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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.

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• 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