the OHSU cancer registry or disease-relevant computed tomography (CT) scans to allow cohort classification. Note that our study includes RNA-Seq, DNA-Seq panel, and TCR-Seq (T-cell Receptor Sequencing) data, but that this dbGaP submission just includes the patients/samples with RNA-Seq and/or DNA-Seq panel data. Therefore, this submission includes 290 samples from 278 patients. TCR sequence data is available on the Adaptive Biotechnologies platform. Clinical course timepoints, patient demographics, stage, grade, nodal involvement, resection margins, and angiolymphatic invasion were provided as deidentified data by the OHSU cancer registry with quality control data verification in a subset by pathologists (BB and TM). We reviewed all available computed tomography (CT) scans for all patients with primary tumor resection dates recorded by the cancer registrar, with tumor samples analyzed by RNA-seq, DNA-seq, or TCR-seq, and/or with additional information indicating metastatic spread (e.g., metastatic samples received for related studies). We abstracted the site of all lesions proven to be metastatic by biopsy and/or that clearly increased in size during progression or decreased in size during treatment as long as a radiologist described the lesion as “likely”, “suspicious for”, “concerning for”, or “favor” metastasis. Clinical imaging was reviewed by a radiologist (AG) to validate patient assignments to the liver, lung, and neither liver nor lung (other recurrence site) cohorts. Time to recurrence was calculated from the earliest of either the recurrence date provided by the OHSU cancer registry, or the date of earliest lesion abstracted from CT reports. The subject attributes reported in this submission were up to date at the time of our data freeze, which occurred July 2021.

  Study phs003597

• Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program - Neuroblastoma

  The goal of NCI's Pediatric In Vivo Testing Consortium (PIVOT) is to advance the development of effective treatments for pediatric cancers through preclinical in vivo testing of novel therapeutic agents. To design impactful experiments that can be rapidly translated to the clinic, PIVOT investigators require comprehensive genomic characterization of the patient-derived xenograft (PDX) models used across the consortium. This robust experimental design enhances collaboration with industry partners by providing proof-of-concept data for drugs in development. As part of this effort, neuroblastoma PDX models are being molecularly characterized to identify promising therapeutic candidates. The molecular profiling includes whole exome sequencing (WES), RNA-seq, MethylEPIC array, CytoSNP array, and DNA fingerprinting for quality control. Additionally, demographic and clinical data (e.g., diagnosis, disease site, disease status) are shared. These characterized PDX models, matched with patient tumors, guide model selection for preclinical drug testing.

  Study phs003163

• Spindle Assembly Checkpoint Competency Determines Sensitivity to KIF18A Inhibition in Small-Cell Lung Cancer

  This study examined the biological determinants of response to KIF18A inhibition in small-cell lung cancer (SCLC), a chromosomal instability-high cancer. The study used patient tumor datasets, SCLC cell line models, genomic and transcriptomic profiling, drug sensitivity testing, live-cell imaging, genetic perturbation, and pharmacologic inhibition to assess chromosomal instability, mitotic regulation, and spindle assembly checkpoint function. Although KIF18A expression was elevated in SCLC and associated with chromosomal instability, proliferation, and neuroendocrine transcriptional programs, these features did not predict drug sensitivity. Instead, response to KIF18A inhibition was primarily determined by spindle assembly checkpoint competency, with SAC-proficient cells undergoing sustained mitotic arrest and apoptosis and SAC-defective cells showing resistance. The dbGaP-accessible data will include de-identified RNA-seq-derived expression data and associated sample metadata for the NIH/NCI patient-derived SCLC cell line component of the study. These data were used to assess selected gene expression features, including KIF18A-related expression and a neuroendocrine-related score based on Neuroendocrine-associated genes. No direct participant identifiers will be included.

  Study phs004869

• Subtyping of Small Cell Lung Cancer Using ChIP-Seq of Plasma Cell-Free Nucleosomes and Matched Tumor Transcriptomes

  We undertook an observational study using plasma collected from patients with small cell cancer who received care at the National Cancer Institute (NCI). Human subjects committee at NCI approved the studies; all patients provided written informed consent for plasma, tumor, and matched normal sample sequencing. Sequence data for 8 samples in phs003628 are available under phs004200.

  Study phs003628

• Blockade of TGF Beta Drive Hyper Progression on Small Cell Lung Cancer

  To uncover mechanisms underlying divergent outcomes in patients with small cell lung cancer (SCLC), a highly aggressive neuroendocrine malignancy, we performed bulk transcriptomics of pre-treatment tumor biopsies from patients enrolled in a clinical trial of bintrafusp alfa, a bifunctional fusion protein targeting PD-L1 and TGF-β. We identified marked elevation of IFN-γ signaling and MHC class II expression. In contrast, Hyperprogressive disease (HPD) was associated with systemic immune suppression, impaired cytotoxicity, and, unexpectedly, tumor-intrinsic activation of TGF-β signaling and stemness. Functional studies confirmed that intact TGFβR2-mediated signaling is required for the hyperproliferative response to TGF-β blockade, revealing a context-dependent tumor-suppressive role for TGF-β.Although TGF-β is widely regarded as an immunosuppressive driver in advanced cancers, our findings reveal a tumor-intrinsic, growth-constraining role for TGF-β signaling in SCLC. Disrupting this restraint can accelerate tumor progression, providing a mechanistic basis for HPD and highlighting the need for biomarker-driven strategies that account for tumor-intrinsic signaling when applying stromal-targeted immunotherapies.

  Study phs004200

• Whole Genome Sequencing for Metastatic Mutational Burden in Extraskeletal Myxoid Chondrosarcoma

  Extraskeletal myxoid chondrosarcoma (EMC) is an ultra-rare cancer. Though it has a favorable prognosis and an indolent course, it has high rates of local recurrence and metastasis to the lungs. EMC is most often characterized by a translocation involving the NR4A3 gene most often fusing with EWSR1, leading to constitutive expression of NR4A3, the biological significance of which is unknown. Our study presents a case of EMC with case-matched lung and advanced pelvic metastases. We conducted Whole Genome Sequencing to examine differences in the mutational landscape at two different stages of metastasis. This is the first study to our knowledge to analyze mega-base scale structural variants (SVs) in EMC. Our data validates copy number variants (CNVs) found in previous studies. While the primary tumor and lung metastasis had similar somatic variations and CNVs, the pelvic metastasis had more SVs with especially increased mutational burden of SVs in chromosome 2. This suggests that different molecular drivers appear in more advanced, relapsing EMC compared with the primary tumor and early lung metastasis. The sequencing data is available through dbGaP.

  Study phs003305

• Childhood Cancer Data Initiative (CCDI): Enhancement of Data Sharing in Pediatric, Adolescent and Young Adult Cancers

  NCI's Childhood Cancer Data Initiative (CCDI) is building a community centered around childhood cancer care and research data. Through enhanced data sharing, we can improve our understanding of cancer biology to improve preventive measures, treatment, quality of life, and survivorship, as well as ensure that researchers learn from every child with cancer. While childhood cancers represent the leading cause of death in children over the age of 1, they are collectively rare, comprising approximately 1%‒3% of cancers diagnosed annually in the United States. Information on diagnosis, treatment, and outcomes is often stored at the hospital or institution where a child is treated, making it difficult to answer scientific questions about childhood cancer. Sharing clinical care and research data generated by children's hospitals, clinics, or networks broadly with the community can help us learn faster and, on a scale much larger than any single institution caring for children can learn on its own. To exploit the rapid advances in high-throughput DNA sequencing technologies and realize the goals of precision cancer medicine, the UMICH Cancer Center established the Michigan Oncology Sequencing Center (MI-ONCOSEQ). This UMICH Cancer Center provisions genomic data derived from the Michigan Oncology Sequencing Center (MI-ONCOSEQ) clinical sequencing assay for patients that fall within the inclusion criteria of the CCDI data sharing initiative. An "integrative sequencing approach" carried out in a CLIA-certified laboratory is utilized to provide a comprehensive landscape of the genetic alterations in individual tumor specimens for the purpose of identifying informative and/or actionable mutations. Using a number of computational pipelines that we have developed in-house or have adapted from the public domain, candidate molecular aberrations are nominated and then analyzed by scientists for clinical significance and/or relevance. This approach enables the detection of point mutations, insertions/deletions, gene fusions and rearrangements, amplifications/deletions, and outlier expressed genes. Furthermore, we can identify certain germline alterations that may also be relevant.

  Study phs002431

• GENomics of CAncer DisparitiEs (GENCADE)

  Genetic ancestry-concordant RNA splicing events in men with prostate cancer (PCa) involve cancer promoting genes and associate with disease recurrence after radical prostatectomy. Patients diagnosed with PCa who were scheduled to undergo radical prostatectomy or biopsy were enrolled in the GENCADE study, according to the Institutional Review Board (IRB)-approved protocol Pro00053535 (NCT02229565). With respect to NCT02229565, the descriptors “African American” and “Caucasian American” refer to the same patients described as “Black” and “White”, respectively, herein. Patients were also co-enrolled to the Duke BioRepository & Precision Pathology Center (BRPC) protocol (Pro00035974) to facilitate tissue collection.

  Study phs003731

• Cardiovascular Cell Therapy Research Network - A Phase I, First-in-Human, Multicenter, Randomized, Double-Blinded, Placebo-Controlled Study of the Safety and Efficacy of Allogeneic Mesenchymal Stem Cells in Cancer Survivors With Anthracycline-Induced Cardiomyopathy (CCTRN-SENECA-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To examine the safety and feasibility of delivering allogeneic human mesenchymal stem cells (allo-MSCs) by transendocardial injection to cancer survivors with left ventricular (LV) dysfunction secondary to anthracycline-induced cardiomyopathy (AIC).Background: Anthracycline-based chemotherapies are effective in treating various forms of cancer. The risk of anthracycline-induced cardiomyopathy (AIC) has been primarily related to the lifetime cumulative dose and every exposure to an anthracycline carried some risk of inducing cardiac dysfunction. Historically, AIC has been irreversible with poor prognosis and most prevalent in young persons and females. Previous studies have determined that patients with AIC have approximately 3.5-higher relative risk of death within 5 years compared to ischemic or nonischemic cardiomyopathy. There is currently no effective treatment for AIC.There are several shared pathological features between AIC and heart failure (HF). A promising approach to treatment of HF is the administration of bone marrow–derived mesenchymal stromal cells (MSCs). The SENECA trial was the first-in-human study of allo-MSCs in patients with LV dysfunction secondary to AIC.Participants: Male and female cancer survivors aged 18 to 79 years, with a diagnosis of AIC, were recruited for the SENECA trial. Inclusion criteria included: initial diagnosis of AIC at least 6 months prior to consent; left ventricular ejection fraction (LVEF) ≤45%; receiving stable, optimally tolerated therapy with beta-blockers, angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers, and/or aldosterone antagonists unless contraindicated; no evidence of ischemic heart disease; cancer-free for at least 2 years with a low likelihood of recurrence (a 5-year risk of recurrence estimated at ≤30%).Participants were excluded for any condition that, in the judgment of the Investigator or Sponsor, would be a contraindication to enrollment, study product administration, or follow-up.Design: The primary objectives of SENECA were the safety of allo-MSC administration, the feasibility of delivering the cells to the subjects, and collecting outcome measures. The secondary objectives were to determine the effects of allo-MSC administration on LV function and functional status from baseline to 6 months and from baseline to 12 months after treatment.The trial was initiated with a 6-subject, open-label lead-in phase. Between September 2016 and December 2016, 6 candidates consented to participate and received 20 transendocardial, electromechanically-guided injections of allo-MSCs. A complete safety report of the 6 subjects was provided for review by the data safety monitoring board and FDA. Subsequently, the study was allowed to proceed to the randomization phase.Baseline evaluations to determine eligibility included: cardiac magnetic resonance imaging (CMR), 6-min walk test (6MWT), Minnesota Living with Heart Failure Questionnaire (MLHFQ), and a comprehensive laboratory panel that included N-terminal pro-brain natriuretic peptide (NT-proBNP).Between March 2017 and October 2018, 31 eligible subjects were randomized 1:1. There were 14 subjects enrolled in the treatment arm and 17 subjects in the placebo arm. Participants received either 1 × 108 allo-MSCs in 8 ml of Buminate 5% solution or a placebo (8 ml of cell-free Buminate solution) delivered via 20 transendocardial injections (0.4 ml each).All subjects were followed for 1 year, with evaluations at: day 0 (day of injection), day 1, day 7, day 30, day 180, and day 365. A physical examination, electrocardiogram, and laboratory evaluations were conducted at each visit, along with the assessment of adverse events and review of medications. In addition, at 6 months and 1 year, subjects performed the following tests: 6MWT, MLHFQ, and CMR. Serum samples were collected at baseline and 1, 6, and 12 months after treatment to determine whether there were any significant changes in panel reactive antibody (PRA).Conclusions: The SENECA trial demonstrated that allo-MSCs are well-tolerated and that transendocardial injections of allo-MSCs are feasible in patients with AIC. Although the SENECA trial was not designed to test efficacy, a subset of participants was included in secondary endpoint analysis. The only statistically significant differences observed were with the MLHFQ and 6MWT assessments which favored the intervention. Larger studies will be required to determine the efficacy of allo-MSCs treatment.

  Study phs004712

• FORCE Trial: Resistance Training Intervention Among Colon Cancer Patients

  Our study population was composed of participants of the FORCE clinical trial, which was a randomized resistance training intervention study for Stage II and III colon cancer patients undergoing chemotherapy. Patients were recruited from Kaiser Permanente of Northern California, the Penn State Cancer Institute, and the Dana Farber Cancer Institute and were assigned to resistance training or usual care within the first weeks of adjuvant chemotherapy. Lean mass was evaluated at the beginning and the end of the study, and participants were monitored for toxicities associated with chemotherapy and chemotherapy dose modifications. Genome-wide DNA methylation was assayed using peripheral blood collected at the FORCE trial baseline and the post-intervention visit using the Infinium MethylationEPIC v1.0 (EPIC) BeadChips (Illumina). EPIC array signal intensities were preprocessed and used to estimate site-specific DNA methylation levels, which were used for the estimation of several epigenetic clocks. Our study hypothesized that those with accelerated epigenetic age at the beginning of chemotherapy would be more likely to have modifications to their assigned chemotherapy regimen driven by a higher burden of chemotoxicities. We also hypothesized that epigenetic age acceleration would significantly increase over the course of chemotherapy and that a resistance training intervention would reduce the rate of change.

  Study phs003671