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.

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• 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.

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• 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.

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• 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.

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• 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.

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• 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

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• 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.

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• 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.

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• 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

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• 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.

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• 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