6048 results for "canc*"

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• NCTN: Treatment of Atypical Teratoid/Rhabdoid Tumors (AT/RT) of the Central Nervous System with Surgery, Intensive Chemotherapy, and 3-D Conformal Radiation (ACNS0333)

  Study ID: ACNS0333NCT Number: NCT00653068 Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: Treatment of Atypical Teratoid/Rhabdoid Tumors (AT/RT) of the Central Nervous System with Surgery, Intensive Chemotherapy, and 3-D Conformal Radiation (ACNS0333)Trial Description: This phase III trial studies the side effects of combination chemotherapy, 3-dimensional conformal radiation therapy, and an autologous peripheral blood stem cell transplant, and to see how well they work in treating young patients with atypical teratoid/rhabdoid tumor of the central nervous system. Giving high-dose chemotherapy before an autologous peripheral blood stem cell transplant stops the growth of cancer cells by stopping them from dividing or killing them. Giving colony-stimulating factors, such as G-CSF, helps stem cells move from the bone marrow to the blood so they can be collected and stored. Chemotherapy or radiation therapy is then given to prepare the bone marrow for the stem cell transplant. The stem cells are then returned to the patient to replace the blood-forming cells that were destroyed by the chemotherapy or radiation therapy. Clinical data presented in the following publication(s): PMID 32105509 Disease type(s): CNS Neoplasm (Primary Tumor) - Embryonal Tumors of the CNSClinical Dataset(s) included:NCT00653068-D1 (PMID 32105509): There are 3 datasets (-D1 through -D3) for ACNS0333's primary publication, PMID 32105509. This dataset, NCT00653068-D1, provides information on the flow of patients enrolled in ACNS0333 through therapy shown in the CONSORT diagram in Figure 2, baseline characteristics, extent of tumor resection, methylation, ATRT subgroup, SMARCB1 status, induction response, survival, and cause of death data. There is one row for each patient enrolled.NCT00653068-D2 (PMID 32105509): There are 3 datasets (-D1 through -D3) for ACNS0333's primary publication, PMID 32105509. This dataset, NCT00653068-D2, provides specific incidence of grade 4 or higher adverse events that occurred in 5% or more of patients in at least one phase of therapy, as presented in Table A2 (Treatment-Associated Toxicity).NCT00653068-D3 (PMID 32105509): There are 3 datasets (-D1 through -D3) for ACNS0333's primary publication, PMID 32105509. This dataset, NCT00653068-D3, provides event-free survival (EFS) data for the primary analytic comparison: ACNS0333 patients 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 phs004137

• MP2PRT: Genomic and Molecular Characterization of Biomarkers Associated with Tumor Angiogenesis, DNA Repair, and Immunologic Tolerance using Samples from the NRG Oncology Phase 3 Randomized Trial, GOG-0240 (NCT00803062)

  The Molecular Profiling to Predict Response to Treatment (MP2PRT) program is part of the NCI's Cancer Moonshot Initiative. The aim of this program is the retrospective characterization and analysis of biospecimens collected from completed NCI-sponsored trials of the National Clinical Trials Network and the NCI Community Oncology Research Program. This study is one of the selected studies under this program. For this study, genomic characterization (WGS, WXS, Total RNAseq, miRNAseq) has been performed on cervical tumor tissue from patients with advanced disease (persistent, recurrent, and metastatic) and matching germline samples. It is hypothesized that the characterization of these tissues using next generation sequencing will lead to the identification of relevant novel genetic aberrations within the immunologic, DNA repair, and tumor angiogenesis domains that dichotomize the study population into exceptional responders and non-responders to systemic therapy, with a spectrum of response manifesting between the two extremes.

  Study phs002293

• SMARCB1 Missense Mutants Destabilize SWI/SNF Complex Stability and Remodeling Activity

  Study Design and Aims: This study utilizes a comprehensive deep mutational scanning (DMS) approach to systematically assess the functional consequences of 8,418 amino acid substitutions in the SMARCB1 gene, a core subunit of the SWI/SNF chromatin remodeling complex. The primary aim is to evaluate how missense mutations affect SMARCB1's tumor suppressor function and its role in the assembly and activity of distinct SWI/SNF subcomplexes (cBAF, PBAF, and GBAF). By addressing functional impacts across the entire coding sequence of SMARCB1, the study seeks to elucidate the molecular mechanisms underlying chromatin remodeling deficiencies caused by SMARCB1 missense mutations and their implications for cancer biology and diagnostics.Population Information: The study focuses on functional variants of SMARCB1, specifically addressing the mutational landscape relevant to cancers such as malignant rhabdoid tumor (MRTK), atypical teratoid rhabdoid tumor (ATRT), and renal medullary carcinoma (RMC). Variants are modeled using in vitro systems to characterize their functional consequences.Molecular Technologies: This study first uses DMS for the systematic identification of functionally disruptive mutations in SMARCB1. Top hits identified through DMS were validated using complementary molecular technologies. These included RNA sequencing (RNA-Seq) to evaluate transcriptional changes associated with specific mutations, ATAC-sequencing (ATAC-seq) to assess chromatin accessibility and remodeling activity, and mass spectrometry to analyze SWI/SNF complex composition in the presence of specific mutations. Principal Findings: The study identifies a subset of missense mutations within the RPT2 domain of SMARCB1 that impair SWI/SNF complex stability and chromatin remodeling, despite retaining detectable protein expression. Notably, these findings challenge current diagnostic methods that rely solely on immunohistochemistry to assess protein presence, as some functionally disruptive mutations retain detectable expression.Data Available through dbGaP: The dataset includes RNA-Seq and ATAC-seq data detailing transcriptional and chromatin accessibility changes associated with validated mutations, mass spectrometry data documenting SWI/SNF complex composition and stability in the context of specific mutations, and functional assay results for all SMARCB1 variants assessed via DMS. This dataset provides a valuable resource for understanding SMARCB1's role in chromatin biology and for improving the classification of variants of uncertain significance (VUS) in clinical diagnostics.

  Study phs003896

• Transcriptome-Wide Association Study (TWAS) to Identify Susceptibility Genes for Colorectal Cancer

  This study included genotype data from 420 study participants of East Asian descent, along with RNA-seq (n=300) and small RNA seq data (n=400) generated from their colorectal tissue samples. We used the transcriptome data and genotype data from these individuals to build a prediction model for each coding gene and long non-coding RNA, and perform a Transcriptome-Wide Association Study (TWAS) of colorectal cancer in East Asian populations.

  Study phs002813

• Transcriptional Profiling of a Dana-Farber Cancer Institute Early-Onset Colorectal Cancer Cohort

  We generated bulk RNA-seq data from 83 early-onset colorectal cancer primary tumors. Tumor samples were obtained from patients seen at the Dana-Farber Cancer Institute's Gastrointestinal Cancer Center with an age of diagnosis less than 50 years.

  Study phs004807

• GWA Study of Oral Cavity, Pharynx and Larynx Cancers in European, and North and South American Populations - CIDR

  There is striking geographical variation in head and neck cancer (HNC) incidence globally. Some of the highest incidence rates have been observed in Southern and Eastern Europe and South America. The goal of this project is to assess susceptibility loci across and within ancestral backgrounds, using the All of Us array. Ten studies have come together in this initiative.

  Study phs002503

• Proteogenomic Characterization of Human Uterine Cervical Cancer

  We report a proteogenomic analysis of human cervical cancer. Mutation-phosphorylation correlations revealed associations of proliferation and invasion-related signaling pathways with somatic mutations in significantly mutated genes. mRNA-protein abundance correlations identified molecules with tumor promoting or suppressing functions correlating with patient survival. Integrated clustering of mRNA, protein, and phosphorylation data provided six subtypes (Sub1-6) of cervical cancer. Compared with the previous subtypes identified from transcriptome data, protein data further identified subgroups of squamous carcinoma and adenocarcinoma based on stromal and immune characteristics. In the squamous subgroups, Sub4 showed higher T-cell immunity than Sub5, and myeloid-derived suppressive immune cells that inhibit T-cell proliferation were enriched in Sub5. In the adeno subtypes, Sub3 had higher myofibroblasts that modulate anti-tumor immunity than Sub6. These stromal and immune features were consistent with the survival patterns of patients in the subtypes. Our proteogenomic analysis provides patient stratification and therapeutic targets in cervical cancer and improves our understanding of cancer biology.

  Study phs002916

• Cancer Associated Fibroblasts Drive Epithelial to Mesenchymal Transition and Classical to Basal Change in Pancreatic Cancer Cells with Loss of IL-8 Expression

  We examined the transcriptional changes induced by cancer associated fibroblasts in pancreatic ductal adenocarcinoma patient-derived tumor organoids. We hypothesized that cancer associated fibroblasts (CAFs) impacted tumor cell transcriptional phenotypes to promote more tumorigenic behavior. Using patient-matched cells from 8 patients, we compared the transcriptional profiles of patient-derived organoids in monoculture to patient-derived organoids co-cultured with autologous CAFs. Similarly, we looked at the transcriptional changes in matched patient-derived CAFs grown in monoculture or co-cultured with patient-derived organoids. With a focus on intercellular crosstalk, we identified crosstalk between CAFs and patient-derived organoids through changes in tumor cell classification (classical vs basal) and a phenotype of more prominent epithelial to mesenchymal transition. We also identified IL8 as a regulator for maintaining a classical tumor cell phenotype. This was identified by bulk RNA sequencing and examined dynamically in organoid-CAF co-culture. This dbGaP deposit is the bulk RNA sequencing data for these 8 patients. The deposit for 3 additional patients from this cohort who did not receive neoadjuvant chemotherapy can be found at: phs003563.

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• Multiomic Landscape of Multiple Myeloma Precursor and Relapsed Disease

  Multiple myeloma (MM) is a treatable, though incurable, plasma cell malignancy. The molecular mechanisms driving disease onset and the emergence of drug resistance remain elusive. To better characterize the mutational, transcriptional, and epigenetic alterations that accompany MM disease evolution, we accessed molecular data from MM patients treated at Moffitt Cancer Center, with bone marrow biopsies collected between 2011 and 2023.We performed scMultiome (single-cell, paired RNA/ATAC-Seq, 10x Genomics) on 18 CD138+-selected bone marrow aspirate samples, including: 2 healthy donors, 3 patients with monoclonal gammopathy of undetermined significance (MGUS), 4 with smoldering myeloma (SMM), 3 with newly diagnosed MM (NDMM), 1 with early relapse MM (ERMM, 1 to 3 lines of therapy), and 5 with late relapse MM (LRMM, 4 or more lines of therapy). Our dataset includes a sequential sample: a patient with a premalignant condition ("scMultiome_SMM_4") that progressed to active myeloma ("scMultiome_NDMM_3"). These data allow for the assessment of transcriptional and epigenetic dysregulation at the cellular level. Our findings illustrate the dynamic epigenetic and transcriptional landscapes that accompany MM disease progression.We also conducted CUT&Tag analysis on 4 NDMM and 4 LRMM samples to map histone modifications, specifically H3K27ac, to investigate their role in transcriptional reprogramming observed in advanced stages of MM. This analysis revealed sample heterogeneity in terms of super-enhancer-regulated genes associated with active transcription.This cohort also includes samples from the clinical trial NCT04151667, “Daratumumab-Based Response-Adaptive Therapy for Older Adults With Newly Diagnosed Multiple Myeloma.” We performed scRNAseq (single-cell RNA sequencing, 10x Genomics) on 30 CD138+-selected bone marrow aspirate samples and 31 pre-sort samples featuring bone marrow mononuclear cells of various cell types from 5 healthy donors and 11 patients with newly diagnosed MM (NDMM). Our dataset includes sequential samples for all 11 NDMM patients, both prior to induction therapy (denoted by ‘a') with Daratumumab and Dexamethasone, and at cycle 2 day 22 (C2D22, i.e., 60 days after induction therapy start, denoted by ‘b'). For three NDMM patients, we also have samples at relapse (denoted by ‘c'). These data allow for the assessment of transcriptional dysregulation at the single-cell level in both the tumor and immune-tumor microenvironment, associated with Daratumumab treatment in NDMM patients.In addition to the molecular data, demographic, and phenotypic information for all samples is provided.

  Study phs003892

• Whole-Exome Sequencing of Acute Myeloid Leukemia

  The Fanconi anemia (FA) pathway is a tumor-suppressive network comprised of at least 22 genes. We demonstrate that the FA pathway disruption sensitizes Acute Myeloid Leukemia (AML) cells to PLK1 inhibition (iPLK1). We obtained cryopreserved mononuclear cells (MNCs) derived from the bone marrow of 16 adult AML patients from the Indiana University Simon Comprehensive Cancer Center (IUSCCC) Biospecimen Collection and Banking Core as a panel for comparative volasertib (iPLK1) sensitivity assessment. Through whole-exome sequencing (WES), we identified multiple pathogenic mutations in FA pathway and FA pathway-associated genes. We found that higher FA pathway mutation burden correlated with sensitivity to volasertib.

  Study phs003966

• Genomic Profiling of Pediatric B-cell Acute Lymphoblastic Leukemia

  Pediatric leukemia is the most common type of childhood cancer and, despite tremendous progress in treatment, remains the second leading cause of cancer deaths in children. B-cell acute lymphoblastic leukemia (B-ALL) is the most common type of pediatric leukemia. Recent studies using transcriptional profiling of large cohorts of pediatric B-ALL have shown that patients can be grouped into transcriptional subtypes that are often defined by specific driver mutations. Interestingly, many of these mutational subtypes are defined by gene fusions or rearrangements that drive altered expression of transcription factors (ETV6-RUNX1, PAX5, DUX4, TCF3-PBX1, ZNF384) or in chromatin regulatory machinery (KMT2A), suggesting that transcriptional dysregulation is a major driver of B-ALL. While the transcriptional distinctions are clear, the relationship between patients in terms of their chromatin regulatory landscape remains unclear. To address this, we profiled gene expression, open chromatin, and 3D genome folding in patient derived B-ALL samples. We identified that at the level of 3D genome organization, many chromatin interactions and looping events are shared across mutational subtypes, suggesting that shared transcriptional programs, in addition to group specific driver mutations, possibly regulate the chromatin landscape in B-ALL. Using RNA-seq and ATAC-seq data, we were able to identify "latent" signatures of expression related to non-mutant transcription factors (TFs) that also contribute to expression heterogeneity across TF subtypes. These are related to patient specific patterns of 3D genome folding, and in some cases, are predictive of disease outcomes. This study helps shed light on the chromatin landscape in B-ALL and furthers our understanding of the interactions between diverse mutant TFs that drive B-ALL and non-mutant TFs that help shape the B-ALL chromatin landscape.

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• Patient-Derived Breast Cancer Organoid Study

  This study uses normal and tumor tissues from breast cancer patients to derive 3D cell culture models called organoids. Organoid technology is an innovative platform that can be used to study a patient's tumor in a dish ex-vivo. As part of this study we have comprehensively characterized these models using next-generation sequencing for: 1) pathogenic SNVs in a targeted gene panel 2) copy number alterations 3) transcriptome analysis using RNA sequencing and 4) single-cell RNA sequencing

  Study phs002722

• NCTN: Radiation Therapy and Cisplatin with or without Cetuximab in Treating Patients with Stage III or Stage IV Head and Neck Cancer (RTOG-0522)

  Study ID: RTOG-0522NCT Number: NCT00265941 NRG OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Phase III Trial of Concurrent Accelerated Radiation and Cisplatin vs Concurrent Accelerated Radiation, Cisplatin, and Cetuximab (C225) [followed by Surgery for Selected Patients] for Stage III and IV Head and Neck Carcinomas (RTOG-0522)Trial Description: RATIONALE: Radiation therapy uses high-energy x-rays to kill tumor cells. Drugs used in chemotherapy, such as cisplatin, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Cisplatin may also make tumor cells more sensitive to radiation therapy. 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. Giving radiation therapy and cisplatin together with cetuximab may kill more tumor cells. It is not yet known whether radiation therapy and cisplatin are more effective with or without cetuximab in treating head and neck cancer.PURPOSE: This randomized phase III trial is studying radiation therapy, cisplatin, and cetuximab to see how well they work compared to radiation therapy and cisplatin in treating patients with stage III or stage IV head and neck cancer. Clinical data presented in the following publication(s):PMID 25154822 Disease type(s): Head and Neck Neoplasm - Squamous Cell CarcinomaClinical Dataset(s) included:NCT00265941-D1 (PMID 25154822): There are two datasets for RTOG-0522's primary publication 25154822 (-D1 and -D2). This dataset, NCT00265941-D1, contains reasons for exclusion, treatment received, treatment discontinuation reasons, baseline characteristics, p16 status, EGFR expression, survival, distant metastases, and use of feeding tube data.NCT00265941-D2 (PMID 25154822): There are two datasets for RTOG-0522's primary publication 25154822 (-D1 and -D2). This dataset, NCT00265941-D2, contains adverse event data. This dataset is limited to grade 1-4 adverse events that were attributed as definitely, probably, or possibly related to protocol treatment and occurred in at least 10% of patients in either arm. The acute and late periods are defined as 90 days or fewer and > 90 days, respectively, from the start of radiation therapy.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 phs004190

• Single-Cell ATAC and RNA Sequencing of Human Breast Cancer Reveals Salient Cancer-Specific Enhancers

  Matched single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq) were performed for 12 human breast tumor samples, 4 normal human mammary reduction samples, and 4 human breast cancer cell lines (HCC1143, SUM149PT, MCF7, and T47D). Both scATAC-seq and scRNA-seq assays resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. In this work, we quantitatively linked variation in chromatin accessibility to gene expression across malignant and non-malignant cell types from patient samples. We then showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.

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• HINTS Geo-Coded Data 2018 (HINTS 5 Cycle 2)

  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 mail-mode data collection cycles over the course of four years. The second round of data collection for HINTS 5 (Cycle 2) was conducted from January 26 through May 2, 2018 with a goal of obtaining 3,500 completed questionnaires. A total of 3,504 respondents are included in the final sample.

  Study phs004217

• Molecular Profiling of Head and Neck Squamous Cell Carcinomas

  This study performed targeted DNA sequencing of key NF-κB signaling pathway regulatory genes in matched tumor and normal tissues from patients with HPV-associated head and neck squamous cell carcinoma (HNSCC). A custom Ion Torrent AmpliSeq panel was designed to interrogate ten genes whose products regulate NF-κB activity and are frequently altered in the NF-κB-active subtype of HPV+ HNSCC: TRAF3, CYLD, TRAF2, NFKBIA, TNFAIP3, TRAF6, BIRC2, BIRC3, MYD88, and MAP3K14. The panel comprised 250 overlapping amplicons in a 2-primer pool format, achieving 93.65% coverage across the 24.86 kb target region. Genomic DNA was isolated from formalin-fixed paraffin-embedded (FFPE) macro-dissected tumor and matched normal tissues at the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab. This sequencing was performed as part of a study developing a clinical assay to identify HPV+ HNSCC subtypes defined by NF-κB activity for the purpose of risk stratification and de-escalation of radiation therapy.

  Study phs004476

• Prediction of Resistance and Sensitivity to HER2 Targeted Therapy in the Neoadjuvant Setting

  Women with breast cancers that overexpress HER2 are at greater risk for disease progression and death than women whose tumors do not overexpress HER2. Trastuzumab, a recombinant humanized monoclonal antibody against the extracellular domain of the HER2 protein blocks downstream signaling of HER2 and substantially improves the efficacy of chemotherapy in women with metastatic and early-stage HER2-positive breast cancers. Because resistance to trastuzumab eventually results in progressive disease in the metastatic setting and contributes to recurrence following adjuvant trastuzumab-based therapy, it is important to develop agents other than trastuzumab that target HER2 signaling through different mechanisms of action. Lapatinib is an oral, small molecule, dual tyrosine kinase inhibitor of HER2 and EGFR. Lapatinib has shown a lack of cross-resistance with trastuzumab in preclinical studies and activity in women with HER2-positive, metastatic breast cancer that has progressed during trastuzumab treatment. Trastuzumab blocks the downstream signaling of HER2 by binding to the extracellular domain of the receptor. Lapatinib binds to the intracellular domains of HER2 and EGFR and prevents activation of downstream signaling pathways. Because of this different mechanism of action, lapatinib may be effective in trastuzumab-resistant disease. The study will also provide important safety information on trastuzumab and lapatinib combinations immediately following anthracycline exposure, and also provide an initial direct comparison of cardiac effects of trastuzumab and lapatinib when incorporated into a standard sequential adriamycin and cyclophosphamide (AC) followed by weekly paclitaxel neoadjuvant regimen. Availability of a second agent that can interrupt HER2-signaling pathways through completely different mechanisms than those of trastuzumab offers the potential for further improvement in the management of patients with HER2-overexpressing breast cancer in both the adjuvant and metastatic setting. Co-administration of both trastuzumab and lapatinib with chemotherapy may be important in improving outcomes in subsets of HER2-positive breast cancers. However, use of two inhibitors of the HER2 pathway will increase costs and may increase toxicity, so it will be important to identify the subsets of patients who would benefit from the dual therapy. Inhibition of HER2 with a single agent clearly is sufficient for many patients as evidenced by the results of the trastuzumab trials. Therefore, co-administration to unselected populations of women with HER2-positive breast cancers would not represent an optimal approach. Given the activity of lapatinib, it is likely that it will also be sufficiently active in inhibiting HER2-pathway activation in some patients to allow for its use as the sole inhibitor of the HER2 pathway. Different populations may also derive greater benefit from one of the HER2-blocking agents relative to the other. Identification of potential predictive factors for pathologic complete response to the combination or to either agent administered alone in neoadjuvant trials would provide important information for adjuvant trials designed to definitively address these important issues. This study will compare 3 combined chemotherapy regimens: AC followed by paclitaxel plus trastuzumab and lapatinib, AC followed by paclitaxel plus lapatinib, and AC followed by paclitaxel plus trastuzumab given before surgery to patients with HER2-positive breast cancer.Tumor samples were collected prior to and post-treatment, and RNA sequencing was performed with this version.

  Study phs003275

• NCTN_NCORP: The Men's Eating and Living (MEAL) Study: A Randomized Trial of Diet to Alter Disease Progression in Prostate Cancer Patients on Active Surveillance (CALGB-70807)

  Study ID: CALGB-70807NCT Number: NCT01238172 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN_NCORP: The Men's Eating and Living (MEAL) Study: A Randomized Trial of Diet to Alter Disease Progression in Prostate Cancer Patients on Active Surveillance (CALGB-70807)Trial Description:RATIONALE: Eating a diet high in vegetables may slow down disease progression in patients with prostate cancer.PURPOSE: This randomized clinical trial is studying how well diet works in altering disease progression in patients with prostate cancer on active surveillance. Clinical data presented in the following publication(s):PMID 31935026 Disease type(s): Reproductive System Neoplasm, Male - Prostate CancerClinical Dataset(s) included:NCT01238172-D1 (PMID 31935026): Dataset NCT01238172-D1 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains baseline characteristics, including baseline serum PSA values.NCT01238172-D2 (PMID 31935026): Dataset NCT01238172-D2 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for the consort diagram (inclusion/exclusion status, treatment arm).NCT01238172-D3 (PMID 31935026): Dataset NCT01238172-D3 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains survival and time to alternative treatment data.NCT01238172-D4 (PMID 31935026): Dataset NCT01238172-D4 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for patient off treatment reasons.NCT01238172-D5 (PMID 31935026): Dataset NCT01238172-D5 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for the dietary patterns analysis included in Table 2 and the eTable.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 phs004238

• The Haplotype-Resolved Genome and Epigenome of the Aneuploid HeLa Cancer Cell Line

  The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes. Reprinted from Adey et. al. 2013, Nature, with permission from Nature Publishing Group.

  Study phs000642

• Study of Novel Approaches for Prevention (SNAP-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 two self-regulation interventions versus control in reducing weight gain in young adults over an average follow-up of 3 years.BackgroundWeight gain occurs commonly throughout adulthood and has been associated with many adverse health outcomes. Weight gain in adults aged 18 – 35 years had stronger negative associations with critical outcomes such as cancer risk and mortality compared to weight gain at later ages. Developing effective approaches to reduce weight gain in young adults was therefore an important public health priority and focus of the SNAP study.ParticipantsSNAP targeted an enrollment of 600 participants (25% men and 25% racial / ethnic minorities), age 18–35, with a BMI of 21–30.9 kg/m2. Eligibility requirements focused on ability to participate in the program (e.g., internet access, English speaking), safety (no history of eating disorders, ability to walk for activity) and completion of screening and baseline assessment visits.Potential subjects were excluded due to pregnancy, diabetes, alcohol or substance dependence, psychiatric disorders, and any medical problem that could cause unintentional weight change.A total of 599 subjects were enrolled and randomly assigned into one of three treatment arms. 202 participants were enrolled in the control group, 197 assigned to the large changes group, and 200 assigned to the small changes group.DesignThe Study of Novel Approaches to Weight Gain Prevention (SNAP) was a 3-armed randomized controlled clinical trial that compared self-regulation with small daily behavior changes (Small Changes), self-regulation with large periodic behavior changes (Large Changes), and a minimal treatment control.The Control group attended one face-to-face meeting where they were introduced to the issue of weight gain, the concept of self-regulation, and an overview of both Small and Large Change approaches to potentially prevent weight gain.The Small and Large Changes interventions both began with 10 face-to-face group meetings over 4 months. Participants in Small Changes were taught to make daily small changes (approximately 100 kcal/day) in both diet and physical activity. Participants were given pedometers and instructed to add 2000 steps per day above their baseline activity level.Large Changes focused on losing weight during the initial four-month program to create a buffer against subsequent weight gain. To achieve this, participants were prescribed a calorie goal based on a 500- 1000 kcal deficit from baseline to use during the initial 8 weeks. They were also encouraged to gradually increase moderate intensity physical activity to a goal of 250 minutes/week, the level recommended for weight loss maintenance.All participants were scheduled to complete assessments at baseline, month 4, year 1 and year 2. To encourage self-regulation, participants were instructed to weigh themselves daily and submit their weight via the study website, text message or email. They received monthly email feedback on their weight, which was based on a color-coded system and either reinforced their success, encouraged problem-solving, or recommended additional strategies to help reverse weight gain. Each year, participants were invited to join two 4-week online refresher campaigns reinforcing the behaviors taught during the initial program. All participants received identical quarterly newsletters and personalized feedback reports on their assessment data, including the Control group.The primary outcome was the mean weight gain over an average follow-up of 3 years. Secondary outcomes were the proportion of participants gaining ≥1 pound (chosen to represent a stringent criterion of weight gain over baseline) and the incidence of obesity (BMI≥30 kg/m2) over the 3 years.ConclusionsSelf-regulation interventions involving small or large changes were both effective in reducing the mean weight gain relative to control over an average follow-up of 3 years. The Large Changes intervention successfully decreased the proportion of participants who experienced weight gains ≥1 pound over the follow-up, and both interventions reduced the incidence of obesity during follow-up by almost 50% relative to Control, representing a clinically significant reduction in risk of developing obesity.Wing RR, Tate DF, Espeland MA, et al. Innovative Self-Regulation Strategies to Reduce Weight Gain in Young Adults: The Study of Novel Approaches to Weight Gain Prevention (SNAP) Randomized Clinical Trial. JAMA Intern Med. 2016;176(6):755-762. doi:10.1001/jamainternmed.2016.1236

  Study phs004682

• Transcriptional Signatures Indicating RB Function Correlate with Response to CDK4/6 Inhibition in Endometrial Cancer

  Here we provide exome-capture RNA sequencing data from 39 endometrial cancer samples from women who participated in two separate abemaciclib combination clinical trials. In addition, whole exome sequencing data are provided for a subset of the tumors for which enough material remained. In the original publication, specific RNA sequencing results were matched to objective response status of the patients in the trials, and it was shown that specific transcriptional signatures could predict function of the RB tumor suppressor and response to abemaciclib in the trials. This study is published. Please cite the original source publication Yang, et al., 2026, PMID: 42531366, for which the data were generated and analyzed.

  Study phs004904

• HINTS Geo-Coded Data 2012 (HINTS 4 Cycle 2)

  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. The second of these cycles (Cycle 2) was conducted from October 2012 through January 2013, including a total of 3,630 respondents.

  Study phs004207

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• Translational Genomics in Cervical Cancer

  This study characterizes the mutational trajectories of locally-advanced cervical cancer (LACC) cases during the course of standard of care chemoradiation therapy (CRT) treatment at Washington University School of Medicine. Tissue biopsied from primary LACC tumors prior to the start of therapy and at mid-treatment and normal blood were collected for sequencing. Whole exome sequencing (WES) was performed on the Illumina NovaSeq 6000 and whole genome sequencing (WGS) was performed on the Illumina NovaSeq X. The most frequently mutated genes and tumor mutational burden were consistent with previously published cervical cancer studies. Raw sequencing reads for all samples are made available here.

  Study phs004441

• NCTN: ASSURE: Adjuvant Sorafenib or Sunitinib for Unfavorable Renal Carcinoma (E2805)

  Study ID: E2805 NCT Number: NCT00326898 ECOG-ACRIN Cancer Research Group Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: ASSURE: Adjuvant Sorafenib or Sunitinib for Unfavorable Renal Carcinoma (E2805) Trial Description: This randomized phase III trial studies sunitinib malate to see how well it works compared to sorafenib tosylate or placebo in treating patients with kidney cancer that has been removed by surgery. Sunitinib malate and sorafenib tosylate may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth and by blocking blood flow to the tumor. Giving sunitinib malate or sorafenib tosylate after surgery may kill any tumor cells that remain after surgery. It is not yet known whether sunitinib malate is more effective than sorafenib tosylate or placebo in treating kidney cancer. Clinical data presented in the following publication(s): • PMID 26969090 • PMID 30130544 • PMID 31471309 • Additional unpublished data from E2805 Disease type(s): Kidney Neoplasm - Renal Cell Carcinoma Clinical Dataset(s) included: • NCT00326898-D1 (PMID 26969090): There are two datasets for E2805's primary publication 26969090 (-D1 and -D2). This dataset, NCT00326898-D1, contains baseline characteristics, stratification factors, treatment dose, number of cycles received, surgery type (radical or partial nephrectomy), and outcome data. Patient ID 1410 corresponds to a duplicate registration for which no data was collected and therefore excluded. NCT00326898-D2 contains toxicity data. Patients in the NCT00326898-D1 through -D7 datasets have the same deidentified patient IDs. • NCT00326898-D2 (PMID 26969090): There are two datasets for E2805's primary publication 26969090 (-D1 and -D2). This dataset, NCT00326898-D2, contains toxicity data. NCT00326898-D1 contains baseline characteristics, stratification factors, treatment dose, number of cycles received, surgery type (radical or partial nephrectomy), and outcome data. Patients in the NCT00326898-D1 through -D7 datasets have the same deidentified patient IDs. • NCT00326898-D3 (Unpublished data): This dataset, NCT00326898-D3, contains data collected on ECOG-ACRIN trial E2805, which are not published in the primary, nonclear cell renal cell carcinoma cohort, or cytokine analysis publication for the trial. NCT00326898-D3 includes information on arm A (Sunitinib) and arm B (Sorafenib) patients that started treatment for E2805 study. The dataset contains information on the time interval from randomization to treatment start date, treatment dose, and reasons for dose modification by cycle. Treatment arm information can be found in D1. Patients in the NCT00326898-D1 through -D7 datasets have the same deidentified patient IDs. • NCT00326898-D4 (Unpublished data): This dataset, NCT00326898-D4, contains data collected on ECOG-ACRIN trial E2805, which are not published in the primary, nonclear cell renal cell carcinoma cohort, or cytokine analysis publication for the trial. NCT00326898-D4 contains toxicity data (by cycle) on hypertension, diarrhea, hand-foot reaction, and/or rash/desquamation while on treatment for E2805 study, including treatment attribution and time interval from randomization to toxicity start date. Patients in the NCT00326898-D1 through -D7 datasets have the same deidentified patient IDs. Treatment arm information can be found in D1. • NCT00326898-D5 (PMID 30130544): There is one dataset for PMID 30130544 (-D5). This dataset, NCT00326898-D5, contains the analysis data published in PMID 30130544, a publication focusing on the nonccRCC subgroup of ECOG-ACRIN trial E2805. This dataset contains recurrence site data, competing risk indicators, and updated survival times. Variables reported in this publication such as age, sex, treatment arm, and histology are identical to those presented in NCT00326898-D1 (for the trial's primary publication, PMID 26969090) and are thus not duplicated in this dataset. NCT00326898-D5 can be used together with the NCT00326898-D6 dataset to obtain updated, complete information on sites of recurrence. Patients in the NCT00326898-D1 through -D7 datasets have the same deidentified patient IDs.• NCT00326898-D6 (Unpublished data): This dataset, NCT00326898-D6, contains data collected on ECOG-ACRIN trial E2805, which are not published in the primary, nonclear cell renal cell carcinoma cohort, or cytokine analysis publication for the trial. NCT00326898-D6 contains information (the time interval from nephrectomy to randomisation, cause of death, histology components, and clarification about what sites the "other" and "other organs" (-D5) include for sites of recurrence) collected on the trial but not published. Both NCT00326898-D5 and NCT00326898-D6 datasets together provide updated, complete information on sites of recurrence. Patients in the NCT00326898-D1 through -D7 datasets have the same deidentified patient IDs. COD data is consistent with survival information presented in D5. • NCT00326898-D7 (PMID 31471309): There is one dataset for PMID 31471309 (-D7). This dataset contains the cytokine analysis data published in PMID 31471309 based on trial NCT00326898. Variables reported in this publication such as treatment arm, T-stage, Fuhrman grade, ECOG PS, DFS, and DFS event are identical to those presented in NCT00326898-D1 (for the trial's primary publication, PMID 26969090) and are thus not duplicated in this dataset. 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 phs004235

• Aberrant Activation of Wound Healing Programs within the Metastatic Niche Facilitates Lung Colonization by Osteosarcoma Cells

  Lung metastasis is responsible for nearly all deaths caused by osteosarcoma, the most common pediatric bone tumor. How malignant bone cells coerce the lung microenvironment to support metastatic growth is unclear. This study delineates how osteosarcoma cells educate the lung microenvironment during metastatic progression.Using single-cell transcriptomics (scRNA-seq), we characterized genome– and tissue-wide molecular changes induced within lung tissues by disseminated osteosarcoma cells in both immunocompetent murine models of metastasis and patient samples. We confirmed transcriptomic findings at the protein level and determined spatial relationships with multi-parameter immunofluorescence. We evaluated the ability of nintedanib to impair metastatic colonization and prevent osteosarcoma-induced education of the lung microenvironment in both immunocompetent murine osteosarcoma and immunodeficient human xenograft models.Osteosarcoma cells induced acute alveolar epithelial injury upon lung dissemination. scRNA-seq demonstrated that the surrounding lung stroma adopts a chronic, non-resolving wound-healing phenotype similar to that seen in other models of lung injury. Accordingly, metastasis-associated lung demonstrated marked fibrosis, likely due to the accumulation of pathogenic, pro-fibrotic, partially-differentiated epithelial intermediates. Inhibition of fibrotic pathways with nintedanib prevented metastatic progression in multiple murine and human xenograft models. Our work demonstrates that osteosarcoma cells co-opt fibrosis to promote metastatic outgrowth. When harmonized with data from adult epithelial cancers, our results support a generalized model wherein aberrant mesenchymal-epithelial interactions are critical for promoting lung metastasis. Adult epithelial carcinomas induce fibrotic pathways in normal lung fibroblasts, whereas osteosarcoma, a pediatric mesenchymal tumor, exhibits fibrotic reprogramming in response to the aberrant wound-healing behaviors of an otherwise normal lung epithelium, which are induced by tumor cell interactions.

  Study phs003569

• Precision Interception of Gastric Cancer Precursors Through Molecular and Cellular Risk Stratification

  The GAstric Precancerous conditions Study (GAPS, NCT04191551) is a cross-sectional study of patients undergoing endoscopy who are at increased risk of gastric cancer. Enrolled patients are administered a standardized questionnaire, undergo clinical biopsy collection using the Sydney system, and consent for the collection of saliva, blood, and additional gastric tissue. All patients are scored for intestinal metaplasia using the operative link on gastric intestinal metaplasia (OLGIM) scoring system.

  Study phs003648

• NCTN: A Randomized Phase III Trial of Three Different Regimens of CPT-11 Plus 5-Fluorouracil and Leucovorin Compared to 5-Fluorouracil and Leucovorin in Patients with Advanced Adenocarcinoma of the Colon and Rectum (N9741)

  Study ID: N9741 NCT Number: NCT00003594 Alliance for Clinical Trials in Oncology Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: A Randomized Phase III Trial of Three Different Regimens of CPT-11 plus 5-Fluorouracil and Leucovorin compared to 5-Fluorouracil and Leucovorin in Patients with Advanced Adenocarcinoma of the Colon and Rectum (N9741) Trial Description: RATIONALE: Drugs used in chemotherapy use different ways to stop tumor cells from dividing so they stop growing or die. Combining more than one drug may kill more tumor cells. It is not yet known which regimen of combination chemotherapy is most effective in treating advanced colorectal cancer. PURPOSE: Randomized phase III trial to compare the effectiveness of various combination chemotherapy regimens in treating patients who have advanced, recurrent, or metastatic colorectal cancer that cannot be treated with surgery or radiation therapy. Clinical data presented in the following publication(s): PMID 14665611 Disease type(s): Gastrointestinal Neoplasm - Colorectal Cancer Clinical dataset(s) included: NCT00003594-D1 (PMID 14665611): The NCT00003594-D1 dataset is one of 4 datasets associated with PubMed ID 14665611. This dataset contains information regarding patient-level information including eligibility, treatment arm, baseline characteristics, grade 4 and 5 toxicity data, and best response. It also includes information to analyze overall survival and time to progression. NCT00003594-D2 (PMID 14665611): The NCT00003594-D2 dataset is one of 4 datasets associated with PubMed ID 14665611. This dataset contains information per patient, per cycle regarding dosing, reasons for treatment delays, and overall response assessment status. NCT00003594-D3 (PMID 14665611): The NCT00003594-D3 dataset is one of 4 datasets associated with PubMed ID 14665611. This dataset contains information per patient, per cycle, per adverse event during treatment. NCT00003594-D4 (PMID 14665611): The NCT00003594-D4 dataset is one of 4 datasets associated with PubMed ID 14665611. This dataset contains information per patient regarding end of treatment timing and reason. Additional genomic data are available for this trial under phs001290. 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 phs004259

• A genotype-phenotype study of tumors from patients with inherited mutations in DNA repair genes

  This study investigated the genomic landscape of tumors from patients with inherited mutations in DNA repair genes. The aim of this study was to determine the relationship between locus-specific loss of heterozygosity (LOH) and genomic signatures of homologous recombination-based DNA repair (HR) deficiency in tumors associated with pathogenic germline variants in DNA repair genes. Cohorts of pathogenic germline variant (PGV) carriers with different cancer types were identified via a cancer genetics registry and clinical practice at Penn Medicine and through our collaborator network. Tumors were analyzed with next generation sequencing (whole exome and/or targeted panel sequencing) with or without transcriptomic analyses. Sub-study #1 "Non-breast/ovarian tumors in germline BRCA1/2 carriers". This study investigated primary non-breast/ovarian tumors that arise in individuals with BRCA1/BRCA2 pathogenic germline variants (PGVs). Whole exome sequencing (WES) using Agilent All-Exon Kit v7 hybrid capture probes was performed on matched tumor and blood germline normal DNA on an Illumina HiSeq. Individual WES data from DNA samples from tumor and normal are available. Sub-study #2: "Breast tumors in germline CHEK2 carriers". This study investigated primary breast tumors that arise in individuals with CHEK2 pathogenic germline variants (PGVs). Whole exome sequencing (WES) using Agilent All-Exon Kit v7 hybrid capture probes was performed on matched tumor and blood germline normal DNA on an Illumina HiSeq. Whole transcriptome RNAseq was performed on tumors. Individual WES data from DNA samples from tumor and normal and RNAseq data from tumor are available. Sub-study #3: "Breast tumors in germline TP53 carriers". This study investigated primary breast tumors that arise in individuals with TP53 pathogenic germline variants (PGVs). Whole genome sequencing (WGS) and/or custom panel targeted sequencing was performed on matched tumor and blood germline normal DNA on an Illumina HiSeq. Whole transcriptome RNAseq was performed on tumors and normal breast tissue. Individual WGS or targeted data from DNA samples from tumor and normal and RNASeq data from tumor and normal are available. Sub-study #4: "Prostate tumors in germline DNA repair carriers". This study investigated prostate tumors that arise in individuals with a variety of pathogenic germline variants (PGVs). Whole genome sequencing (WGS) and/or custom panel targeted sequencing was performed on matched tumor and blood germline normal DNA on an Illumina HiSeq. Whole transcriptome RNAseq was performed on tumors and normal prostate tissue. Individual WGS or targeted data from DNA samples from tumor and normal and RNASeq data from tumor and normal are available.

  Study phs003348

• Cellular and Molecular Profiling of Epithelial Ovarian Cancers and Associated Normal Tissues

  This collection of data includes bulk RNA-seq and whole genome bisulfite sequencing (WGBS) for ovarian cancer samples (microdissected into carcinoma and stroma compartments), as well as single-cell RNA-seq (scRNA-Seq) and bulk WGBS and enzymatic methyl-seq (EM-seq) normal human Fallopian tube samples. The data from the ovarian cancer samples was collected to understand cellular and molecular alterations associated with histological and molecular subtypes of ovarian cancer. Data for these samples are included in Djirackor, Heinze et al. (accepted at Cancer Research). The scRNA-Seq data was generated to identify the developmental trajectory, cell type composition, and point towards the cell-of-origin for high grade serous ovarian carcinoma (HGSOC). Further, this was intended to establish a normal RNA reference for the cancer data. Results from this study are described in Johnson, Majewski et al. (accepted at Nature Communications, preprint PMID: 40475517). The data from bulk DNA methylation on normal Fallopian tubes was used to optimize the bisulfite-conversion process for the cancer samples and to serve as an epigenetic reference in the cancer studies. This data is described in Morrison et al. (PMID: 34147133). Any questions can be directed to Hui Shen (hui.shen@vai.org).

  Study phs004702

• FIGHT-207: Anonymized Genomic Alterations and Clinical Responses

  Background: FIGHT-207 was a phase 2 study of the FGFR1-FGFR3 inhibitor pemigatinib in patients with previously treated, locally advanced/metastatic or unresectable solid tumor malignancies harboring activating fibroblast growth factor receptor (FGFR) gene alterations. Population information: 107 patients were divided into 3 cohorts: FGFR1–FGFR3 fusions/rearrangements; n=49 Activating FGFR1–FGFR3 non-kinase domain single nucleotide variants (SNVs); n=32 FGFR1–FGFR3 kinase domain mutations or variants of unknown significance (VUS) with potential pathogenicity; n=26 Participants on study had tumors that were grouped into the following histologies based on ≥ 5 patients: Cholangiocarcinoma, gynecologic cancers (cervical, endometrial, uterine), central nervous system (glioblastoma, low-grade pediatric glioma, astrocytoma), pancreatic cancer, breast cancer, urothelial tract/bladder cancer, non-small cell lung cancer, and other (adrenal cancer, anal cancer, cancer of unknown primary origin, colorectal cancer, gastric/gastroesophageal cancer, gallbladder cancer, giant cell bone tumor, head and neck cancer, lung neuroendocrine cancer, nasopharyngeal cancer, ovarian cancer, prostate cancer, renal cell cancer, sarcoma, solitary fibrous tumor). Among the efficacy-evaluable participants, 99 had both independent review committee (IRC) central best overall response (BOR) and tissue NGS- data; 2 additional patients had Not Evaluable (NE) as central BOR Baseline tissue targeted NGS data (F1CDx, Foundation Medicine Inc.) of genomic alterations are reported for N=101 participants Baseline plasma targeted NGS analysis (PredicineCare, Predicine Inc.) of genomic data are reported for N=83 participants; data at disease-progression are reported for N=78 participants. Principal Findings: The FIGHT-207 study provided evidence of clinical benefit of pemigatinib in multiple histologies, explored the clinical actionability of various FGFR1-FGFR3 gene alterations, and leveraged the depth of translational data from targeted NGS analysis of baseline samples and plasma samples obtained at baseline and end of treatment to provide key insights into the biology of FGFR inhibition and the clinical utility of FGFR inhibitors. The FIGHT-207 article (pending in Nat.Med. NMED-A128973B) reports evidence suggesting clinical acquired resistance to FGFR inhibition via secondary FGFR mutations as well as emerging co-mutations in other oncogenic and tumor suppressor pathways. This study also provides evidence of acquired resistance to FGFR inhibition in multiple histologies beyond cholangiocarcinoma and urothelial cancers in a systemic correlative analysis of post-progression ctDNA in a trial. Data available through dbGaP: Anonymized information for 101 participants with both IRC central BOR evaluation (including 2 patients with NE as BOR) and tissue NGS data, including tumor histology, enrollable FGFR alteration, and outcome. Genomic alterations determined by baseline tissue NGS (F1CDx, Foundation Medicine Inc.) Genomic alterations determined by plasma NGS analysis (PredicineCare, Predicine Inc.) of ctDNA analysis at baseline (n=83) and at end of treatment/ disease progression (n=78) including genomic alterations that were not assessed to be Germline SNPs.

  Study phs003590

• Pursuing Molecular Biomarkers to Guide Adjuvant Therapy for HPV+ Head and Neck Cancers After Transoral Robotic Surgery

  Human papillomavirus-positive oropharyngeal squamous cell carcinomas (HPV+ OPSCCs) represent a distinct subset of head and neck cancers that are rapidly increasing in incidence. Despite the generally favorable prognosis of HPV+ OPSCCs, compared to HPV-negative counterparts, due to higher treatment responsiveness and improved survival, a subset of patients experiences disease recurrence, leading to poor clinical outcomes. The identification of high-risk patients through molecular stratification could enable personalized therapeutic strategies, including intensified treatment or novel interventions. This study focuses on the molecular profiling of treatment-naïve primary HPV+ OPSCCs, aiming to identify molecular characteristics associated with tumor recurrence. In this study, we compared molecular profiles of primary tumors that recurred with those of non-recurrent control tumors to uncover key molecular features linked to recurrence.

  Study phs003889

• HINTS Geo-Coded Data 2013 (HINTS 4 Cycle 3)

  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. The third of these cycles (Cycle 3) was conducted from September 2013 through December 2013, including a total of 3,185 respondents.

  Study phs004208

• Basal-to-Inflammatory Transition Contributes to Basal Cell Carcinoma Therapy Resistance via Crosstalk with a Pro-Inflammatory Stromal Niche

  Overcoming tumor evolution and inducible resistance states remain the main challenge to creating successful anti-tumor therapies. The body's cancer-associated inflammatory response is a double-edged sword having ill-defined pro- and anti-tumor properties. Our group previously identified a basal cell carcinoma (BCC) tumor-intrinsic resistance pathway called basal to squamous cell carcinoma transition (BST). However, tumor resistance driven through the complex dynamics of tumor interactions with the inflammatory response remains poorly studied. Here, employing a multipronged approach combining human tumor single-cell transcriptomics, single-cell chromatin accessibility (scATAC-Seq) study, CODEX multiplexed imaging, spatial transcriptomic along with functional validation, we have identified a surprising inflammation-associated SMOi therapy enriched tumor epithelial cell state we term basal-to-inflammatory transition (BIT). Marked by CHI3L1, TAGLN, ITGAV, and VCAM1, BIT arises in spatially distinct neighborhoods from BST in a subset of naive BCCs. While BST tumor epithelium occurs within the central cores of tumor nodules, BIT tumor epithelium arises in a specialized inflammatory environment defined by a tumor associated TREM1 myeloid signature. IL1 and OSM secreted by TREM1 myeloid cells activate the inflammatory NF-kB family of transcription factors within the BIT tumor epithelium. Strikingly, IL1 and OSM ligands are sufficient not only in inducing the BIT tumor state in vitro and in vivo in a synergistic fashion but also in lowering the sensitivity of human BCC explant tumors to SMOi treatment. This work provides critical insights into the BIT-resistant state as a novel targetable tumor state driven by a specialized inflammatory microenvironment.

  Study phs003437

• Blood and Marrow Clinical Trials Network Evaluating Corticosteroids with Mycophenolate Mofetil vs. Corticosteroids with Placebo as Initial Systemic Treatment of Acute GVHD (BMT-CTN-0802-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.ObjectivesExplore the difference in response and survival rates for individuals with acute graft versus host disease (aGVHD) who received mycophenolate mofetil (MMF) plus corticosteroids versus corticosteroids alone.BackgroundIndividuals with certain cancers, genetic blood diseases, autoimmune diseases, and skeletal dysplasia may be candidates to receive an allogeneic hematopoietic stem cell transplantation (HSCT) as a potentially curative measure. A common and often fatal complication of receiving the transplant is acute graft-versus host disease (aGVHD). Historically, aGVHD has been treated with corticosteroids alone but favorable response rates are less than half prompting the need for better treatment options.ParticipantsAdult and pediatric participants were eligible for this study if they were the recipient of an allogeneic HSCT and newly diagnosed with aGVHD. Participants also needed to be able to swallow the MMF or placebo capsules and have an absolute neutrophil count > 500 cells per μL without growth factors. Disqualifiers for study eligibility included receipt of MMF or mycophenolic acid within 7 days of screening, uncontrolled infections, hepatic veno-occlusive disease, chronic GVHD, or renal failure on dialysis.A total of 235 patients participated in the study. Participants were randomized into either a treatment or placebo group. There were 116 participants in the treatment or MMF arm and 119 participants in the placebo arm.DesignBMT CTN 0802 was a phase 3 multicenter randomized double-blinded trial. Randomization was stratified by transplant center and grade of aGVHD (I-II vs III-IV) at study entry. Eligible participants who required GVHD therapy were treated within 72 hours of enrollment. All patients in the study received corticosteroids at a dose of prednisone 2 mg/kg per day orally (or methylprednisolone 1.6 mg/kg per day IV). Patients were also given MMF or the placebo at a dose of 1000 mg or 20 mg/kg (for patients Response to treatment was classified as complete, partial, progression, no response, or flare. Complete response (CR) was defined as complete resolution of all signs and symptoms of aGVHD, and a partial response (PR) was defined as improvement of 1 stage in 1 or more organs involved by GVHD without progression in others. Progression was defined as worsening in 1 or more organs, and no response was defined as stable disease or absence of improvement in any organ involved by GVHD within 14 days of therapy initiation. A flare in GVHD was defined as any increase in symptoms or therapy for aGVHD after an initial response (CR or PR). All toxicities were reported regardless of whether they were thought to be related to the study treatment.Adult study participants who were able to communicate in English also completed the MD Anderson Symptom Inventory (MDASI), a tool used to measure quality of life. Participants completed the inventory at enrolment and at day 56 ± 7 days.The primary end point was acute or chronic GVHD-free survival at day 56 after initiation of therapy.ConclusionsResults for this study concluded that the addition of MMF to corticosteroids as initial therapy for acute GVHD does not improve GVHD-free survival compared with corticosteroids alone. There was also no difference between the treatment arms in regards to quality of life measures (Bolanos-Meade J, Logan B, Alousi A et al., Blood. 2014;124(22):3221-3227).

  Study phs004840

• Genetic Studies of Homologous Recombination Deficiency in Hispanic Gastric Cancer

  Approximately 10% of gastric cancer cases show familial clustering and a hereditary cause is likely, however, only 1-3% cases result from known hereditary syndromes – which are predominantly associated with CDH1 and CTNNA1 genes. Hispanics are > 2 times more likely to be diagnosed and to die from gastric cancer compared to non-Hispanic whites. Not only does gastric cancer precision medicine lag behind other cancers – there is an urgent need to understand its etiology. Germline mutations in homologous recombination genes have been implicated as important risk factors for gastric cancer. The purpose of this study is to continue to generate knowledge to improve gastric cancer outcomes and disparities by 1) characterizing prevalence of germline mutations in homologous recombination genes and identify new genes associated with gastric cancer 2) perform molecular characterization of gastric tumors in Hispanic patients. Participants for germline analysis were enrolled from Chile, Colombia, Mexico, Portugal, Spain, Uruguay.Whole exome sequence capture was performed for all germline and somatic samples using Agilent SureSelect Human All Exon v7 Kit. All sequencing was performed on an Illumina NovaSeq 6000. Germline Analysis: Whole exome sequencing was performed on 536 Hispanic patients (290 males, 246 female)

  Study phs003251

• Sequencing Data from Patient-Derived Models of Pediatric Cancer

  Pediatric cancer can take decades of life from patients and devastate families. To design improved treatments we must understand the pathogenesis and molecular mechanisms underlying development of these diseases. Tumor samples from patients are precious resources that give unique biological insights. To extend the utility of these samples, we utilize patient derived xenograft (PDX) models. These models are created by growing patient tumor samples in immune compromised mice. This increases the volume of samples available for study and enables in vivo testing. We generated single cell RNAseq data from pediatric PDX models to characterize the tumor, explore microenvironmental interactions and test treatments. This study aims to provide a warehouse for data generated from PDX models. Additional data will be added as it becomes available and is published.

  Study phs004719

• Genomic Characterization CS-MATCH-0007 Arm Q

  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 Q is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with HER2 amplification are treated with Kadcyla® (ado-trastuzumab emtansine). This subprotocol is one of the treatment arms included in the CS-MATCH-0007 protocol and will provide specimens for the program including tumor tissue and whole blood.

  Study phs001926

• Structure of the Mucosal and Stool Microbiome in Lynch Syndrome

  The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched in both stool and mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.

  Study phs002343

• PE-CGS: Optimizing Engagement of Hispanic Colorectal Cancer Patients in Cancer Genomic Characterization Studies

  Colorectal Cancer (CRC) is the second leading cause of cancer death in the US. Hispanic/Latinos (H/L) are the largest and fasting growing ethnic group in the US, and cancer is the leading cause of death among H/L in the US. Therefore, we need to fully understand the full complexity of the molecular etiology of cancer in this ethnic group. For instance, although incidence rates of CRC are lower among Latinos as compared to Whites or African Americans, Hispanics with metastatic disease have shorter overall survival when adjusted for health care setting, demographics, disease characteristics and treatment factors. H/L also tend to be diagnosed at a younger age and with higher stage, and we have previously reported that Mexican H/L in California have the greatest proportion of young (The Cancer Genome Atlas has provided a deep overview of the molecular taxonomy of CRC in 594 cases, however, less than 1% of the cases (n=5) were H/L. Therefore, it is imperative for us to take more detailed assessment of the molecular genomic landscape of CRC in H/L. One of the major issues likely limiting our ability to perform these large genomic initiatives in minority patients is that Patient or Participant Engagement practices may not be investigated to identify best practices for accruing and consenting patients into clinical translational biomedical research studies. This concept of Participant Engagement is critically important for both the patients and the translational cancer research community. Optimizing and improving our approaches for directly engaging patients at initial contact, throughout the course of a translational genomic study, and during the time of return of results is likely to lead to stronger relationships between the medical community and patients, but could also lead to significant improvement in outcomes for patients and for the cancer care community as a whole. As such, we propose the creation of the USC Center for Optimization of Participant Engagement in Cancer Characterization (COPECC) with a focus on optimizing the engagement of Latinos in CRC Genomic Characterization research studies. USC COPECC would serve as a member of the NCI U2C Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Our investigative team includes experts in all relevant areas of research for genomic characterization, participant engagement, and engagement optimization. We have an established platform for consenting patients into cancer genomics studies that will serve as a standard process. The overall goal of USC COPECC is to generate results on participant engagement optimization and CRC genomic research that will be shared with the broader community to distribute best practices for engaging Latinos in hopes of improving overall outcomes for CRC in this underserved population.

  Study phs003985

• Molecular Analysis of Alliance A031201 Study

  This is the first study examining the relationship between clonal hematopoiesis and clinical outcomes in prostate cancer patients. We used a targeted gene sequencing panel to identify patients in the A031201 clinical trial with and without clonal hematopoiesis. We found that clonal hematopoiesis did not affect overall or progression free survival in A031201 but was associated more adverse cardiac events.

  Study phs003717

• Clonal Hematopoiesis Dynamics and Evolutionary Fitness During Breast Cancer Treatment Impact Clinical Outcomes

  We investigated the impact of cancer therapies on clonal hematopoiesis (CH), the age-associated expansion of somatically mutated hematopoietic stem cells, in patients with breast cancer. We examined 392 serial peripheral blood samples collected before and after treatment using chemotherapy, radiation, and/or hormone therapy from a prospective cohort of 171 patients. Ultra-deep targeted DNA exon sequencing was performed across 81 genes (custom Agilent SureSelectXTHS2 panel, median coverage > 5000x) implicated in hematologic malignancies and CH, enabling precise characterization of the mutational spectrum and longitudinal tracking of clonal dynamics. The primary objective was to understand how different cancer treatments (i.e., chemotherapy, radiation, and hormone therapy) alter the effective hematopoietic population and select for or against specific CH clones. Our analysis revealed that cytotoxic therapies induced significant reductions in allelic diversity, creating therapeutic bottlenecks that led to selective clonal expansion. These selective dynamics were associated with worse clinical outcomes, where patients with positively selected CH during treatment experienced significantly shorter progression-free and overall survival. Data generated from this study, including the sequencing data, treatment exposure data, and clinical outcomes will be made available through dbGaP. Mutation calls used for analyses are included in the medRxiv (2025.08.27.25334581) supplement and will be available in the published version of the manuscript.

  Study phs004283

• The Formation and Propagation of Human Robertsonian Chromosomes

  Robertsonian chromosomes are a type of variant chromosome found commonly in nature. Present in one in 800 humans, these chromosomes can underlie infertility, trisomies, and increased cancer incidence. Recognized cytogenetically for more than a century, their origins have remained mysterious. Recent advances in genomics have allowed us to assemble three human Robertsonian chromosomes completely. We identify a common breakpoint and epigenetic changes in centromeres that provide insight into the formation and propagation of common Robertsonian translocations. Further investigation of the assembled genomes of chimpanzee and bonobo highlights the structural features of the human genome that uniquely enable the specific crossover event that creates these chromosomes. Resolving the structure and epigenetic features of human Robertsonian chromosomes at a molecular level will pave the way to understanding how chromosomal structural variation occurs more generally, and how chromosomes evolve.

  Study phs003920

• Childhood Cancer Data Initiative (CCDI): Whole Genome Landscapes of Patient Derived Osteosarcoma Xenograft Models

  Osteosarcoma is the most common primary bone malignancy in children and young adults and has few treatment options. As a result, there has been little improvement in survival outcomes over the past few decades. The need for models to test novel therapies is especially great for this disease because it is both rare and unresponsive to most therapies. To address this need, an NCI-funded consortium has characterized and utilized a panel of patient-derived xenograft models of osteosarcoma for drug testing. The exomes, transcriptomes, and copy number landscapes of these models have been described previously. This study adds whole-genome sequencing (WGS) and reverse-phase protein array profiling data, which can be correlated with drug testing results. In addition, four new osteosarcoma models are described for use by the research community.

  Study phs004232

• Integrated Somatic and Germline Molecular Properties Dictating Biological and Clinical Phenotypes in Cancer

  Study version 1: We performed single-nuclei matched RNA- and ATAC-sequencing of frozen biopsies from normal adjacent tissue, primary and metastatic esophageal adenocarcinoma specimens. The data was then further stratified into a tumor microenvironment and malignant compartment and was computationally analyzed to reveal cancer cell subtypes and programs driving malignancy.Study version 2: We performed single nucleus multiome sequencing (simultaneous ATAC and RNA sequencing) on snap frozen adipose and liposarcoma patient samples.

  Study phs003438

• Molecular Characterization of the Immunological Landscape in Human Brain Tumors

  We are performing a comprehensive cellular and molecular characterization of the immunological landscape of human brain tumors. This work includes single-cell RNA and T cell receptor (TCR) sequencing of T cells isolated from the tumor and blood of patients with advanced primary (high-grade glioma) and metastatic (non-small cell lung cancer) cancers. Whole exome sequencing on tumor and normal tissue was also performed.

  Study phs004853

• Direct Transposition of Native DNA for Sensitive Multimodal Single-Molecule Sequencing

  STUDY GOALS: This study focuses on elucidating the epigenetic modulators of prostate cancer progression and metastasis at high resolution. This is achieved by applying a novel, high-sensitivity single molecule sequencing assay that measures chromatin state on single DNA molecules (SMRT-Tag) to matched primary and metastatic tumor samples from the same patient. Samples are obtained from patient derived xenograft (PDX) models. STUDY DESIGN: Individuals diagnosed with primary and metastatic prostate cancer in the course of routine care were consented and enrolled, and biopsies of primary and/or metastatic lesions performed to obtain sample material used for generating PDX models. Samples collected from these models were processed with a novel strategy developed for highly-sensitive multimodal profiling of single chromatin fibers using the third generation long-read sequencing. The resulting data indicates genetic variants, chromatin organization, and m5dCpG methylation status across the genome. PRINCIPLE FINDINGS: We determined characteristic single-molecule patterns of chromatin organization (spacing of nucleosomes, presence and absence of m5dCpG marks, etc.) that were altered in the transition from primary malignancy to metastasis. Broadly, global chromatin organization was severely disrupted in metastatic samples, resulting in increased accessibility at CTCF motifs, which may be relevant for disease progression. We further identified specific genomic domains including constitutive heterochromatin significantly enriched for irregular or hyper-accessible chromatin. Together, these findings suggest the involvement of ATP-dependent chromatin remodelers in evicting nucleosomes as a facet of metastatic prostate cancer. DATA AVAILABILITY: SAMOSA-Tag, the assay used in this study, is a sequencing assay that uses the third generation long read sequencing, specifically the SMRT sequencing platform from Pacific Biosciences. Demultiplexed raw SMRT sequencing BAM files generated in this study are deposited. Individual raw subread BAM files correspond to replicate sequencing assays performed on either primary or metastatic PDX prostate tumors.

  Study phs003511

• Spatial Transcriptomics of Vaccine Therapy With or Without Cyclophosphamide in Treating Patients Undergoing Chemotherapy and Radiation Therapy for Stage I or Stage II Pancreatic Cancer That Can Be Removed by Surgery

  Pancreatic ductal adenocarcinoma (PDAC) is a rapidly progressing cancer that responds poorly to immunotherapies. Intratumoral tertiary lymphoid structures (TLS) have been associated with rare long-term PDAC survivors, but the role of TLS in PDAC and their spatial relationships within the context of the broader tumor microenvironment remain unknown. Here, spatial transcriptomics data were generated from 16 pancreatic cancer patients treated with GVAX, whose tumors presented with induced intratumoral TLS. Resected tumor specimens were embedded in OCT media and freshly frozen. Sections were cut into 6.5 x 6.5 mm dimensions compatible with Visium spatial transcriptomics slides. TLS-positive tumor sections from 14 patients (14 tumor samples in total) and lymph nodes from remaining patients (2 lymph node samples in total) were selected by an expert pathologist for profiling. We used 4 Visium slides and covered the 16 capture areas with sections cut in a cryostat at 10 µm. The fresh frozen Visium protocol was followed according to manufacturer's recommendations (10x Genomics Spatial 3' v1). Tissue permeabilization and library construction was carried out according to the manufacturer's protocols. Permeabilization time was optimized to 30 minutes. The captured tissue sections were permeabilized to allow RNA to be captured onto the slide where it reverse-transcribed to cDNA. The cDNA was then amplified, and sequencing libraries were prepared using the 10x Genomics Visium Spatial Gene Expression Reagent Kit for Library Preparation. The libraries were then sequenced using an Illumina NovaSeq sequencer. The raw data obtained from the sequencing were processed using the SpaceRanger (spaceranger-1.2.0) pipeline for alignment onto the GRCh38-2020-A reference transcriptome quantification of gene expression. Unsupervised learning generated a TLS-specific spatial gene expression signature that significantly associates with improved survival in PDAC patients. These analyses demonstrate TLS-associated intratumoral B cell maturation.

  Study phs003862

• Childhood Cancer Data Initiative (CCDI): Identification and Targeting of Treatment Resistant Progenitor Populations in T-cell Acute Lymphoblastic Leukemia

  Our goal with this study was to identify the mechanisms of treatment resistance in T-cell acute lymphoblastic leukemia (ALL) using single-cell genomics. We profiled 40 T-ALL cases from the Children's Oncology Group AALL0434 clinical trial using CITE-seq/snATAC-seq, capturing a breadth of immunophenotypes, including early T-cell precursor (ETP) and near-ETP/non-ETP subtypes. By integrating analyses of T-ALL cells with the normal T-cell developmental trajectory, the study identified a specific subgroup of leukemia cells resembling bone marrow progenitors (BMP-like cells). These BMP-like cells were associated with treatment failure and poor overall survival in T-ALL patients. Overall, this study reveals comprehensive multiomic signatures for rapidly assessing risk and tailoring targeted treatment for high-risk T-ALL patients.

  Study phs003432

• Understanding Determinants of Racial Disparities in Lung Cancer Incidence

  This is a nested case-control study designed to evaluate the association between common genetic variants and the risk of lung cancer. The study included 1258 cases and 1252 controls selected from the Southern Community Cohort Study (SCCS), a large, prospective observational cohort. Cases were identified from cancer registries across the catchment area of the SCCS. Cases and controls were frequency matched on age, sex, race, and enrollment site (community health center vs general population).

  Study phs003789

• Genomic Profiling of Rare Tumors

  Utilizing the rare and unique patient samples provided by Pattern Medicine, LLC, MD Anderson will molecularly characterize rare cancer samples, and potentially generate a collection of preclinical models to enable identification of novel therapeutic targets and concepts, as well as evaluation of innovative treatment strategies.

  Study phs003916

• Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program –Sarcoma, Kidney, and Liver Cancers

  The goal was to complete whole exome sequencing (WES) and RNA sequencing (RNA-Seq) on patient derived xenograft samples. Cancer in children is rare with approximately 15,700 new cases diagnosed annually in children 21 years or younger in the U.S. Through use of multimodality therapy (surgery, radiation therapy, and aggressive chemotherapy), 70% of patients will be 'cured' of their disease, and 5-year Event-Free Survival (EFS) exceeds 80%. Consequently, the number of patients that can be enrolled in phase I/II clinical trials is small, and most patients will have been extensively treated, hence drug/radiation resistant. Thus, preclinical studies that accurately translate into effective clinical therapy are an essential component of pediatric drug development. Our group has contributed to studies in the Pediatric Preclinical Testing Program (PPTP) and Pediatric Preclinical Testing Consortium (PPTC) that have led to clinical studies through Children's Oncology Group (COG). Of importance, we have developed and characterized over 330 Patient Derived Xenografts (PDX), developed from tumors both at diagnosis and relapse, that can be used to facilitate pediatric drug development as directed by FDA under the Research to Accelerate Cures and Equity for Children Act (RACE for Children Act).

  Study phs003160

• NCTN: Phase III Randomized Study of Sorafenib Plus Doxorubicin versus Sorafenib in Patients with Advanced Hepatocellular Carcinoma (HCC) (CALGB-80802)

  Study ID: CALGB-80802NCT Number: NCT01015833 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: Phase III Randomized Study of Sorafenib plus Doxorubicin versus Sorafenib in Patients with Advanced Hepatocellular Carcinoma (HCC) (CALGB-80802)Trial Description: This randomized phase III trial studies sorafenib tosylate and doxorubicin hydrochloride to see how well they work compared with sorafenib tosylate alone in treating patients with liver cancer that has spread to nearby tissue or lymph nodes or has spread to other places in the body. Sorafenib tosylate may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth and by blocking blood flow to the tumor. Drugs used in chemotherapy, such as doxorubicin hydrochloride, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. It is not yet known whether giving sorafenib tosylate together with doxorubicin hydrochloride is more effective than sorafenib tosylate alone in treating liver cancer. Data presented in the following publication(s): PMID 31486832 Disease type(s): Gastrointestinal Neoplasm - Liver and Hepatobiliary CancerClinical Dataset(s) included:NCT01015833-D1 (PMID 31486832): Dataset NCT01015833-D1 is the only dataset associated with PubMed ID 31486832. This dataset contains baseline characteristics, treatment arm and number of cycles, treatment discontinuation reasons, hepatitis status, toxicity, 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 phs004239

• Collagen XVII Promotes Pancreatic Cancer Through Regulation of PIK3R5

  Pancreatic ductal adenocarcinoma (PDAC) contains a desmoplastic stroma that promotes the aggressive biology of this disease. While the varied mechanisms by which fibrillar collagens contribute to PDAC have been defined, little is known about the contribution of transmembrane collagens. Among this class of collagens, Collagen XVII uniquely contains an extensive intracellular domain that connects intracellular cytoplasmic components with the extracellular matrix. Collagen XVII is best characterized as the defining component of the type I hemidesmosome, an anchoring complex that attaches epithelial cells to the underlying basement membrane. In this study, we characterize the expression of collagen XVII in PDAC and the mechanisms by which it contributes to PDAC biology. We demonstrate that crosstalk between PDAC cells and cancer associated fibroblasts drive collagen XVII expression in vitro and xenograft tumor models in vivo. Genetic depletion of collagen XVII in low-passage patient derived cell lines diminishes their metastatic potential and ability to form tumors in mice. Whole transcriptome sequencing of tumors formed by cells with diminished collagen XVII levels revealed dramatically lower levels of PIK3R5, a regulatory subunit of class IB phosphatidylinositol-3-kinase (PI3K) that interacts with G protein-coupled receptors. Consistent with this, collagen XVII-deficient tumors exhibited lower levels of phosphorylated AKT, a downstream effector of PI3K. The studies highlight the importance of collagen XVII signaling in PDAC and define a novel mechanism by which collagen XVII mediates activation of PI3K.

  Study phs003641

• Integrating Circulating Tumor DNA Analysis and Radiomics for Dynamic Risk Assessment in Localized Lung Cancer

  DNA was isolated from pre-treatment and mid-treatment plasma samples and matched germline samples from patients undergoing chemoradiation therapy for stage IIB-IIIB non-small cell lung cancer. Sequencing libraries were hybrid captured using custom selector pools designed to target genes frequently mutated in non-small cell lung cancer prior to ultra-deep next generation sequencing.

  Study phs003947

• Dynamic Evolution of Fibroblasts Revealed by Single Cell RNA Sequencing of Human Pancreatic Cancer

  Understanding the constituents of the pancreatic ductal adenocarcinoma (PDAC) microenvironment may illuminate more efficacious targets for treating this aggressive malignancy. However, the compositional changes occurring in untreated and treated PDAC relative to both normal and inflamed pancreas have not been well characterized. To provide a more comprehensive understanding of the PDAC tumor microenvironment relative to the non-cancerous pancreas, we performed single-cell expression profiling (10X Genomics Chromium) on samples of upfront resectable PDAC, FOLFIRINOX-based treated PDAC, chronic pancreatitis, and normal pancreas specimens from 19 patients. Spatial gene expression profiling (10X Genomics Visium) was performed to gain additional insight into cell populations. Our analysis revealed that fibroblasts are central mediators of cell-cell communication in both inflamed and malignant settings and defined unique roles for these cell populations in different disease contexts.

  Study phs003751

• Blood and Marrow Transplant Clinical Trials Network - A Phase II Multicenter Trial of Single Autologous Hematopoietic Cell Transplant Followed by Lenalidomide Maintenance for Multiple Myeloma with or without Vaccination with Dendritic Cell/Myeloma Fusions (BMT CTN-1401-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 compare response at one year post transplant between participants receiving dendritic cell/myeloma vaccine along with granulocyte macrophage colony-stimulating factor (GM-CSF) and lenalidomide maintenance therapy to those receiving lenalidomide maintenance therapy with or without GM-CSF.Background: The advent of combination biologic therapy for multiple myeloma (MM) has significantly improved patient outcomes. Induction therapy followed by consolidation with autologous hematopoietic stem cell transplantation (auto-HCT) prolongs progression-free survival in patients with MM. The addition of post-transplant lenalidomide maintenance therapy further extends the duration of remission. However, the vast majority of patients ultimately experience disease progression due to the emergence of resistant disease. The development of strategies to enhance the durability of post-transplant response remains a major unmet need in the field. Since MM is associated with immune suppression, the development of cancer vaccines is being investigated in MM with the goal of stimulating tumor-specific immunity. Dendritic cells (DC) are the most potent antigen-presenting cells that prominently express costimulatory signaling necessary for optimal T-cell activation, cross-presentation of antigen to reactive CD8 T cells, and the development of primary immunity. The BMT CTN developed a personalized cancer vaccine in which patient-derived tumor cells are fused with autologous monocyte-derived DCs. The BMT CTN-1401 study examined the efficacy of the DC/MM fusion vaccine in conjunction with lenalidomide maintenance therapy after auto-HCT, compared with maintenance alone.Participants: Participants with symptomatic MM were eligible if they were 18-70 years old, were candidates for auto-HCT, had a Karnofsky Performance status of ≥70%, had >20% plasma cells in the bone marrow aspirate differential A total of 140 participants were randomized. 68 participants were randomized to the vaccine arm, 37 to the lenalidomide plus GM-CSF arm, and 35 to the lenalidomide alone arm.Design: BMT CTN-1401 was a phase II, multicenter, open label trial. All participants underwent bone marrow aspiration following enrollment. Myeloma cells were isolated, preserved, and for participants randomized to the vaccine arm, used for vaccine generation. All participants received standard-of-care induction therapy and auto-HCT conditioned with melphalan. Participants were randomized approximately 2 months post-transplant. Participants were randomized in a 2:1:1 ratio to the vaccine arm (DC/MM vaccine, GM-CSF, plus lenalidomide), or one of two control arms (lenalidomide plus GM-CSF or lenalidomide alone). All participants began maintenance lenalidomide between day 90 and 100 post-transplant at a dose of 10 mg a day for 28 days of a 28-day cycle. On day 1 of cycles 2, 3, and 4 of lenalidomide maintenance, patients assigned to the vaccine arm underwent subcutaneous administration of the DC/MM fusion vaccine along with 100 μg GM-CSF administered subcutaneously adjacent to the vaccine site on days 1 to 4. Participants randomized to the control arms received either lenalidomide alone or lenalidomide with GM-CSF at the same dose and schedule as the vaccine arm.The primary outcome was a comparison of participants in complete response (CR)/stringent CR (sCR) at 1-year post-transplant between the vaccine and control arms. The primary immunologic endpoint of the study was a comparison of the percentage of circulating multiple myeloma–reactive T cells between participants in the vaccine and control arms. PFS (progression-free survival) and OS (overall survival) were secondary endpoints of the study.Conclusions: There was not a statistically significant difference in the percentage of participants achieving complete response 1-year post-transplant in the vaccine arm compared to the control arms.

  Study phs004718

• NCTN: Postoperative Chemotherapy With or Without Bevacizumab for Patients With Stage II or III Rectal Cancer (E5204)

  Study ID: E5204NCT Number: NCT00303628 ECOG-ACRIN Cancer Research GroupSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: Randomized Phase III Study of Postoperative Oxaliplatin, 5-Fluorouracil and Leucovorin vs Oxaliplatin, 5-Fluorouracil, Leucovorin and Bevacizumab for Patients with Stage II or III Rectal Cancer Receiving Pre-operative Chemoradiation (E5204)Trial Description: Drugs used in chemotherapy, such as oxaliplatin, leucovorin, and fluorouracil, 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 bevacizumab, 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. Bevacizumab may also stop the growth of tumor cells by blocking blood flow to the tumor. Giving more than one drug (combination chemotherapy) together with bevacizumab after surgery may kill any tumor cells that remain after surgery. It is not yet known whether oxaliplatin, leucovorin, and fluorouracil is more effective with or without bevacizumab in treating rectal cancer. This randomized phase III trial is studying combination chemotherapy to see how well it works with or without bevacizumab in treating patients who have had surgery for stage II or stage III rectal cancer. Clinical data presented in the following publication(s):PMID 31852811 Disease type(s): Gastrointestinal Neoplasm - Colorectal CancerClinical dataset(s) included:NCT00303628-D1 (PMID 31852811): There are five different datasets for PMID 31852811 from trial E5204. This dataset, NCT00303628-D1, contains baseline characteristics, stratification factors, surgery information, treatment, second primary cancer and efficacy data. NCT00303628-D2 (PMID 31852811): There are five different datasets for PMID 31852811 from trial E5204. This dataset, NCT00303628-D2, contains toxicity data. NCT00303628-D3 (PMID 31852811): There are five different datasets for PMID 31852811 from trial E5204. This dataset, NCT00303628-D3, contains PRO Bowel function/uniscale data. NCT00303628-D4 (PMID 31852811): There are five different datasets for PMID 31852811 from trial E5204. This dataset, NCT00303628-D4, contains PRO FACT-Diarrhea Data. NCT00303628-D5 (PMID 31852811): There are five different datasets for PMID 31852811 from trial E5204. This dataset, NCT00303628-D5, contains PRO FACT/GOG-Ntx 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 phs004621

• Establishment and Genomic Validation of Novel Patient-Derived Xenograft Models for Drug Discovery in Gastrointestinal Stromal Tumor

  This dataset contains targeted next-generation sequencing data generated with the Illumina TruSight Oncology 500 (TSO500) assay from six gastrointestinal stromal tumors (GIST) and matched patient-derived xenograft (PDX) models established at Fox Chase Cancer Center (Philadelphia, PA). GIST are most commonly driven by activating mutations in KIT or PDGFRA, and this study focused on KIT-mutant tumors. All PDXs were derived from metastatic patient tumors previously treated with one or more tyrosine kinase inhibitors (TKIs). PDXs were maintained through series of passages and represents in vivo models of differential TKI sensitivity. The dataset represents a detailed comparison of mutational profiles between primary tumors and corresponding PDXs across passages, enabling studies of genomic stability, resistance mechanisms, and the evaluation of novel therapeutic strategies in GIST.

  Study phs004185

• The Electronic Medical Records and GEnomics Network Genomic Risk Assessment (eMERGE IV)

  The eMERGE (electronic MEdical Records and GEnomics) network enrolled ~25,000 individuals not typically involved in research in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report along with recommended actions. The GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports and was returned to participants, their providers, and their EHR. The network is examining the uptake of care recommendations after return of results.Children's Hospital of Philadelphia (CHOP)The Center for Applied Genomics (CAG) is a specialized Center of Emphasis at the Children's Hospital of Philadelphia (CHOP) with the primary goal of translating basic research findings to medical innovations. The mission of CAG is to develop new and better ways to diagnose and treat children affected by rare and complex medical disorders. We aim to discover genetic causes for the most prevalent diseases of childhood including ADHD, asthma, autism, diabetes, epilepsy, obesity, schizophrenia, pediatric cancer, and a range of rare diseases. Ultimately, our objective is to generate new diagnostic tests and to guide physicians to the most appropriate therapies. Our participants are recruited from the CHOP Health Care Network, which includes over 50 sites throughout Pennsylvania and New Jersey, 100% of which use Epic EMR system. This constitutes the country's largest pediatric integrated delivery system, supporting >1.1 million visits/year within the primary and specialty care networks, community-based inpatient pediatric and neonatal programs, a rehabilitation hospital, and a home care service. It provides acute- and well-care to patients in urban, rural, and suburban settings.Cincinnati Children's Hospital Medical Center (CCHMC)CCHMC has proposed ambitious initiatives for eMERGE IV. The major goals are to generate, return as appropriate along with clinical recommendations, individualized genomic risk assessments that include polygenic risk scores for 2500 minority participants ascertained on dyads (mother/child) and extended to families (dyad + biologic father, siblings). The informatics initiatives include integration of electronic medical records and development, implementation and evaluation of clinical decision support at two different hospital systems, one pediatric and one adult. Participant preferences, education needs, and ethical and social implications will be studied throughout the 5 year period. Columbia UniversityColumbia University in partnership with the New York-Presbyterian hospital has a long and strong tradition of patient-centered research and community engagement in the urban, medically underserved communities of Washington Heights and Harlem in Northern Manhattan, and has established Precision Medicine as a major university-wide initiative (PMI), of which eMERGE is a vital program. We possess broad and deep expertise in clinical genetics, genomics, informatics, EHR phenotyping, systems biology, public health, and ELSI, including return of genetic results and secondary findings to diverse patients. Columbia will share lessons learned in linking EHR and sequence data for genomic decision support, developing scalable genomic education methods and assessing the impact of returning genetic results on patients, families, and clinicians. We are poised to contribute novel comprehensive risk prediction and management solutions for diverse patients as part of eMERGE IV efforts.Icahn School of Medicine at Mt. Sinai (Mt. Sinai)Mt. Sinai investigators have been at the center of many NHGRI-led genomic research (GSP, PAGE) and genomic medicine (eMERGE, CSER, IGNITE) consortia. Building on our decade-long track record in genomic research, clinical trials, and genomic medicine in diverse, underserved patients from New York City, we propose to develop new frameworks to bring genomic risk into clinical care to promote health equity. In addition to genomic discovery and risk prediction, we are creating analytical and data resources, and digital health applications tailored to diverse populations, as part of the eMERGE IV Network. The Mt. Sinai team is composed of clinicians and scientists who work closely with community members and industry partners to develop flexible and innovative strategies to bring leading-edge research into clinical care. Having recently announced a large institutional investment to scale the integration of genomics and artificial intelligence into patient care, Mt. Sinai is poised to contribute to eMERGE IV's mission to implement and learn from genomic risk assessment in clinical care. Mt. Sinai's team will contribute to progress in multiple areas across eMERGE, including developing and deploying electronic phenotypes; discovering new genotype-phenotype associations; and facilitating the communication of genomic results to patients and their healthcare providers.Mass General BrighamThe eMERGE IV Clinical Center at Mass General Brigham leverages a large biobank, clinical data in the electronic health records (EHR) for >6 million patients from the largest integrated health care provider in New England, advanced bioinformatics expertise, prior leadership in PRS development, established expertise in returning genomics results, and experience using information technology to transform clinical processes and assess medical, behavioral and economic outcomes. We have developed highly specific machine learning algorithms for e-phenotypes and implemented eMERGE algorithms for multiple phenotypes and have considerable experience in developing decision support tools and analyzing outcomes that can be leveraged to study the integration of PRS data into clinical practice. We will test the hypothesis that PRS will allow us to stratify eMERGE participants based on genetic risk for common complex traits. We will focus on coronary artery disease, atrial fibrillation, type 2 diabetes, colorectal cancer and depression in GWAS populations and validate multi-ethnic PRS in the Mass General Brigham Biobank and eMERGE III dataset. We will conduct an analysis of the effect of disclosing results to high risk participants to determine how personalized results changed patient outcomes in laboratory values, risk reduction behaviors, or health care utilization.Mayo Clinic (Mayo)The goal of Mayo eMERGE investigators is to leverage the electronic health record (EHR) for genomic discovery and to implement genomic medicine to improve health care outcomes, working closely with other eMERGE sites and the Mayo Center for Individualized Medicine. In eMERGE I we used genotype data and electronic phenotyping algorithms for genomic discovery. In eMERGE II we conducted a clinical trial of disclosing a polygenic risk score (PRS) for coronary heart disease (CHD) and placed pharmacogenomic variants in the EHR with linkage to clinical decision support (CDS). In eMERGE III, we returned actionable findings from targeted sequencing of 68 genes and collaborated with a Federally Qualified Health Center (FQHC) to bring genomic medicine to an under-represented population. In eMERGE IV, as part of the Genomic Risk Assessment & Management Network, we will test the hypothesis that individuals at high polygenic risk for common diseases will have a higher uptake of risk reduction measures than those at lower risk. We will build on our prior work in genomic discovery, EHR integration and return of results (RoR) to develop and validate PRS and combine these with clinical risk scores and family history to compute comprehensive risk profiles for 2500 individuals. Our prior work in disclosing a PRS for CHD to research participants as part of a comprehensive risk profile enables us to efficiently expand the approach to other common diseases that pose a significant public health burden. To assess the utility of PRSs, we will recruit 1800 adults and 200 adolescents from Rochester MN and 500 adults from Phoenix AZ. DNA will be sent for CLIA-certified genomic testing and we will calculate ancestry specific PRSs for each participant. Individualized risk estimates will be reported to participants and health care providers (HCPs) and placed in the EHR with linkage to CDS that includes guideline-based risk-management information. For participants who are at significantly higher polygenic risk of developing at least 1 of the diseases, results will be disclosed in-person by a HCP followed by assessment of outcomes including new tests ordered, risk reduction measures, and changes in modifiable risk factors. We will examine the economic, behavioral and psychosocial implications of returning PRS. Our focus on PRS for common cardiovascular diseases brings genomic medicine to the population. We will continue our partnership with Mountain Park Health Center, a FQHC serving low-income, minority communities in Phoenix AZ, to address concerns about health disparities in the context of genomic medicine.Northwestern University (NU)Northwestern University is dedicated to translational genomics, with a strong focus on unified, interdisciplinary research bridging the informatics, clinical, basic science, and bioethics domains. Over the phases of eMERGE, Northwestern has applied this interdisciplinary approach to study the feasibility, utility, outcomes, and effectiveness of EHR-linked genomic information as a member of the network. Particular areas of focus include: novel informatics approaches to integrate genomic results into EHR systems; development of open-source, EHR-based phenotyping algorithms to empower translational research across a variety of clinical domains; and studies of participant, patient, and provider interaction with EHR-based genomic results. In phase IV of eMERGE, Northwestern is building on this expertise to develop, deploy, and evaluate systems of EHR-based, genomics-guided clinical risk assessment and management tools across a variety of common, impactful conditions. Northwestern's cross-disciplinary approach to this work is empowered by an innovative smartphone app to consolidate outreach, enrollment, engagement, return of results, and dissemination of health education materials surrounding genetic risk and risk management. Focusing recruitment on community-based clinics, Northwestern aims to engage participants from communities that, though not traditionally included in academic research settings, could benefit significantly from these risk management approaches. By combining expertise in informatics and EHR integration with innovative return-of-results strategies rooted in behavior theory, Northwestern aims to provide valuable data on accuracy, utility, and uptake of genetic risk assessment as the field moves towards integrating genetic risk scores into clinical practice.University of Alabama at Birmingham (UAB)Our eMERGE team aims to bring our experience and expertise in research with medically underserved (>75%) populations to identify genomic signatures of common diseases, conduct genomic risk assessments within the clinical workflow and where appropriate, pre-treat at-risk patients with common diseases including diabetes, chronic obstructive pulmonary disease, obesity, coronary artery disease and prostate cancer. Our aims will also allow us to develop genomic risk assessments, and address challenges involved in bringing genomic medicine into routine medical care. Working with the eMERGE network, we will select the eleven diseases of public health impact and select polygenic risk scores for clinical implementation. We will conduct an ethical legal social implications (ELSI) study, to explore patient perspectives on the use of family history and polygenic risk scores for estimating disease risk among Alabama Genomic Health Initiative (a statewide cohort) participants. The results will inform the development of consent, educational materials, and a communication strategy to enhance recruitment and retention of eMERGE participants. Recruiting over 75% of patients from medically underserved communities, we will incorporate genomic risk, family history, and clinical data to identify high-risk patients, recommending risk reduction recommendations in concordance with practice guidelines. For high-risk patients, we will deploy clinical decision support and present the genomic risk assessments and risk reduction recommendations. We will assess three outcomes: uptake of recommendations (implementation outcome), adherence to clinic visits (engagement outcome), and surrogates of disease/control (clinical outcome; e.g. blood sugar, cholesterol). We bring our expertise and experience to collaborate with the eMERGE investigative team to leverage the power of genomics to prevent disease.University of Washington (UW)The eMERGE IV Northwest partnership includes clinicians, scientists, and professionals in other fields from University of Washington (UW) Medicine, UW Health Sciences, the Fred Hutchinson Cancer Research Center, and the Brotman Baty Institute for Precision Medicine. The eMERGE IV Northwest partnership aims to evaluate the use of genomic information in the health care of diverse participants at the University of UW. Our site is expected to lead work on the prediction of colon cancer, glaucoma, and cardiovascular disease; other conditions expected to be studied include diabetes, liver disease, high cholesterol, and osteoporosis. Working with our eMERGE colleagues, we will aggregate, into a single score that informs about the risk of a disease, a participant's polygenic test information, which looks at variants from across the genome, as well as other known risk factors, such as personal and family medical history, environmental and social determinants, and physical and lab results. This score would let clinicians know which patients might benefit from screenings or other interventions to reduce the risk of disease or make an early diagnosis. In addition to experts specializing in each of the medical conditions that are the focus of the Northwest site, leaders in health economics, and in the ethical and societal aspects of genomics and health care will also be part of the research team. Medical, as well as economic, outcomes will be measured. Stakeholder engagement will be encouraged to obtain comments from participants and their families.Vanderbilt University Medical Center (VUMC)Vanderbilt University Medical Center has embraced Personalized Health and Healthcare as a key pillar of our Research Strategic Plan. This institutional commitment has taken multiple forms including the development of key infrastructure resources (the institutional Biobank (BioVU); the program in preemptive pharmacogenetic testing; the genotyping and sequencing core) and support of faculty in key disciplines such as genomics, informatics, ethics, privacy science, and clinical pharmacology. VUMC's team has contributed importantly to progress in multiple areas across eMERGE, including developing and deploying phenotype algorithms; developing and managing the genotype quality control pipeline for the network (eMERGE I); discovering new genotype-phenotype relations in VUMC and cross-network datasets; actively participating in the PGx clinical implementation project, community consultation, and return of results initiatives; developing methods to resolve tensions between data access and individual privacy; developing sampling methodology for the CERC survey; and developing new software tools for the field, including for developing and validating phenotypes, de-identification and for the phenome-wide association study paradigm (“PheWAS”)eMERGE Network Coordinating Center (CC)Vanderbilt University Medical Center has been the coordinating center of the eMERGE Network since inception. During this phase of eMERGE we have partnered with the Broad Institute to to add expertise in large-scale genotyping, cloud computing, and genomic data analysis and management, and with Duke University to leverage its proficiency in the implementation of patient-oriented family history tools and delivery of risk assessments. To meet the needs of the Network, the CC continues to serve NHGRI, the Network, and its members in all coordination, communication, and collaboration functions while providing a nationally visible home for eMERGE authored tools and scientific productivity. The CC is also assisting the Network with selecting and validating polygenic risk scores (PRS) for approximately eleven complex diseases and developing genomic risk assessments (GRAs) which combine the PRS with other clinical risks, family history, and monogenic risks. Finally, The CC will coordinate a prospective study for 25,000 participants which calculates clinical and genomic risks for participants and their providers. In addition to providing the genotyping and PRS reporting services, we will develop with the Network scalable EHR-based methods to assess uptake of risk-reduction recommendations and clinical impact.

  Study phs003905

• Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined with Nivolumab and Ipilimumab for Patients with Resected MMR-p Colorectal and Pancreatic Cancer

  Phase 1 study for patients with resected PDAC after neoadjuvant and/ or adjuvant chemotherapy and/or radiation, as well as patients with metastatic colorectal cancer who have exposure to 2 or more lines of chemotherapy, to evaluate safety and the immune response to pooled mutant-KRAS peptide vaccine (KRAS peptide vaccine) with poly-ICLC adjuvant in combination with nivolumab and ipilimumab.

  Study phs003425

• Genomic Landscape and Preclinical Therapeutic Insights Developed from Xenograft, Organoid, and Cell Line Models in the NCI's Patient-Derived Models Repository

  Patient-derived xenografts (PDXs), organoids (PDOrgs), and two-dimensional cell cultures (PDCs) are powerful tools for translational cancer research. The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR) features preclinical models from primary and metastatic lesions across a broad array of solid tumors, including rare and pediatric cancers, each annotated with genomic data as well as clinical information about the patient from whom the model originated (https://pdmr.cancer.gov). We used these models to demonstrate stable propagation of genomic aberrations over multiple passages, to evaluate patient-specific tumor heterogeneity, and to examine the relationship of the preclinical activity of a panel of approved and investigational anticancer agents in PDXs and PDOrgs to known levels of therapeutic activity in the clinic.

  Study phs003984

• Comprehensive Genomic Data Deposition for Pancreatic Cancer Precision Medicine Studies: Clinical Trials NCT02451982 and NCT02648282

  This submission includes specimens from 89 pancreatic cancer patients at Johns Hopkins Hospital, comprising 41 surgically resectable and 48 locally advanced pancreatic cancer (LAPC) cases. These samples originate from two clinical studies, NCT02451982 and NCT02648282, following the Johns Hopkins Medical Institution Institutional Review Board-approved registry protocol at the Pancreatic Cancer Precision Medicine Center of Excellence Program. Written consent for specimen use, obtained from participants in the original studies, covers additional research, including this one. Biopsy specimens collected through endoscopic ultrasound-guided fine needle core biopsies or surgically resected tumors are included. NCT02451982 is a platform trial evaluating immunotherapy combinations for surgically resectable pancreatic ductal adenocarcinoma in the neo-adjuvant and adjuvant settings. It investigates the GVAX pancreatic cancer vaccine with immune-boosting cyclophosphamide, exploring immune cell trafficking and the impact of PD-1 blocking. NCT02648282 focuses on the efficacy and safety of combining cyclophosphamide, pembrolizumab, GVAX, and stereotactic body radiotherapy (SBRT) in locally advanced pancreatic cancer, with an emphasis on anti-tumor activity. Both studies provide valuable insights into innovative pancreatic cancer treatment approaches.

  Study phs003600

• NCTN: A Non-Randomized Phase III Study of Response Adapted Therapy for the Treatment of Children with Newly Diagnosed High Risk Hodgkin Lymphoma (AHOD0831)

  Study ID: AHOD0831NCT Number: NCT01026220Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Non-Randomized Phase III Study of Response Adapted Therapy for the Treatment of Children with Newly Diagnosed High Risk Hodgkin Lymphoma (AHOD0831)Trial Description: This phase III trial is studying how well giving combination chemotherapy together with radiation therapy works in treating young patients with newly diagnosed Hodgkin lymphoma. 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. Radiation therapy uses high energy x-rays to kill cancer cells. Giving combination chemotherapy together with radiation therapy may kill more cancer cells. Clinical data presented in the following publication(s):PMID 31180135Disease type(s): Hematopoietic Neoplasm/Lymphoma - Hodgkin LymphomaClinical Dataset(s) included:NCT01026220-D1 (PMID 31180135): There is one dataset for AHOD0831's primary publication 31180135. This dataset contains patient demographics, baseline characteristics, PET results, and survival endpoints. This dataset is presented at patient level and includes one record per patient.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 phs004161

• Multi-Modal Single-Cell, Spatial, and Genomic Analyses of Human Non-Small Cell Lung Cancer Brain Metastases

  We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of 12 treatment-naive non-small cell lung cancer (NSCLC) primary tumors (PTs) and 31 treatment-naive NSCLC brain metastases (BMs). In total, we recovered 277,206 cell transcriptomes in 43 samples. Single-nuclei suspension from frozen NSCLC metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020, PMID:32405060) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST) followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 10,000-14,000 and were loaded using a Chromium controller (10X genomics) and Chromium Single Cell 5' Reagents (V1.1 and V2). Complementary DNA libraries were generated according to manufacturer's instructions, with the modification of one additional cycle of amplification. Matched single nuclei T cell receptor (snTCR) sequencing libraries were prepared from amplified cDNA libraries using either Chromium Single Cell V(D)J Enrichment Kit for human T cells Reagent Kit, v1.1, or single cell human TCR amplification kit. Final snTCR sequencing libraries were prepared using Single Index Kit T Set A for V1.1 libraries or Library construction kit and Dual Index Kit TT set A for V2 libraries. Sequencing libraries were quantified using Tapestation D5000 reagents and a 2200 TapeStation and pooled for sequencing. Pool matched low pass whole-genome sequencing (lp-WGS) was performed in addition to snRNA-seq to improve the identification of the malignant and non-malignant cell compartments. Nuclei from snRNA-seq sample preparations were collected by centrifugation (500g, 5 min), snap frozen after removing excess ST buffer, and stored at -200C until further processing. If insufficient nuclei (0C for 9 minutes. Adapters were not diluted, and the optional PCR (5 cycles) and cleanup were performed. After library cleanup with AMPure beads (Beckman Coulter, Brea, CA), libraries were quantified with Tapestation D5000 HS tapes (Agilent) and stored at -200C until sequencing.Using multiplexed immunofluorescence in an independent cohort of treatment-naïve pairs of primary tumors and brain metastases from the same patients with NSCLC, we validated genomic and tumor-microenvironmental findings and identified a cancer cell population characterized by neural features that strongly enriched in brain metastases. This comprehensive analysis provides insights into human NSCLC brain metastasis biology and serves as an important resource for additional discovery.

  Study phs003865

• NCORP: Vitamin D and Breast Cancer Biomarkers (CALGB-70806)

  Study ID: CALGB-70806NCT Number: NCT01224678 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCORP: Vitamin D and Breast Cancer Biomarkers (CALGB-70806)Trial Description: RATIONALE: Vitamin D may help prevent breast cancer.PURPOSE: This randomized clinical trial is studying vitamin D and breast cancer biomarkers in female patients. Clinical data presented in the following publication(s):PMID 33849913 Disease type(s): Breast Neoplasm - Breast Neoplasm, MiscellaneousNon-neoplastic Disorder - Non-neoplastic Disorder, MiscellaneousClinical Dataset(s) included:NCT01224678-D1 (PMID 33849913): Dataset NCT01224678-D1 is one of 2 datasets associated with PubMed ID 33849913. This dataset contains baseline and change in breast density, baseline characteristics, change in Vitamin D levels, and off treatment reasons.NCT01224678-D2 (PMID 33849913): Dataset NCT01224678-D2 is one of 2 datasets associated with PubMed ID 33849913. This dataset contains data presented in the safety analyses.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 phs004250

• Disentangling the Effect of Black/African Ancestry from Confounding Variables on Colorectal Cancer Biology

  This study examined the effect of African ancestry on AI assisted computation of tumor infiltrating lymphocytes (TIL%) scores from hematoxylin and eosin stained whole slide images (WSI) assembled from three cohorts: 1.) African vs. European ancestry WSI downloaded from the TCGA-COAD-READ database; 2.) African vs. European ancestry WSI assembled from three US medical centers; 3.) Nigerian WSI assembled from a single Nigerian medical center. There were 33 African ancestry WSI suitable for analysis in the TCGA cohort and 48 African ancestry WSI in the independent US cohort. In addition to self-described African ancestry, the additional independent covariables were: 1.) Mismatch repair enzyme-deficient/ microsatellite instability-high vs. MMR-proficient/MSI-Low +microsatellite stable (MMR-d/MSI-H vs. MMR-p/MSI-L+MSS); 2.) Categorical age at diagnosis/resection (75 y); 3.) Sex (Male vs. Female); tumor location (Right vs. Left + Rectum); tumor stage (I+II vs. III+IV), tumor grade [G1+ G1/G2+G2 vs. G2/G3 +G3+mucinous (regardless of G)]. For the 242 TCGA cohort there were 241 parallel whole transcriptome data generated from parallel frozen tumor samples. For the independent US cohort there were 87 parallel targeted whole exome transcriptome data generated from the same formalin fixed paraffin embedded (FFPE) block. The TCGA and independent US cohort computed TIL% scores were correlated separately with CIBERSORTx derived total lymphocyte and T-cell abundance scores, and with CXCL10 and CCL5 gene expression values. mRNA gene expression count data (from STAR processing of the RNA-sequence data) and WSI for the subjects used in this study are available from the Genome Data Commons (GDC).

  Study phs004622

• Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer: DNA and RNA Sequencing

  This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. All participants in this study were female. RNA sequencing (RNA-Seq) data from the same patients were previously published under phs001863. This comprehensive dataset (phs003801) includes all data published under phs001863 and new RNA and DNA data for patients in CALGB 40603.

  Study phs003801

• Germline Sequence Variation in Cancer Genes Among Rwandan Breast and Prostate Cancer Cases

  Inherited genetic information can reduce cancer risk and mortality using protocols for patient ascertainment, testing, counseling, prevention, and treatment. For example, carriers of germline BRCA1/BRCA2 or Lynch Syndrome mutations are at increased risk of breast, ovarian, prostate, endometrial, colorectal, and other cancers. Genetic testing is of clinical value because many mutations are actionable in reducing risk or determining appropriate treatment regimens. There is growing evidence that inherited genetic mutations represent a large proportion of cancer cases in sub-Saharan Africa (SSA). It is also well known that most cancer genetic testing data does not represent the racial and ethnic diversity of the US or global population. Despite the high proportion of cancer cases diagnosed at an early age and late stage, as well as the potential for interventions to reduce cancer risk and death by using genetic tools, genetic testing, counseling, and clinical management protocols have largely not been widely developed in SSA. In order to develop and evaluate the potential for genetic testing in SSA, we propose to undertake a proof of concept feasibility study of hereditary cancer that will contribute data on the prevalence of hereditary cancer mutations in SSA and inform the development of SSA-specific guidelines for cancer genetic testing. In this study, we undertook a pilot evaluation of research genetic testing and counseling in breast and prostate cancer cases in Rwanda that involved genetic testing of breast and prostate cancer cases.

  Study phs003927

• DNA Repair Capacity for Lung Disease Risk Assessment

  A focus of this work was to address the extent to which susceptibility for lung cancer varies by gene-environment-phenotype interactions involving DNA repair capacity and differences in risk from environmental stressors. GWAS from a subset of subjects from the Lovelace Smokers Cohort and New Mexico Lung Cancer cohort were used to derive polygenic risk scores for DNA repair pathways (nucleotide excision, base excision, single strand break, non-homologous, homologous recombination). Logistic regression analysis was used to examine the association between polygenic risk score and lung cancer status. Polygenic risk scores were grouped by quartiles. Only diminished base excision repair was associated with increased risk for lung cancer at the 25-50% quartile and approached significance at the 50-75% quartile.

  Study phs004063

• National Cancer Institute Multi-Ancestry Genome-Wide Association Study of Kidney Cancer (NCI-3)

  The National Cancer Institute (NCI) multi-ancestral genome-wide association study (GWAS) of kidney cancer ("NCI-3") was performed by NCI to further investigate common genetic variants associated with risk of kidney cancer and its two major subtypes across individuals of different ancestries (European, African, East Asian, Latin American). The NCI-3 GWAS includes 12,315 cases and 73,091 controls from 25 centers in North America, South America and Europe, genotyped using the Illumina Global Screening Array v2.0. SNP-level results from this GWAS were combined by meta-analysis with results from two earlier NCI European-ancestry GWAS (RCC; phs000351: 1,311 cases and 3,424 controls and phs001736: 2,417 cases and 4,391 controls), a NCI GWAS of African Americans (phs000863; 255 cases and 375 controls), GWAS conducted at other institutions [International Agency for Research on Cancer (scan 1: 2,438 cases and 5,071 controls; scan 2: 2,781 cases and 2,940 controls), The University of Texas MD Anderson Cancer Center (scan 1: 893 cases and 556 controls, scan 2: 1,241 cases and 1,712 controls) and the Institute for Cancer Research, UK (944 cases and 4,024 controls)] and GWAS analyses of data from three large biobanks (Biobank Japan: 523 cases and 86,306 controls; FinnGen: 2,095 cases and 304,956 controls; UK Biobank: 1,807 cases and 348,824 controls). Only individual-level data from NCI-3 and the two MD Anderson Cancer Center scans are included in this dbGaP submission. All study-specific and meta-analysis summary statistics are included.

  Study phs003505

• Rearrangements of Viral and Human Genomes at Human Papillomavirus Integration Events and Their Allele-Specific Impacts on Cancer Genome Regulation

  We discovered genomic and epigenomic dysregulation originating at sites of human papillomavirus (HPV) integration following the Oxford Nanopore long-read analysis of 72 cervical cancer genomes. The integration events had allele-specific effects on the genome, methylome, and transcriptome, which sometimes resulted in the activation of cancer genes. We also examined the 72 samples using Illumina short-read analysis in phs000528. We also produced long-read cDNA-sequencing data on 29 cervical cancer samples from phs000528 (of which 27 also have long-read WGS data available) for further analysis of HPV-human transcripts derived from HPV integration events.

  Study phs003780

• HINTS Geo-Coded Data 2019 (HINTS 5 Cycle 3)

  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 mail-mode data collection cycles over the course of four years. The third round of data collection for HINTS 5 (Cycle 3) was conducted from January 22 to April 30, 2019 with a goal of obtaining 3,500 completed questionnaires. A push-to-web pilot test was conducted alongside the fielding of Cycle 3 (referred to as the Web Pilot). The Web Pilot was conducted from January 29 to May 7, 2019 with a goal of obtaining 2,046 additional completed questionnaires. A total of 5,438 respondents are included in the final sample.

  Study phs004216

• Incidental Detection of Maternal Neoplasia through Non-Invasive Cell-Free DNA Analysis (IDENTIFY), a Natural History Study

  Prenatal cell-free (cf) DNA sequencing for fetal aneuploidy incidentally detects circulating tumor DNA in the plasma of asymptomatic pregnant women. Distinguishing the subset of women with malignant tumors detected by prenatal sequencing from those with benign conditions, such as uterine fibroids, is critical to maternal medical management. The Incidental Detection of Maternal Neoplasia Through Non-Invasive Cell-Free DNA Sequencing (IDENTIFY) study at the National Institutes of Health in Bethesda, MD, offers standardized cancer screening and cfDNA sequencing to asymptomatic or minimally symptomatic pregnant women with nonreportable prenatal cfDNA sequencing results. We previously reported that whole-body magnetic resonance imaging (WB-MRI) and a specific genome-wide sequencing pattern of chromosomal gains and losses involving three or more chromosomes could reliably differentiate which women had cancer. We continue to explore additional noninvasive biomarkers to identify the subset of women with nonreportable prenatal cfDNA sequencing results who have cancer and to predict tissues of origin, particularly when patients or their providers are reluctant to pursue diagnostic testing, WB-MRI studies are unavailable, or imaging findings are indeterminate. Here, cfDNA sequence analysis was performed to identify cancer driver somatic mutations that might aid in distinguishing between pregnant women who have a high likelihood of occult malignancy from those who do not. In this pilot study, prospectively collected blood samples from 65 pregnant or postpartum women with and without occult cancers were analyzed blindly for cfDNA somatic mutations in 275 cancer-associated genes.

  Study phs004107

• GU16-257: Neoadjuvant Gemcitabine, Cisplatin, Plus Nivolumab in Patients with Muscle-Invasive Bladder Cancer with Selective Bladder Sparing

  This is a phase 2 trial seeking to define the safety and activity of gemcitabine, cisplatin, plus nivolumab as neoadjuvant therapy in patients with muscle-invasive bladder cancer and to define the role of clinical complete response (cCR) in predicting benefit in patients opting to avoid cystectomy. Primary Objectives Determine the cCR rate with gemcitabine, cisplatin, plus nivolumab;Determine the ability of cCR (cT0 or cTa) to predict benefit from treatment. Benefit was defined as, among the patients achieving a cCR, either being (a) 2-year metastasis-free in patients forgoing immediate cystectomy or (b) FindingsSeventy-six patients were enrolled; of these, 33 achieved a cCR (43%, 95% confidence interval (CI): 32%, 55%), and 32 of the 33 who achieved a cCR opted to forgo immediate cystectomy. The positive predictive value of cCR was 0.97 (95% CI: 0.91, 1).

  Study phs003372

• Methylation-Based Immune Deconvolution in Prostate Cancer Patients Before and After Radical Prostatectomy

  To explore whether surgical treatment for prostate cancer leads to long-term immune changes, we conducted a pilot study of n=11 prostate cancer patients treated with radical prostatectomy. We also included n=8 patients managed with active surveillance as a comparison group. We examined intra-individual changes in circulating immune cell subsets using serial blood samples collected pre- and approximately 6-months post-prostatectomy, and from matched time points for the patients managed on active surveillance. Immune cell subsets were deconvoluted using genome-wide methylation data. We observed no meaningful changes in circulating immune cell subsets in either patient group, suggesting that any surgery-induced immune changes to the circulating immune profile may not be long-lasting. The genome-wide methylation data from the two time points will be made available through dbGaP.

  Study phs003660

• A Prospective Study of the Oral Microbiome and Pancreatic Cancer

  Two prospective cohort studies - the Black Women's Health Study and the Southern Community Cohort Study - were used to investigate the oral microbiome in relation to pancreatic cancer risk. Using a nested case-control study design, 148 cases and 510 matched controls were included (122 Black American pancreatic cancer cases and 409 matched controls). DNA was extracted from oral wash samples, using the PowerSoil Pro kit. Paired-end whole metagenomic shotgun sequencing was performed, using the Illumina HiSeq2000 platform with a read length of 100 bp (insert size 350 bp).

  Study phs002454

• Integrative Analysis for Multi-Omics Data in Non-Small-Cell Lung Cancer

  We conducted epigenetic and transcriptomic mapping of primary non-small cell lung tumors and non-neoplastic tissues. 20 non-neoplastic lung tissues and 18 non-small cell lung tumors were obtained from Biorepository and Tissue Technology Shared Resource at Moores Cancer Center, UC San Diego. All tumor samples were in pathological stages I and II. 8 pairs of samples were "matched", meaning that the tumor and normal tissues came from the same patient. Microfluidic oscillatory washing–based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq) was used to profile the binding of H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3. SmartSeq-2 was used to map mRNA expression. We identified a large number of differentially modified regions for both epigenetic and transcriptomic markers between tumors and normal tissues. Deep learning model showed extensive transcription factor network rewiring. Raw sequencing data of the ChIP-seq and RNA-seq libraries are available through this dbGaP submission.

  Study phs003113

• APOLLO-BRCA-1: Proteogenomic Analysis of Invasive Breast Tumors in Young (less than 40 years old) vs Older Patients (greater than or equal to 60 years old)

  Breast cancer in women under the age of 40, accounting for ~5% of breast cancer diagnosed in the U.S., is more aggressive with worse outcomes than breast cancer in older women. The aim of this study is to to identify molecular features that may underlie the worse outcomes in young women with breast cancer. We performed a first-ever integrated proteogenomic study from a matched cohort of laser-microdissected tumors of 34 young (age Proteomic Data Commons at the National Cancer Institute.

  Study phs003636

• Kids First: Genomic Analysis of Pediatric Rhabdomyosarcoma

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the genomic and phenotypic data from this study are accessible through dbGaP. The data is also available at the Kids First Portal, where other Kids First datasets can also be accessed in the cloud for data analysis, data visualization, collaboration and interoperability, open to all researchers and developers. Rhabdomyosarcoma (RMS) is one of the most common and deadly sarcomas in children and adolescents, but very little is known about its genetic epidemiology. This study will explore the role of new (i.e., de novo) mutations in both known cancer predisposition genes and novel susceptibility genes on the risk of RMS. A better understanding of the genetic risks for RMS may lead to prevention strategies, better risk stratification, and even the identification of new therapeutic targets.

  Study phs004306

• Detecting and Subtyping Lung Cancer Through Analysis of Circulating Tumor DNA

  Small cell lung cancer (SCLC) is among the most aggressive tumors with poor clinical outcomes. Tumors are rarely resected, which is a major barrier to molecular profiling of tumor tissue; therefore, non-invasive approaches using circulating tumor DNA (ctDNA) from liquid biopsies are needed to help advance research and clinical care for patients with SCLC. We developed a targeted capture panel that profiles SCLC genes and transcriptional regulation sites, including transcription start sites (TSS) and transcription factor binding sites (TFBS). This is a single assay that detects genomic mutations and transcriptional regulation activity based on ctDNA fragment patterns reflecting epigenetic nucleosomal positions. We applied this assay to sequence patient-derived xenograft (PDX) and patient plasma samples. We also performed whole genome sequencing (WGS) for a subset of the PDX plasma samples to validate the capture data. We developed new algorithms to quantify activity of key SCLC marker genes of ASCL1, NEUROD1, POU2F3, and ATOH1 and to classify SCLC subtypes based on activity of these markers. Furthermore, we developed a model to classify SCLC from non-small cell lung cancer (NSCLC), which has potential important applications for monitoring transdifferentiation and tumor plasticity.

  Study phs003570

• NRG-GY017: Atezolizumab before and/or with Chemoradiotherapy in Immune System Activation in Patients with Node Positive Stage IB2, II, IIIB, or IVA Cervical Cancer

  Locally advanced cervical cancer remains an area of high therapeutic unmet need, with ~50% of patients developing disease recurrence despite treatment with chemotherapy combined with radiation. Combination of immune checkpoint blockade with chemoradiation has been explored in this setting, but optimal sequencing of these modalities is unknown. To address this question, we developed and conducted the NCI sponsored trial “Anti PD-L1 (Atezolizumab) as an Immune Primer and Concurrently with Extended Field Chemoradiotherapy for Node Positive Locally Advanced Cervical Cancer”, randomizing patients to atezolizumab administration prior to and concurrent with chemoradiation therapy (CRT) vs. concurrent with CRT (NRG-GY017; N=40, ClinicalTrials.gov Identifier: NCT03738228). Patients were randomized to atezolizumab neoadjuvant and concurrent (Arm A) or concurrent with CRT (Arm B). The study closed to successful accrual of 36 evaluable patients in June 2020. Out of 40 patients consented patients, 4 were never treated. The reasons for that are: 2 were screen failures, 1 withdrew consent, and 1 was not treated due to physician preference. The study incorporated comprehensive collection of pre- and on-treatment tumor biopsies as well as multitime point blood collections. T cell receptor (TCR) sequencing was performed on the tumors as well as pre- and on-treatment peripheral blood, and the data are included with dbGaP submission. Among the 36 eligible and treated patients, there were 30 (17 on Arm A and 13 on Arm B) with pre- and on-treatment peripheral TCR sequencing data. Twenty-five patients (14 in Arm A and 11 in Arm B) had additional tumor TCR sequencing data available, which enabled tracking of tumor-associated TCR clones in peripheral blood. We demonstrate that neoadjuvant atezolizumab administration results in peripheral expansion of higher proportion of tumor-associated TCR clones in Arm A than in Arm B and is associated with favorable 2-year disease-free survival (DFS). No new safety signals were identified. These findings support further evaluation of the neoadjuvant IO and CRT sequencing strategy in locally advanced cervical cancer.

  Study phs003833

• NCTN: Risk-Stratified Therapy for Acute Myeloid Leukemia in Down Syndrome (AAML1531)

  Study ID: AAML1531 NCT Number: NCT02521493 Children's Oncology Group (COG) Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: Risk-Stratified Therapy for Acute Myeloid Leukemia in Down Syndrome (AAML1531) Trial Description: This phase III trial studies response-based chemotherapy in treating newly diagnosed acute myeloid leukemia or myelodysplastic syndrome in younger patients with Down syndrome. Drugs used in chemotherapy 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. Response-based chemotherapy separates patients into different risk groups and treats them according to how they respond to the first course of treatment (Induction I). Response-based treatment may be effective in treating acute myeloid leukemia or myelodysplastic syndrome in younger patients with Down syndrome while reducing the side effects. Clinical data presented in the following publication(s): • PMID 34320162 Disease type(s): • Hematopoietic Neoplasm/Leukemia - Acute Myeloid Leukemia • Hematopoietic Neoplasm/Leukemia - Myelodysplastic Syndrome Clinical Dataset(s) included:• NCT02521493-D1 (PMID 34320162): There are 2 datasets associated with PMID 34320162, NCT02521493-D1 through NCT02521493-D2. The NCT02521493-D1 dataset is a patient level dataset (single row per patient) containing patient characteristics, laboratory findings (hemoglobin, peripheral WBC, peripheral platelet), cytogenetics, outcome (overall survival and event-free survival), neutrophil recovery, ICU admission, select toxicity data, and targeted sequencing data for eligible myeloid leukemia in children with Down syndrome (ML-DS) enrolled on the AAML1531 clinical trial. • NCT02521493-D2 (PMID 34320162): There are 2 datasets associated with PMID 34320162, NCT02521493-D1 through NCT02521493-D2. The NCT02521493-D2 dataset is an adverse event level dataset (single row per adverse event, period, and patient) containing information of the micro-organisms associated with adverse events by period in the AAML1531 clinical trial. Additional genomic data are available for this trial under phs002187.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 phs004081

• Genomic Alterations in Normal Breast Tissues Preceding Breast Cancer Diagnosis (GANPBC)

  This study was designed to examine the genomic alterations in histologically normal breast tissues of women who subsequently developed breast cancer and compare it to breast tissues from women who did not. Breast core needle biopsy tissues from 160 healthy women at the Susan G. Komen Tissue Bank were requested for this study and sequenced using whole exome sequencing. The samples included tissues from 79 participants who, during the annual follow-up with Susan G. Komen self-reported a subsequent diagnosis of invasive or non-invasive breast cancer after tissue submission; these cases were classified as pre-diagnosis normal tissues. The remaining 81 samples were from women who had no cancer diagnosis at their last follow-up and were classified as healthy control samples. Among the pre-diagnosis samples, the average time from tissue donation to breast cancer diagnosis was 4.7 years (range: 0-11). For the healthy controls, the average time from tissue donation to the last follow up was 6.1 years (range: 0-14).

  Study phs003822

• NCTN: A Randomized Double-Blinded Phase III Study Comparing Gemcitabine, Cisplatin, and Bevacizumab to Gemcitabine, Cisplatin, and Placebo in Patients with Advanced Transitional Cell Carcinoma (CALGB-90601)

  Study ID: CALGB-90601NCT Number: NCT00942331 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Double-Blinded Phase III Study Comparing Gemcitabine, Cisplatin, and Bevacizumab to Gemcitabine, Cisplatin, and Placebo in Patients with Advanced Transitional Cell Carcinoma (CALGB-90601)Trial Description: This randomized phase III trial studies gemcitabine hydrochloride, cisplatin, and bevacizumab to see how well they work compared with gemcitabine hydrochloride and cisplatin in treating patients with urinary tract cancer that has spread to other places in the body. Drugs used in chemotherapy, such as gemcitabine hydrochloride and cisplatin, 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. Immunotherapy with bevacizumab, may induce changes in body's immune system and may interfere with the ability of tumor cells to grow and spread. It is not yet known whether gemcitabine hydrochloride and cisplatin are more effective when given with or without bevacizumab in treating patients with urinary tract cancer. Clinical data presented in the following publication(s):PMID 33989025 Disease type(s): Urothelial Tract Neoplasm - Urothelial Tract/Bladder CancerClinical Dataset(s) included:NCT00942331-D1 (PMID 33989025): Dataset NCT00942331-D1 is one of 3 datasets associated with PubMed ID 33989025. This dataset contains all patient level data including baseline characteristics, survival status and time to event, progression free survival and time to event, treatment summaries, off treatment reasons for chemotherapy and bev/placebo, best response, tumor scans, the occurrence of grade 3/4 thrombocytopenia, the occurrence of a serious adverse event, and the occurrence of a dose delay or reduction.NCT00942331-D2 (PMID 33989025): Dataset NCT00942331-D2 is one of 3 datasets associated with PubMed ID 33989025. This dataset contains dose modification reasons for all patients with at least one dose reduction or delay. There is also a variable distinguishing the dose modification between cisplatin and gemcitabine.NCT00942331-D3 (PMID 33989025): Dataset NCT00942331-D3 is one of 3 datasets associated with PubMed ID 33989025. This dataset contains adverse event information.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 phs004243

• Targeting SS18-SSX Biology in Synovial Sarcomagenesis

  This study investigates the biological consequences of BRD9 degradation in synovial sarcoma, a cancer driven by the SS18::SSX (SSX1 or SSX2) fusion oncoprotein. The study includes human synovial sarcoma cell lines, patient-derived xenograft (PDX) models. Molecular profiling was performed using RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq).The primary aim was to determine how depletion of the GBAF chromatin remodeling complex subunit BRD9 affects chromatin remodeling activity, transcriptional regulation, and tumor growth in synovial sarcoma. The study found that BRD9 degradation does not disrupt GBAF complex assembly but instead enhances chromatin remodeling activity, maintains or increases chromatin accessibility, and promotes expression of SS18::SSX target genes despite reduced chromatin occupancy. These findings provide a mechanistic explanation for the limited clinical efficacy of BRD9 degraders in synovial sarcoma.Data available through dbGaP will include raw and processed human genomic and epigenomic datasets generated from patient-derived tumors, including RNA-seq, ChIP-seq, ATAC-seq, together with associated experimental and clinical metadata necessary for data interpretation.

  Study phs004771

• Sequencing of Rare Pancreatic Tumors That Respond to PD-1 Blockade

  Pancreatic cancer is nearly always refractory to immunotherapy, except in a rare subset of patients whose tumors have a high mutational burden (TMB), usually due to mismatch-repair deficiency. We collected tumors and matched blood from patients with pancreatic cancer, some of whom had high-TMB disease. We performed single-cell RNA-seq analyses of those samples to understand the correlates in the pancreatic tumor microenvironment of productive responses to immunotherapy. We found that different T cell populations responded to PD-1 blockade in TMB-high vs TMB-low tumors. This dataset consists of Illumina NovaSeq sequencing output (as FASTQ files) for blood and tumor libraries prepared using 10X Genomics Single Cell 5' Immune Profiling kits. FASTQs are provided for GEX, TCR, and (for multiplexed samples) HTO libraries.

  Study phs004257

• Transfer Learning Associates CAFs with EMT and Inflammation in Tumor Cells in Human Tumors and Organoid Co-Culture in Pancreatic Ductal Adenocarcinoma

  This study examined the transcriptional changes induced by cancer associated fibroblasts (CAFs) in pancreatic ductal adenocarcinoma patient-derived tumor organoids. We hypothesized that cancer associated fibroblasts impacted tumor cell transcription to promote tumorigenic behavior. Using patient-matched cells from 3 patients, we compared the transcriptional profiles of patient-derived organoids in monoculture to patient-derived organoids co-cultured with CAFs. Similarly, we looked at the transcriptional changes in matched patient-derived cancer associated fibroblasts grown in monoculture or co-cultured with patient-derived organoids. With a focus on intercellular crosstalk, we identified crosstalk between cancer associated fibroblasts and patient-derived organoids through VEGFA and NRP1. This was identified by bulk RNA sequencing and examined dynamically in organoid-CAF co-culture. This dbGaP deposit is the bulk RNA sequencing data for these 3 patients.

  Study phs003563

• Lung Cancer Genetic Study Among Asian Never Smokers

  The Lung Cancer Genetic Study Among Asian Never Smokers includes data from four population-based studies conducted among Asian women: the Shanghai Women's Health Study (SWHS), the Hwasun Cancer Epidemiology Study (HCES1 and HCES2), the Female Lung Cancer Consortium in Asia (FLCCA, including sFLCA), and the Guangzhou Lung Cancer Study (GLCS). Shanghai Women's Health Study (SWHS): The SWHS is a population-based prospective cohort study of approximately 75,000 adult women who were recruited between 1997 and 2000. The cohort has been followed by a combination of record linkage and active follow-ups. Lung cancer patients identified in the SWHS and non-cases were included in the current study.Hwasun Cancer Epidemiology Study-Lung Cancer (HCES1 and HCES2): The HCES is a hospital-based case-control study whose goal is to identify factors of the cancer development and clinical progression in a Korean population. Included in this project were 299 female lung cancer cases from HCES2, who were diagnosed between April 2004 and February 2013 at Chonnam National University Hwasun Hospital, a cancer specified hospital in Jeollanam-do province, South Korea. Controls were randomly selected from women with no previous cancer diagnosis at enrollment in the Namwon Study and the Dong-gu study, ongoing community-based cohort studies in South Korea. A total of 1,103 controls (273 from HCES1 and 830 from HCES2) were genotyped by MEGA. Guangzhou Lung Cancer Study (GLCS): The GLCS is a case-control study including never-smoking women lung cancer cases and controls from Guangzhou, China.In this study, the DNA samples of 1,195 subjects from SWHS and GLCS were genotyped using whole exome sequencing (WES), and the DNA samples of 7,174 subjects from SWHS, HCES1, HCES2, FLCCA, and sFLCA were genotyped using the Multi-Ethnic Global Array (MEGA).

  Study phs002366

• Atezolizumab and Bevacizumab in Treating Patients With Rare Solid Tumors

  This phase Ib/II single-arm study evaluated atezolizumab + bevacizumab for patients with treatment-refractory metastatic HPV+ anal cancer. The primary endpoint was best overall response, and secondary endpoints included progression-free survival, overall survival, and safety/tolerability. Paired tissue biopsies were collected in patients before treatment and at the time of first restaging and analyzed for whole-exome sequencing, RNAseq (Bulk), and multiplex immunofluorescence. The overall response rate among 20 patients was 10%. WES and RNAseq data are provided here.

  Study phs003845

• A Clone's Genomic Stability as a Biomarker of Its DNA-Damage Resilience

  A main problem in the treatment of advanced cancers, including gastric cancers and glioblastoma, is the incertitude at which we predict how individual patients will respond to DNA-damaging agents, especially on the long run. Knowing the mechanism behind a patient's response, or the lack thereof, will help us depart from the oversimplified “more-is-better” and “one-size-fits-all” principles according to which DNA-damaging agents are administered. This will improve clinical outcome by allowing us to pinpoint those who would respond better and longer to lower doses than to higher doses of DNA-damaging agents. Under the assumption that the success of DNA-damaging therapy increases with the proliferation rate of a relatively homogeneous tumor population, there was little reason to assume anything other than monotonic dose-response relations. With the recent paradigm shift that most cancers are in fact DNA mosaic products of ongoing evolution, comes the urgency to reconsider these fundamental principles behind DNA-damaging therapy administration. As the developers of one of the first DNA deconvolution methods and with access to technologies to profile the transcriptomes of up to 10,000 cells simultaneously, we are equipped to embark on first personalized dose-finding strategies for DNA-damaging therapies. We will test the potential of the very long-term legacy that DNA-damage entails on a cell “genomic instability” as new biomarker of DNA-damage response. Our preliminary studies showed that, for most cancer types, DNA-damaging agents change a clone's genomic instability and that clones succumb to a limit in the amount of genomic instability they can tolerate. In particular, our results showed that patients with intermediate genomic instability have a very poor outcome and that this relation is only evident among treatment-naive patients, but not among patients treated with DNA-damaging agents. Further they show that we can measure genomic instability per clone and that clones with extreme genomic instability typically don't grow large. Our hypothesis that genomic instability, rather than proliferation rate, determines how sensitive a tumor is to DNA-damaging agents on the long-term, is founded on two unexpected findings. Patients with extremely high genomic instability per tumor clone have an exceptionally good outcome. Aim 1 will integrate exome- and single cell RNA-Seq (scRNA-Seq) data to characterize clones and to measure how much genomic instability they can tolerate. Low genomic instability is associated with reduced benefit from DNA-damaging agents. Aim 2 will use comet assays and treatment history to quantify DNA damage per clone, relating it to the clones' ability to tolerate DNA damage and to changes in the genomic instability of therapy-surviving clones.

  Study phs003762

• NCTN: A Randomized Double-Blind, Placebo-Controlled Phase III Study of Early versus Standard Zoledronic Acid to Prevent Skeletal Related Events in Men with Prostate Cancer Metastatic to Bone (CALGB-90202)

  Study ID: CALGB-90202NCT Number: NCT00079001Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Double-Blind, Placebo-Controlled Phase III Study of Early versus Standard Zoledronic Acid to Prevent Skeletal Related Events in Men with Prostate Cancer Metastatic to Bone (CALGB-90202)Trial Description:RATIONALE: Zoledronate may prevent or decrease skeletal (bone)-related events (such as pain or fractures) caused by bone metastases and androgen deprivation therapy. It is not yet known whether treatment with zoledronate is effective in preventing bone-related events in patients who have prostate cancer and bone metastases.PURPOSE: This randomized phase III trial is studying how well zoledronate works in preventing bone-related events in patients who are receiving androgen deprivation therapy for prostate cancer and bone metastases. Clinical data presented in the following publication(s):PMID 24590644Additional unpublished data from CALGB-90202Disease type(s): Reproductive System Neoplasm, Male - Prostate CancerClinical dataset(s) included:NCT00079001-D1 (PMID 24590644): NCT00079001-D1 is one of 3 datasets that contain the data published in the analyses of PubMed ID 24590644 (-D1 through -D3). This dataset contains baseline characteristics, stratification factors, prior therapy, and metastatic site data.NCT00079001-D2 (PMID 24590644): NCT00079001-D2 is one of 3 datasets that contain the data published in the analyses of PubMed ID 24590644 (-D1 through -D3). This dataset contains primary analysis (time to skeletal-related event), time-to-event analysis, and treatment discontinuation data.NCT00079001-D3 (PMID 24590644): NCT00079001-D3 is one of 3 datasets that contain the data published in the analyses of PubMed ID 24590644 (-D1 through -D3). This dataset contains the toxicity data reported.NCT00079001-D4 (Unpublished data): Dataset NCT00079001-D4 contains data collected on Alliance trial CALGB-90202 which are not published in the primary publication for the trial. NCT00079001-D4 includes data on type of progression, time to progression, cause of death and clinical follow-up 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 phs004392

• Evaluation of Local Response of Prostate Cancer to Irradiation Using Multiparametric MRI and MR-Guided Biopsies

  The purpose of this study was to determine the rate of local recurrence in patients with intermediate and high risk prostate cancer treated with radiotherapy. In this study, multiparametric MRI was first performed, and biopsy tissue was acquired from cancerous regions detected on MRI. Blood samples were also taken. DNA and RNA were extracted from tissue taken at baseline. DNA was used for whole exome sequencing (WES). RNA was used for gene expression microarray. Each patient then received radiation therapy with androgen deprivation therapy.

  Study phs001821

• Multi-Omics Study of Lung Cancer in Smokers From EAGLE

  EAGLE (Environment And Genetics in Lung cancer Etiology) is a population-based case-control study examining the full spectrum of lung cancer etiology from smoking initiation, smoking dependency to lung cancer development and outcome. It combines a traditional molecular epidemiology design with more integrative approaches by examining epidemiological, molecular, and clinical data together. To comprehensively investigate the effect of tobacco smoking behaviors on genomic or epigenomic alterations, we performed a multi-omics study including whole-genomic, transcriptomic, and epigenomic profiles in a total of 221 individuals from the EAGLE study.

  Study phs002992

• DirectHRD Enables Sensitive Scar-Based Classification of Homologous Recombination Deficiency (HRD)

  Homologous recombination deficiency (HRD)-induced genomic scars are an FDA-approved biomarker for identifying cancers likely to respond to PARP inhibitors. However, detecting HRD scars from blood biopsies has been challenging due to the low tumor content in blood samples. To address this limitation, we developed DirectHRD, a genomic scar-based HRD classifier leveraging whole-genome sequencing (WGS) data for non-invasive blood biopsy testing. DirectHRD was applied to 90 cell-free DNA (cfDNA) samples across four cancer types: breast, ovarian, prostate, and pancreatic. The method achieved an AUC of 0.87 and demonstrated the ability to detect HRD at tumor fractions as low as 1%, offering a tenfold increase in sensitivity compared to state-of-the-art methods.

  Study phs003760

• Genomic and Immune Profiling of Breast Cancer Brain Metastases

  Previous work has shown that breast cancer brain metastases (BCBrM) can have unique molecular profiles compared to extracranial tumors (ECTs), resulting in some patients demonstrating subtype switching between primary/extracranial tumors and brain metastases. Description of the biology of BCBrM and associations between biological features and clinical outcomes, particularly between molecular intrinsic subtypes, will facilitate the design of rational therapies for patients with BCBrM. To better characterize the molecular profiles of BCBrM, we conducted whole exome sequencing (WES) and total RNA sequencing (RNA-Seq) on BCBrM tissues, regardless of clinical or molecular subtype, obtained from a cohort of 42 patients from Duke University Medical Center. This cohort adds valuable patient samples to the field and enables strengthened investigation of somatic mutations, copy number alterations, gene expression profiles, and immune populations within and between BCBrM patients and other similar cohorts. The Duke BCBrM cohort includes clinical and molecular annotation of the 42 patient specimens and their associated WES and RNA-Seq data. Clinical and molecular (PAM50) intrinsic subtypes in ECTs and brain metastases were largely concordant within patients. There were observed differences in intrinsic subtype calls between frozen and FFPE specimens of the same tissue, with discordance mostly observed with LumB calls. Copy number alterations in chromosomal regions included clinically relevant genes, and somatic alterations were largely conserved within patients across matched samples, with few genes, including TP53, being recurrently altered in the majority of patient specimens. In matched FFPE brain metastasis and ECT samples, we observed differentially expressed genes and pathways that had increased or decreased expression in brain metastasis, including in oxidative phosphorylation and DNA repair. Survival outcomes for patients differed by intrinsic molecular subtypes, with some association between expression of select gene pathways and survival. Data available through dbGaP will be the sequencing data and sample attributes from BCBrM tissues obtained from 42 patients from Duke University Medical Center.

  Study phs003673

• Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

  We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

  Study phs003638

• California Teachers Study (CTS): Whole Genome Sequences From Under-Represented Populations

  The California Teachers Study (CTS) is a prospective observational cohort of N=133,477 adult women who have been followed since 1995. Participants completed up to six surveys and have been linked with cancer, hospitalization, and mortality data. In 2013-2016, over 14,000 CTS participants donated blood samples for future research. For this project, DNA was extracted in 2023 from 1694 buffy coats and 56 blood clots from N=1750 CTS participants whose self-reported race/ethnicity was Asian (398), Asian or Pacific Islander (18), Black or African American (189), Native American (128), Native Hawaiian or Other Pacific Islander (66), White Hispanic (719), or more than one race (232). Whole genome sequencing (WGS) was performed at CIDR in 2023-2024. WGS data and accompanying phenotype data are available through dbGaP. In addition, all CTS data are available to the research community via the CTS Researcher Platform (www.calteachersstudy.org), a secure cloud-based environment that includes data, software, documentation, and collaboration workspaces.

  Study phs002918

• Phase 2 Study of Pembrolizumab in Combination with Gemcitabine and Cisplatin as Neoadjuvant Therapy

  The purpose of the clinical trial (NCT02690558) is to evaluate whether adding pembrolizumab (Keytruda) to the combination of gemcitabine and cisplatin will improve shrinkage of the tumor before having a cystectomy, for people with muscle-invasive bladder cancer (MIBC).

  Study phs003452

• A Randomized Trial of Combined PD-L1 and CTLA-4 Inhibition with Targeted Low-Dose or Hypofractionated Radiation for Patients with Metastatic Colorectal Cancer

  Brief SummaryThis randomized phase II trial studies the side effects of durvalumab and tremelimumab to see how well they work with or without high or low-dose radiation therapy in treating patients with colorectal (CRC) or non-small cell lung cancer (NSCLC) that has spread to other parts of the body (metastatic). Immunotherapy with durvalumab and tremelimumab may induce changes in body's immune system and may interfere with the ability of tumor cells to grow and spread. Radiation therapy uses high energy x-rays to kill tumor cells and shrink tumors. Giving durvalumab and tremelimumab with radiation therapy may work better in treating patients with colorectal or non-small cell lung cancer.Detailed DescriptionPRIMARY OBJECTIVES:I. To assess safety and tolerability of combined checkpoint blockade with MEDI4736 (durvalumab) and tremelimumab alone or with high or low-dose radiation in non-small cell lung cancer (NSCLC). (NSCLC Cohort) II. To compare the overall response (excluding the irradiated lesion[s]) between combined checkpoint blockade with MEDI4736 and tremelimumab alone or combined checkpoint blockade with low or high dose radiation. (NSCLC Cohort) III. To assess safety and tolerability of combined checkpoint blockade with MEDI4736 and tremelimumab with high or low-dose radiation. (Colorectal Cohort) IV. To determine the overall response rate (excluding the irradiated lesion[s]) with combined checkpoint blockade with MEDI4736 and tremelimumab with either low or high dose radiation. (Colorectal Cohort)SECONDARY OBJECTIVES:I. To estimate median progression-free survival and overall survival. (NSCLC Cohort) II. To determine local control within the irradiated field(s) and abscopal response rates. (NSCLC Cohort) III. To evaluate associations between PD-L1 expression as well as levels of infiltrating CD3+, CD8+ T-cells and overall response. (NSCLC Cohort) IV. To explore changes in PD-L1 expression, circulating T-cell populations, T-cell infiltration, ribonucleic acid (RNA) expression, spatial relationship of immune markers, and mutational burden as a result of low or high dose radiation. (NSCLC Cohort) V. To estimate median progression-free survival and overall survival. (Colorectal Cohort) VI. To determine local control within the irradiated field and abscopal response rates. (Colorectal Cohort) VII. To evaluate associations between PD-L1 expression as well as levels of infiltrating CD3+ CD8+ T-cells and overall response. (Colorectal Cohort) VIII. To evaluate changes between PD-L1 expression as well as levels of infiltrating CD3+, CD8+ T-cells induced by targeted low or high dose radiation. (Colorectal Cohort) IX. To explore changes in circulating T-cell populations, T-cell infiltration, RNA expression, spatial relationship of immune markers, and mutational burden as a result of low or high dose radiation. (Colorectal Cohort)OUTLINE: Patients are assigned to 1 of 2 cohorts. NOTE: This Study is only for Cohort 2. Please see phs003295 for Cohort 1COHORT 1: Patients with NSCLC are randomized to 1 of 3 arms.ARM A: Patients receive tremelimumab and durvalumab and as in Arm C. Beginning at week 2, patients receive high dose radiation therapy once per day (QD) over 10 days for up to 3 fractions.ARM B: Patients receive tremelimumab and durvalumab and as in Arm C. Beginning at week 2, patients receive low dose radiation therapy every 6 hours twice per day (BID) on weeks 2, 6, 10 and 14.ARM C: Patients receive tremelimumab intravenously (IV) and durvalumab IV over 60 minutes every 4 weeks for up to 16 weeks in the absence of disease progression or unacceptable toxicity. Patients then receive durvalumab IV over 60 minutes 4 weeks after last combination dose for up to 9 additional doses.COHORT 2: Patients with CRC are randomized to 1 of 2 arms.ARM A: Patients receive tremelimumab intravenously (IV) and durvalumab IV over 60 minutes every 4 weeks for up to 16 weeks in the absence of disease progression or unacceptable toxicity. Patients then receive durvalumab IV over 60 minutes 4 weeks after last combination dose for up to 9 additional doses. Beginning at week 2, patients receive high dose radiation therapy once per day (QD) over 10 days for up to 3 fractions.ARM B: Patients receive tremelimumab intravenously (IV) and durvalumab IV over 60 minutes every 4 weeks for up to 16 weeks in the absence of disease progression or unacceptable toxicity. Patients then receive durvalumab IV over 60 minutes 4 weeks after last combination dose for up to 9 additional doses. Beginning at week 2, patients receive low dose radiation therapy every 6 hours twice per day (BID) on weeks 2, 6, 10 and 14.After completion of study treatment, patients are followed for up to 12 weeks.Official TitleA Phase 2 Study of MEDI4736 (Durvalumab) and Tremelimumab Alone or in Combination With High or Low-Dose Radiation in Metastatic Colorectal and NSCLC Conditions Metastatic Colorectal CarcinomaMetastatic Lung Non-Small Cell CarcinomaStage IV Colorectal Cancer AJCC v7Stage IV Lung Non-Small Cell Cancer AJCC v7Stage IVA Colorectal Cancer AJCC v7Stage IVB Colorectal Cancer AJCC v7 Intervention/Treatment Biological: DurvalumabRadiation: Radiation TherapyBiological: Tremelimumab Other Study ID Numbers NCI-2016-01325NCI-2016-01325 ( Registry Identifier ) (REGISTRY: CTRP (Clinical Trial Reporting Program))17-71910021 ( Other Identifier ) (OTHER: Dana-Farber - Harvard Cancer Center LAO)10021 ( Other Identifier ) (OTHER: CTEP) Molecular Technologies/AssaysIHCmIFOlinkCyTOFRNAseqWES

  Study phs003294