5617 results for "canc*"

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• Transcriptomic Profiles of Neoantigen-Reactive T Cells in Human Gastrointestinal Cancers

  This study explores the transcriptomic profiles of neoantigen-reactive tumor-infiltrating lymphocytes (TILs) from human bile duct and pancreatic cancer. The submitted data are bulk tumor RNA-Seq, tumor and germline whole-exome sequencing from 10 patients, and single cell RNA-Seq data from TIL of 5 of these patients.

  Study phs002765

• Pan Cancer Investigation of Human Leukocyte Antigen Loss of Heterozygosity

  Cancer cells can escape immune recognition through human leukocyte antigen (HLA) loss of heterozygosity (LOH) which results in deletion of HLA alleles, causing a reduction in presentation of tumor neoantigens. Despite its influence on immunotherapy response, few methods exist to detect HLA LOH, and accuracy of the approaches is poorly defined. Here, we present DASH (Deletion of Allele-Specific HLAs), a machine learning-based algorithm developed to detect HLA LOH from paired tumor-normal sequencing data. Using DASH to characterize HLA LOH in 610 patients across 15 cancer types, we found that 18% of patients had loss of heterozygosity in at least one HLA allele, suggesting the HLA LOH is a widespread, and potentially key immune resistance strategy in multiple cancers.

  Study phs002783

• Personalized Breast Cancer Vaccines Based on Genome Sequencing

  This study is from a phase I clinical trial of neoantigen DNA vaccines in triple negative breast cancer patients with persistent disease following neoadjuvant chemotherapy. The exome and RNA sequences used to identify somatic mutations, predict neoantigens, and design vaccines is within.

  Study phs002787

• Childhood Cancer Data Initiative (CCDI): Molecular Characterization Initiative

  The National Cancer Institute's (NCI) Childhood Cancer Data Initiative (CCDI) focuses on the critical need to collect, analyze, and share data to address the burden of cancer in children, adolescents, and young adults (AYAs). The Molecular Characterization Initiative (MCI) will further the CCDI's goals by providing access to better diagnostic tests for pediatric and AYA patients. The molecular characterizations of solid tumors, soft tissue sarcomas, and rare diseases are performed in a CLIA-certified setting as results may be used to screen for and/or confirm clinical trial eligibility, direct treatment, or otherwise contribute to the conduct of the trial. The following molecular characterization assays were performed:Tumor/Normal Whole Exome sequencing Methylation arraysArcher fusion panel Deidentified clinical reportsNote: New data will be added periodically, please check the SBG site for updates.

  Study phs002790

• Characterization of Neoantigen-reactive T cells by Single-Cell Analysis

  Through CITE-seq and TCR-seq analysis of non-small cell lung cancer (NSCLC) tumor-infiltrating lymphocytes (TIL), we developed a neoantigen-reactive T-cell signature based on clonotype frequency and CD39 protein and CXCL13 mRNA expression. There are four datasets from four NSCLC cases. Each dataset includes (1) Transcriptome of tumor infiltrating lymphocytes (TIL), (2) Cell surface protein expression on TIL by Feature barcoding, (3) T-cell receptor analysis of TIL, and (4) Reference file for feature-barcoding antibodies.

  Study phs002792

• Phase IB/II Study of Bazedoxifene in Combination with Palbociclib in Patients with Endocrine Resistant Hormone Receptor-Positive Breast Cancer

  In this phase Ib/II clinical trial, the investigators evaluated the efficacy and safety of the combination of palbociclib with bazedoxifene in patients with a metastatic endocrine-resistant hormone receptor-positive, HER2-negative breast cancer. Furthermore, whole exome sequencing of cell-free tumor DNA was done on serial samples from these patients, revealing potential molecular changes associated with mechanisms of resistance.

  Study phs002802

• Genome-Wide Pleiotropy Scan Across Multiple Cancers

  A whole-exome sequencing (WES) study was conducted in 3,233 cases diagnosed with multiple primary cancers and 3,229 matched cancer-free controls (90% non-Hispanic white, 3% African-American, 3% East Asian, and 4% Latino) selected from individuals in the Kaiser Permanente Research Bank (KPRB) who were members of the Kaiser Permanente Northern California (KPNC) health plan. Cancer-free controls were matched to cases on age at specimen collection (within 2 years), sex, genotyping array (which matched on self-reported race/ethnicity), closest distance using the first two principal components for genetic ancestry, and reagent kit. Cases and controls were drawn from two prospective KPRB cohorts: the Research Program on Genes, Environment and Health (RPGEH) and the ProHealth study. Participants were sequenced by the Regeneron Genetics Center using the Illumina NovaSeq 6000 platform, and sample preparation and quality control were performed using a high-throughput, fully-automated system [PMID: 33087929]. Reads were aligned to the GRCh38 reference genome, and variants were called using WeCall [PMID: 33087929]. Participants with sex discordance, 20x coverage at less than 80% of targeted sites, and/or contamination greater than 5% were excluded. After quality control, we retained n = 6,247 (3,111 cases, 3,136 controls) individuals for downstream analyses. Among participants selected for this WES study, n = 5,432 (2,299 cases; 3,133 controls) consented to deposition of data to the National Institutes of Health (NIH).Further quality control was applied to filter low quality variants. Genotype calls with low depth of coverage (DP) were updated to missing (DP < 7 for SNPs and DP < 10 for indels), after which sites with low allele balance (AB) - variants without at least one sample having AB ≥ 15% for SNPs or AB ≥ 20% for indels - were removed. Lastly, variants with missingness > 10% and Hardy-Weinberg equilibrium p-value < 10-15 were excluded. Further description of quality control and downstream single-variant and gene-based analyses is available in Cavazos et al, 2022 [medRxiv].

  Study phs002809

• Genetic Analysis of Latin American Cervical Cancer

  HPV16 is the most oncogenic type of human papillomaviruses (HPV). Integration of HPV into the human genome is an important mechanism of carcinogenesis but is absent in at least 30% of HPV16+ tumors. We applied long-read whole-genome sequencing (WGS) to cervical cancer cell lines and tumors to characterize HPV16 carcinogenesis in the absence of integration. WGS of HPV16+ cervical tumor samples from Latin America revealed that 11/20 tumors with only episomal HPV (EP) had intact monomer episomes. The remaining 9 EP tumors had multimer and rearranged HPV genomes. The majority (80%) of the HPV rearrangements and deletions disrupted the E1 and E2 genes, and EP tumors overexpressed the E6 and E7 viral oncogenes, a similar profile to tumors with HPV integration. Tumors with putative multimer HPV integrations display HPV multimers and concatemers of human and viral sequences. Our data uncovered a novel mechanism for HPV16 to cause cancer without integration through aberrant episomal replication, and forming rearranged, mutated, and multimer episomes.

  Study phs002810

• Esophageal Squamous Cell Carcinoma Precursor Study

  Esophageal cancer is the sixth most common cause of cancer death in the world. High-risk areas occur across central Asia and from eastern to southern Africa, and in these populations, nearly all of the cases are esophageal squamous cell carcinoma (ESCC). ESCC has a dismal prognosis, largely because symptoms usually appear late in the course of the disease, when the tumors are incurable. Early detection and treatment of curable precursor lesions and early invasive ESCC in asymptomatic high-risk adults offers the potential for long-term survival and reduced mortality from this disease. Previous studies have shown that routine cytology of non-endoscopically collected esophageal cell samples is not sensitive and specific enough to be clinically useful, so we are now looking for molecular markers of high-grade esophageal squamous dysplasia (HGD), the proven clinically important precursor lesion of ESCC, that can be used to increase the accuracy and utility of this initial screening exam. National Cancer Institute (NCI) and Cancer Institute and Hospital, Chinese Academy of Medical Sciences (CAMS) began collaborative studies of ESCC since the mid-1980s in China. The present proposal is designed to characterize the type and prevalence of DNA mutations in tissue samples of HGD and to establish biologic and questionnaire resources for further study. The proposed study has two components, a field study to obtain questionnaire data and biological samples, and a genomic analysis to perform sequencing of the biological samples and bioinformatics analysis of the sequencing. 

  Study phs002814

• Intercepting Progression from Pre-Invasive to Invasive Lung Adenocarcinoma

  An improved understanding of the biology of lung cancer is needed to intercept the disease at an early point in its progression. In this project we have used multidimensional methods to profile the tumor microenvironment (TME) and to determine the crosstalk between cancer cells and the TME in pre-invasive to invasive human lung non-solid adenocarcinomas. Comparative analysis of the cellular and molecular events associated with the distinct histological stages will lead to identification of the critical events triggering progression and thereby identify targets to intercept disease progression. The data being submitted represents the genomic profiles of patient samples with pre-invasive and invasive human lung adenocarcinomas.

  Study phs002818

• Cancer Risk Estimates Related to Susceptibility Genes (CARRIERS)

  The CARRIERS study utilized custom amplicon-based variant screening of known cancer predisposition genes in germline DNA from breast cancer cases and age matched unaffected controls taken from predominantly cohort-based breast cancer case-control studies to establish the risks of breast cancer associated with pathogenic variants in these genes.

  Study phs002820

• SU2C-MARK Lung Cancer Consortium - Checkpoint Blockade Response Project

  Immune checkpoint inhibitors have become a critical part of the armamentarium against advanced Non-Small Cell Lung Cancer (NSCLC). While early studies have identified Tumor Mutation Burden (TMB) and PD-L1 staining as important biomarkers of response, they remain imperfect predictors. Here we describe a multi-institutional effort as part of the SU2C-MARK Lung Cancer Consortium in which Whole Exome Sequencing (WES) - and in select cases, RNA sequencing – was performed on a large collection of NSCLC samples prior to immune checkpoint blockade therapy, along with matched clinical response data following therapy. (Profiling of a small number of on- or post-treatment samples was also performed.) We anticipate this dataset to be of high value for the development of a deep understanding of the molecular determinants of immune checkpoint blockade response as well as the discovery of novel biomarkers.

  Study phs002822

• A Phase 2 Study of Lamivudine in Patients with p53 Mutant Metastatic Colorectal Cancer

  This was an open-label, single-arm Phase II study of lamivudine in patients who had progressed on systemic therapy for advanced colorectal cancer with TP53 mutations. The phase II study had a two-stage design, with a target accrual of 20 evaluable patients for the first stage and a total of 32 patients for the whole study. The first 9 patients were treated with lamivudine at 150 mg PO bid continuously for 28-day cycles. Subsequent patients (10-32) received a higher dose of 600 mg PO bid continuously for 28-day cycles. Tumor assessments were performed every 8 weeks until documented disease progression by Response Evaluation Criteria in Solid Tumors (RECIST) or drug intolerance. Whole genome sequencing (WGS) and total RNA-seq were performed on pre- and post- treatment biopsies on this trial.

  Study phs002833

• Clinical and Molecular Features of Acquired Resistance to Immunotherapy in Non-Small Cell Lung Cancer

  PD-(L)1 blockade has been shown to promote durable responses in non-small cell lung cancer (NSCLC) patients and has been rapidly incorporated into the treatment regimens for many with advanced disease. Despite this, mechanisms of acquired resistance (AR) to PD-(L)1 have not been well understood. To address the clinical and molecular landscape of AR to PD-(L)1 blockade in NSCLC patients, a large clinical cohort of AR to PD-(L)1 blockade in lung cancer was examined. In conjunction, a systematic genomic and transcriptomic analysis in a subset of patients (n = 29) with available tissue samples was conducted. To investigate the molecular mechanisms of AR to PD-1 blockade from pre- and/or post-treatment tumors, microarray-based whole transcriptome expression data for 29 tumor samples, and whole exome sequencing (WES) data from 34 tumor samples was generated from this subset. Microarray data was uploaded to the Gene Expression Omnibus (GEO) database. Most AR tumors showed retained or increased inflammatory characteristics with significant upregulation of IFNγ which was suggestive of persistent albeit insufficient anti-tumor immune response. This finding expounds upon the prior pre-clinical and translational data supporting the intricate role of IFNγ in sensitivity and resistance to immunotherapy. Whereas initial IFNγ exposure may be fundamental to T cell activation (a hallmark of immune response), persistent IFNγ related effects and upregulation may potentially signal immune dysfunction and IFNγ insensitivity in contrast. The inflammatory phenotypes identified have implications for future rational development of new immunotherapy strategies for patients with AR.

  Study phs002834

• Breast Cancer Family Registry

  The Breast Cancer Family Registry (BCFR) is a multi-center prospective cohort, comprised of over 30,000 women and men from nearly 12,000 families from the United States, Canada, and Australia. Our BCFR resource has been used, and continues to be used, by breast cancer researchers around the world in order to find new ways to prevent, diagnose, and treat cancer. The BCFR provides an extensive and diverse range of resources, expertise, and specialized skills, and has several unique strengths: 1) the collection of a large number of individuals and families across a wide spectrum of breast cancer risk, including both affected and unaffected individuals; 2) the large collection of families with early-onset breast cancer; 3) the large collection of racial/ethnic minority families not replicated elsewhere; 4) the extensive molecular characterization performed to date; and 5) active follow-up of both probands and family members. Thus, the BCFR comprises a unique cohort of probands and family members at familial/genetic risk of breast cancer that will continue to facilitate a wide range of research studies, such as gene discovery, examination of cancer-related outcomes and risk factors in high-risk subjects, investigation of novel behavioral interventions, and cancer prevention trials among at-risk family members. Consequently, the BCFR Cohort, as one of the few cohorts available worldwide with biospecimens and extensive molecular and genetic characterization, combined with epidemiologic data and long-term follow up, will be an invaluable resource for translational research in the genetic epidemiology of breast cancer.

  Study phs002835

• The Transcriptomic Landscape of Oncogenic PI3K Reveals Key Functions in Splicing and Gene Expression Regulation

  This study includes RNA-seq of paired tumor biopsies from PIK3CA-mutated breast cancer patients that underwent treatment with PI3Kα inhibitors.

  Study phs002840

• A Pilot Study of NKTR-214 and Nivolumab in Selected Patients with Locally Advanced/Metastatic Sarcoma

  Study cohort comprises samples derived from patients that received treatment on an open-label, non-randomized, non-comparative pilot study of bempegaldesleukin, a CD122-preferential interleukin-2 pathway agonist, with nivolumab in refractory sarcoma at Memorial Sloan Kettering/MD Anderson Cancer Centers (NCT03282344). Patient tumors include a variety of sarcoma subtypes. Samples include whole exome sequencing of tumor/normal pairs, poly-A RNA and TCR sequencing of tumors.

  Study phs002852

• MSK SPECTRUM - SPatiotemporal Evolution of Cancer Traced Using Multimodalities

  MSK SPECTRUM is a multi-modal, interdisciplinary prospective study of spatiotemporal determinants of high-grade serous ovarian cancer (HGSOC) evolution, treatment and response. Accounting for ~80% of ovarian cancers, HGSOC is the most lethal gynecological malignancy and is a cancer of major unmet clinical need. Challenges in disease management relate to several unresolved questions about disease biology and diagnostic modalities. Prospective longitudinal collection of tissues and blood from laparoscopic biopsies and debulking surgeries enable multi-modal molecular measurements. The program brings together formidable expertise at Memorial Sloan Kettering Cancer Center (MSKCC) across the disciplines of high-resolution genomics and computer science, radiology and radiomics, surgery, tissue banking and sample preparation, medical oncology, immuno-oncology and high-resolution tissue profiling to generate a comprehensive and integrative dataset that will allow us to address the following major aims: i) characterize malignant and immune diversity at diagnosis, ii) survey the co-evolution of malignant cells and the immune response, and iii) stratify patients on standard-of-care and investigational compounds based on their genomic and transcriptomic signatures and changes to relevant genes (TP53, CCNE1, BRCA1/2, CDK12). The goal is to create a framework to utilize integrated multi-modal data as a route to advanced diagnostics and to ultimately establish a proof-of-concept for integrated diagnostics.

  Study phs002857

• RB1 Loss Triggers Dependence on ESRRG in Retinoblastoma

  Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed whole exomes from primary Rb tumors to identify novel Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. ESRRG is an essential mediator of hypoxic adaptation and cell survival in retinoblastoma, representing a promising new therapeutic target.

  Study phs002859

• Improved T Cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer

  This study characterized the evolution of the peripheral immune cell function and composition across the course of standard of care platinum and taxane chemotherapy in ovarian cancer using bulk and single cell transcriptomic approaches. Serial blood samples were collected from ten patients with advanced high-grade serous ovarian cancer treated with chemotherapy. Single cell sequencing was performed on five patients' samples collected before the initiation of chemotherapy and after the third cycle of chemotherapy.

  Study phs002862

• Genomic Analyses in Neoadjuvant Immunotherapy-Treated Head and Neck Cancers

  This is a phase 2 multicenter interventional trial involving the preoperative (neoadjuvant) administration of pembrolizumab, an anti-programmed cell death protein-1 (anti-PD-1) agent, to patients with pathologically confirmed, surgically resectable advanced head and neck squamous cell carcinoma (HNSCC). Participating centers were Dana-Farber/Harvard Cancer Center, Alvin J. Siteman Cancer Center, Washington University and Memorial Sloan Kettering Cancer Center. The trial (NCT02296684) consisted of two cohorts: Cohort 1 enrolled and treated patients received one dose of pembrolizumab prior to surgical resection with curative intent, and adjuvant pembrolizumab was planned for patients with high risk pathological features (positive margins and/or extranodal extension) in the surgical specimen. Cohort 2 enrolled and treated patients received 2 doses of pembrolizumab prior to surgical resection with curative intent. Adjuvant treatment was not dictated by the trial protocol for Cohort 2. The primary endpoint was rate of at least 50% pathological tumor response (pTR), defined as the presence of tumor necrosis/keratinous debris in the tumor bed following neoadjuvant pembrolizumab. pTR was graded as follows: pTR0 (<10%), pTR1 (10-49%) and pTR2 (≥50%). Baseline, pre-treatment tumor biopsy and post-neoadjuvant pembrolizumab surgically resected tumor specimens were dissociated, and CD3+CD45+ cells were analyzed for T cell receptor (TCR) expression and 5' gene expression analysis using single cell sequencing technologies for a subset of patients.

  Study phs002864

• Accurate Genome-Wide Germline DNA Profiling from Decade-Old Archival Tissue Specimens

  We evaluate the validity of repurposing archival tissue specimens for germline genetic studies. We performed lc-WGS and imputed genotypes on 10 pairs of matching blood and tumor tissue and benchmarked the accuracy of genome-wide genotypes, HLA haplotypes, and several polygenic risk scores (PRSs). The reported results indicate the high accuracy of germline genotypes and haplotypes obtained from archival tissue DNA. Using this methodology, we estimate breast cancer PRS in 36 Ductal carcinoma in situ (DCIS) patients and demonstrate its association with breast cancer subsequent event (BCSE).  

  Study phs002865

• Blood Somatic Mutations in TCGA Donors Suffering from Solid Tumors

  Blood somatic mutations identified across 8,530 solid tumor patients in TCGA cohort. We reasoned that low-coverage whole-genome sequencing of blood samples routinely carried out in cancer genomics projects may be repurposed to detect clonal hematopoiesis (CH). Thus, inspired by a previous approach to identify early mutations in the development of the hematopoietic system, we implemented a pipeline to systematically carry out this "reverse" somatic mutation calling on the paired blood/tumor samples. Blood somatic mutations were called using a 'reverse' approach, in which the tumor sample taken from each patient was used as control of their germline genome. Blood somatic mutations are thus detected as variants in the blood (with respect to the human reference genome) that are absent in the tumor sample. The variant calling was carried out in our in house cluster on downloaded blood/tumor BAM files. The matched blood and tumoral BAM files -- masked and deduplicated using GATK -- of 8,530 whole-exome patients were obtained as described above. The variant calling was carried out using Strelka2 (employing default parameters) with the blood sample as the tumoral input and the tumor sample as control (reverse calling). All variants with two or more supporting reads matching the caller PASS filter and with VAF<0.5 were kept. Mutations in lowly mappable regions as defined by the DUST algorithm (k=30) and UMAP68 (36-kmers) were excluded. Contiguous variants were merged into double-base substitutions. Variants with greater frequency across the cohorts than the DNMT3A R882H or JAK2 V617F hotspot in a cohort-specific Panel of Normals and in gnomAD v2.1 were removed. This was equivalent to discarding variants present in these datasets with an allele frequency greater than 0.008 in PoN TCGA and 0.0003 in gnomAD v2.1. Additionally, common SNPs as defined by the dbSNP 151 Common UCSC track and dbSNP were excluded. Mutations within segmental duplications, simple repeats and masked regions as defined in UCSC tracks were also removed. Finally, samples with the mutation count above the 97.5 percentile of the mutation burden across the cohort were deemed unreliable and excluded for further analyses. We call the set of variants obtained after the application of these filters the full set. A more conservative subset of somatic mutations was generated from the full set of blood somatic mutations. To this end, we applied MosaicForecast, a software designed to phase mutations to polymorphisms with the aim of identifying somatic mutations in a small number of cells and also predict mosaicism for the unphased ones with a random forest classifier. As a result, we obtained a subset of mosaic-phased mutations, and a subset of mutations likely to be somatic (mosaic set).In order to obtain access to this study, please first obtain access to TCGA study (phs000178).

  Study phs002867

• The Role of CDX2 in Controlling ABCB1 Expression and Chemosensitivity in Human Colon Cancer

  This study reports the results of RNA sequencing (RNA-seq) experiments performed on two human colon cancer cell lines (HT-29, DLD-1) that were genetically engineered to achieve either the constitutive expression (in HT-29 cells) or the selective inactivation (in DLD-1 cells) of the transcription factor CDX2, a master regulator of embryonic gut development and a key regulator of multi-lineage differentiation in adult colon epithelial cells. Our previous studies had identified lack of CDX2 expression as a prognostic biomarker of poor prognosis and a predictive biomarker of benefit from adjuvant chemotherapy in Stage-II and Stage-III colon cancer patients (Dalerba et al., NEJM, 374:211-222, 2016; PMID: 26789870). The molecular basis of these associations, however, remained poorly understood. The present study was designed to identify which genes are under the transcriptional control of CDX2, in order to clarify their role in shaping colon cancer resistance to chemotherapy. Of the two lines included in this study, the first (HT-29) is CDX2-negative at baseline, and was infected with a lentivirus vector encoding for the cDNA of the human CDX2 gene under the control of a constitutive promoter (CMV). The second line (DLD-1) is CDX2-positive at baseline, and was infected with a series of lentivirus vectors encoding for CRISPR/Cas9 constructs designed to selectively inactivate the CDX2 gene. In both cases, infected cells were purified by fluorescence-activated cell sorting (FACS), based on the differential expression of a green fluorescent reporter (EGFP) that was also encoded by the lentivirus vectors, and transcribed in tandem with either the CDX2 cDNA (HT-29) or CRISPR/Cas9 gRNAs targeting CDX2 (DLD-1). The experiments were designed to include 3 experimental replicates per condition, and to compare the transcriptional profile of genetically engineered cells with that of autologous controls (i.e., HT-29 cells infected with an "empty" version of the same lentivirus vector used to over-express CDX2, DLD-1 cells engineered with a "non-targeting" CRISPR/Cas9 gRNA). In the specific case of DLD-1 cells engineered with CRIPSR-Cas9 constructs targeting CDX2, infected cells were sorted based on the differential expression of EGFP and then plated as single-cells, in order to sub-culture three isogenic clones, all of which were genetically sequenced to confirm bi-allelic knock-out of the CDX2 gene, and confirmed to lack CDX2 protein expression by Western blot. The results of our experiments demonstrate that, in human colon epithelial cells, CDX2 controls the expression of the ABCB1 efflux pump, by positively regulating the transcription of the corresponding gene.

  Study phs002903

• Adoptive Cell Therapy of Autologous T cell Receptor-Engineered T Cells Targeting the p53 Neoantigens in Human Solid Tumors

  Adoptive T cell therapy (ACT) using T cell receptor (TCR)-engineered T cells can mediate regression of advanced human cancers. How TCR-transduced T cells change post-ACT in vivo is currently not well understood. We screened 78 patients for TP53 mutations by whole exome sequencing and whole transcriptome sequencing. Of the 78 patient samples, 49 patient samples were previously reported (phs001003) and 2 additional patients were reported in phs002735. In this accession we report the sequencing data of remaining 23 patients and include 6 additional samples from previously published patients. Additionally, we treated a patient with chemo-refractory breast cancer that expressed mutant p53 R175H with autologous T cells transduced with an allogeneic TCR targeting p53 R175H with human leukocyte antigen (HLA) restriction of A*02. The patient had a partial response for 6 months with 55% tumor regression. The T cells from the infusion product and the peripheral blood T cells at 6 weeks post-ACT were analyzed using 10X single cell transcriptome analysis.

  Study phs002928

• CALGB/SWOG 80405 ct DNA Biomarker Evaluation

  To investigate treatment-specific mutations that underlie resistance to treatment with chemotherapy +/- bevacizumab or cetuximab in first line metastatic Colorectal Cancer (mCRC) patients, we performed targeted sequencing of circulating free DNA (cfDNA) from longitudinal plasma samples. These samples were collected at baseline (PRE, n=354), during treatment (OTH, n=254), and/or at progression or end of the protocol treatment (EOT, n=345) from CALGB/SWOG 80405, a randomized phase III trial that evaluated the efficacy of chemotherapy plus bevacizumab or cetuximab treatment in first line colorectal cancer patients (NCT00265850).

  Study phs002941

• Molecular Biomarkers of Obesity and Metformin Response in Endometrial Cancer: Analysis of GOG-0286B

  The primary endpoint for the phase 2 study was progression free survival (PFS), and the primary endpoint for the phase 3 study was overall survival (OS). Data from phase 2 were included in the phase 3 analysis. Tissue was collected from patients with endometrial cancer who participated in the study (NCT02065687). The tissue will be analyzed for genetic data and combined with the clinical data to see if some gene variants are associated with longer PFS or OS, particularly on the metformin arm of the study.

  Study phs002934

• Transcriptomic Profiling of Oropharyngeal Squamous Cell Carcinoma

  The study is a retrospective transcriptomic profiling of oropharyngeal squamous cell carcinoma. The pathologic database was queried for squamous cell carcinoma tumors originating from the anatomic oropharynx (tonsil or tongue base) with available samples from surgical archives. This retrospective RNA sequencing cohort included cases dating prior to the routine implementation of p16 immunohistochemistry (IHC) testing at our institution, therefore, p16 status was not required for inclusion in this study. Formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center (LCCC) Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer's protocol (Promega 9FB167). After a pathology review of a hematoxylin and eosin (H&E) stained slides to identify tumor area, RNA was extracted from unstained slides using macrodissection. Total RNA quality was measured using a NanoDrop spectrophotometer (Thermo Scientific ND-2000C) and a TapeStation 4200 (Agilent G2991AA). Total RNA concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies Q33216). Libraries were prepared with Illumina TruSeq Stranded Total RNA with Ribo-Zero protocol. Libraries were sequenced on an Illumina HiSeq2500 sequencer. Paired end read data, with read lengths of 75 were collected.

  Study phs002935

• NCI-Maryland Prostate Cancer Case-Control Study

  The study seeks to examine the genetic and ancestral basis of prostate cancer-associated inflammation using a genome-wide association approach. The study population are the participants of the NCI Maryland Prostate Cancer Case-Control study. This study recruited both African American and European American men, and investigated the causes for the excessive burden of prostate cancer among African American men in more general terms. We measured 82 blood-based immune-oncology markers, and genotyped the participants using the HumanOmni5-Quad BeadChip, which provides a significant genome coverage for genetically-admixed and diverse populations, to evaluate the genetic basis and evidence for causality of any immune-inflammation marker that is associated with prostate cancer risk. We want to assess how germline genetics influence the abundance levels of these 82 markers in African American and European American men, which may contribute to differences between them.

  Study phs002939

• Methylation Profiles of Cell-Free DNA Using Nanopore Sequencing

  Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to hundreds of millions of reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment.Control subjects consist of healthy individuals without a positive diagnosis of cancer. cfDNA was obtained through purification of plasma from blood draws. Genomic DNA (gDNA) was derived from extraction of primary tumor tissue or from leukocytes from blood draws.

  Study phs002950

• Exploring the Microbiome-Gut-Brain Axis with Respect to Psychoneurological Symptoms for Children with Solid Tumors

  The human body hosts tens of trillions of microbes, a number 10 times greater than the number of human body cells. The collection of these human-associated microbes and their genomes is called the “human microbiome”. More than 90% of these microbes live in the gastrointestinal (GI) tract, representing 500 species on average. With the development of high-throughput sequencing technology and bioinformatics tools (e.g., 16S ribosomal RNA or 16S rRNA sequencing and shotgun metagenomics analysis), recent progress has been made to elaborate the critical role that the gut microbiome plays in human health and disease. A significant disruption (dysbiosis) of the composition and function of the gut microbiome is associated with carcinogenesis, chemotherapeutic metabolism, and treatment-related symptom toxicities. The current state of science on the gut microbiome in cancer has only recently started in animal models and adults, and has not been well investigated in children diagnosed and treated for cancer, nor with respect to associations with cancer treatment-related toxicities. This proposed study will explore the hypothesis that dysbiosis of the gut microbiome is associated with cancer treatment-related GI and psychoneurological symptoms. We will collect both stool samples (for the gut microbiome) and patient-reported outcomes across chemotherapy.

  Study phs002960

• Germline Genetics of Myelodysplastic Syndromes (MDS) and Acute Myeloid Leukemia (AML)

  Myelodysplastic syndromes (MDS) are part of a heterogeneous and overlapping group of clonal diseases including acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), and the hybrid MDS/MPN entities that arise in hematopoietic stem or progenitor cells. Individuals with MDS have a high risk of progressing to leukemia, with approximately 30% expected to develop AML. Epidemiologic studies have identified common risk factors for MDS and AML, including smoking, chemical exposures, and previous treatment with chemotherapy and radiation. Analyses of the role of common germline genetic variation in MDS and AML have been limited to date. Our study used data from population-based case-control studies of MDS and AML in Minnesota to evaluate genetic contributions to disease. Cases were enrolled through rapid case ascertainment from the Minnesota Cancer Reporting System, a registry that collects information on all cancers diagnosed in Minnesota. Minnesota State driver's license/identification lists were used to identify controls. Medical record review was completed for cases and centralized review was conducted for diagnosis confirmation and MDS subtype verification. Additionally, saliva was collected from cases and controls and genotyped for genetic studies. Genotyping was conducted using the Illumina Human Global Diversity Array.

  Study phs002962

• Functional Analysis of Genetic Variants in African Americans with Breast Cancer

  The goal of this study is to identify and characterize novel genetic variants associated with a predisposition to breast cancer (BCa) in African Americans (AAs) using a family case-family control study design. Variants of unknown clinical significance (VUS) were characterized using bioinformatics tools. Future studies will further characterize select VUSs using in vitro genomic editing methods and functional assays to determine the functional consequences. The targeted sequencing data is made available for 85 actionable cancer genes. These genes have been previously classified with deleterious mutation(s) and whose phenotype results in a specific, defined medical recommendation(s).

  Study phs002977

• AC-ICAM: An Atlas and Compass of Immune-CAncer-Microbiome Interactions in Colon Cancer

  Fresh frozen tumor samples and matched normal colon specimens from chemotherapy naïve, consecutive patients with a histological diagnosis of colon adenocarcinoma at Leiden University Medical Center (LUMC) were subjected to multi-omics profiling at Sidra Integrated Genomics Services, part of Sidra Medicine, Doha, Qatar. This resulted in a high-quality dataset of samples collected between 2001 and 2015. Multi-step QC was performed, including assessment of the quality of the nucleic acid extraction, sequencing, and genetic concordance between DNA/RNA sequences from the same patient. After QC, this resulted in RNA sequencing on 348 tumor samples, whole exome sequencing (WES) on 281 tumor-normal sample pairs (n=562 samples), TCR sequencing of the TCR β locus (TRB) for 114 tumor and 10 matched normal samples, and 16S rDNA sequencing on 246 tumor-normal sample pairs (n=492 samples) and 42 tumor only samples, and 167 WGS non human-aligned reads of the tumor samples. Extensive clinicopathological and survival data of the cohort are available. The median follow-up time for this cohort is 4.6 years, and the distribution of gender and pathological stage are within expected ranges for this patient population with a mean age of 68. We refer to this resource as the Sidra-LUMC (SILU) colon adenocarcinoma (COAD) Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM)."Reprinted from Nature Medicine,Roelands, J., Kuppen, P.J.K., Ahmed, E.I. et al. An integrated tumor, immune and microbiome atlas of colon cancer. Nat Med (2023). https://doi.org/10.1038/s41591-023-02324-5, with permission from Nature."

  Study phs002978

• A Randomized Multi-Institutional Phase II Trial of Everolimus as Adjuvant Therapy in Patients with Locally Advanced Squamous Cell Cancer of the Head and Neck

  This genomic study was an analysis of DNA samples from subjects enrolled in a randomized, interventional, parallel assignment trial of everolimus versus placebo in advanced Head and Neck Cancer. Next Generation Sequencing was performed on samples obtained from primary tumors before treatment. The purpose was to evaluate potential associations between intervention, mutations and outcomes.

  Study phs002986

• A Platform Study of Combination Immunotherapy for the Neoadjuvant and Adjuvant Treatment of Patients with Surgically Resectable Adenocarcinoma of the Pancreas

  This is a single-institutional, randomized, open label platform clinical trial testing various immunotherapy combinations. Patients with newly diagnosed and surgically resectable pancreatic ductal adenocarcinoma (PDA) and scheduled to undergo the Whipple procedure at Johns Hopkins Hospital were eligible to participate in this study. Criteria for determining resectability strictly followed National Comprehensive Cancer Network (NCCN) guidelines. The study consisted of 6 parts: parts 1-5 constituted the Prime Phase (see below), and part 6 was the Extended Treatment Phase. Part 1: Participants received one cycle of immunotherapy two weeks prior to undergoing the Whipple procedure. Part 2: Subjects underwent the Whipple procedure. Part 3: Subjects received a second cycle of immunotherapy 4-10 weeks following the Whipple procedure (2-4 weeks prior to adjuvant chemoradiation). Part 4: Subjects underwent chemoradiation. Part 5: Subjects received 4 additional 28-day cycles of immunotherapy beginning 1-2 months after completing chemoradiation for a total of six cycles (two before chemoradiation and 4 following chemoradiation). Eligible subjects were randomized to Arms A and B in a 1:1 ratio, stratified up-front by age (≤65, >65). Arm A participants received Cy/GVAX. Arm B participants received the combination of Cy/GVAX and nivolumab. GVAX Vaccine consists of equal numbers (2.5 x 108 each) of Panc 6.03 pcDNA1GM-CSF and Panc 10.05 pcDNA1GM-CSF combined into a single vaccination. Each vaccination consisted of six total intradermal injections. A single intravenous (IV) dose of 200 mg/m2 Cy (CytoxanR) was given one day prior to GVAX. Anti-PD-1 Therapeutic Antibody Nivolumab 480 mg every 4 weeks was administered as an intravenous infusion. The primary objective for Arms A and B was to compare IL17 expression (Th17) in vaccine-induced lymphoid aggregates between resected PDAs from patients treated with the combination of Cy/GVAX and anti-PD-1 blockade antibody vs. the treatment of Cy/GVAX alone. Secondary objectives were to assess the safety, overall survival (OS), and disease free survival (DFS) of patients treated with each of the study drug combinations, and to assess the effects of each of the immunotherapy study drug combinations on PD-L1/PD-1 associated pathways, vaccine-induced immune regulatory signatures, and peripheral and intratumoral antigen specific T cell responses. The exploratory objective was to explore the effects of therapy on tumor and peripheral blood and tumor infiltrating immune cells, and to explore potential molecular determinants of response, progression and disease stability. To these ends, tumor infiltrating immune cells (TIICs) were obtained from surgically resected tumors following the neoadjuvant treatment of the study immunotherapy. TIICs were sorted into CD3+CD4+ T cells, CD3+CD8+ T cells, CD3-CD19+ B cells, and CD3-CD19-CD11b+ myeloid cells by flow cytometry. The sorted immune cell subtype pellets were sent to the commercial vendor (Eurofins) for RNA extraction and sequencing. SMART-seq v4 Ultra Low Input mRNA Sample Prep Kit was used for library preparation with 100bp paired end reads. FASTQ files, that were returned from the vendor, are deposited here.

  Study phs003002

• Transcriptional and Epigenetic Profiles of Male Breast Cancer at Single-Cell Resolution Nominate Salient Cancer Specific Enhancers

  We performed matched single-cell RNA sequencing (scRNA-seq) and single-cell chromatin accessibility sequencing (scATAC-seq) for two fresh human tumors collected from male breast cancer patients. The integration of these datasets revealed the intratumoral heterogeneity in both transcription and chromatin accessibility for each male breast cancer patient and allowed for comparisons to be made between male and female breast cancer. We hope these data will be a useful reference in the field of breast oncology, specifically for the treatment of males, as few studies have explored male breast cancer genetics.

  Study phs003006

• Genomic Characterization of Duke Melanoma Brain Metastases

  Previous work has shown that melanoma brain metastases (MBM) have a unique molecular profile compared to extracranial metastases (ECM). Description of the biology of MBM and associations between biological features and clinical outcomes will facilitate the design of rational therapies for patients with MBM. To better characterize the molecular profile of MBM, we conducted whole exome sequencing (WES) and total RNA sequencing on MBM tissues obtained from an independent cohort of 14 patients from Duke University Medical Center. This cohort adds valuable patient samples to the field and enables strengthened investigation of somatic mutations and gene expression profiles within and between cohorts. The mutational landscape and gene expression of MBM from the Duke cohort resembled those previously reported in a previously published dataset of WES and RNA sequencing in MBM and matched ECM tissues from UT MD Anderson Cancer Center (Fischer et al., 2019 30787016). Duke MBM demonstrated similar rates of mutations in genes associated with melanoma, including BRAF, NRAS, and PTEN, as the MD Anderson cohort. Immune populations in MBM were similar between Duke and MD Anderson MBM, though Duke samples demonstrated more resting CD4+ memory T cells. The ratio of M2 to M1 macrophages in the Duke cohort was similar to that of the MD Anderson cohort. In MBM, a higher M2:M1 ratio may contribute to an immune-suppressive tumor microenvironment. Sequencing data and sample attributes from MBM tissues obtained from 14 patients from Duke University Medical Center will be available through dbGaP.

  Study phs003009

• APOLLO1: Proteogenomic Analysis of Lung Adenocarcinoma

  APOLLO is a proteogenomic study seeking to describe the major genome, transcriptome, proteome and phosphoproteome alterations, subtypes, and molecular predictors of patient outcomes. This study includes 87 lung adenocarcinomas and matched normal tissues from the Lung Cancer Biospecimen Resource Network (https://lungbio.sites.virginia.edu/). Tumor tissues were profiled by whole genome sequencing, transcriptome sequencing, MS-based proteomics and phosphoproteomics, and reverse phase protein arrays. Matched normal tissues were profiled by whole genome sequencing. Clinical and sample data include survival times, patient features, and tumor characteristics.

  Study phs003011

• Ipilimumab and Decitabine in Treating Patients With Relapsed or Refractory Myelodysplastic Syndrome or Acute Myeloid Leukemia

  The NCI Experimental Therapeutics Clinical Trials Network (ETCTN)/Cancer Therapy Evaluation Program (CTEP) 10026 study (NCT02890329) tested combined ipilimumab and decitabine treatment in two cohorts: Arm A consisted of patients with relapsed acute myeloid leukemia after allogeneic hematopoietic stem cell transplantation. Arm B consisted of patients with advanced myelodysplastic syndrome or acute myeloid leukemia that did not previously undergo stem cell transplantation. During the study, peripheral blood and bone marrow samples were obtained from study participants at study entry (screening), following the first lead-in cycle of decitabine monotherapy, during combined treatment with decitabine and ipilimumab, and at the end of treatment.This study tested the combination of the CTLA-4 blocking antibody ipilimumab and the DNA methyltransferase inhibitor decitabine in advanced myeloid disease in the transplant-naive and post-transplant context. The samples were used for bulk and single cell RNA sequencing as well as whole exome sequencing.

  Study phs003015

• Phase I Study of the Oral PI3kinase Inhibitor BKM120 or BYL719 and the Oral PARP Inhibitor Olaparib in Patients with Recurrent Triple Negative Breast Cancer or High Grade Serous Ovarian Cancer

  We analyzed massive parallel sequence data from patients with breast and ovarian cancer and identified single base substitution mutational signature 3 (Sig3) - extracted using SigMA - as a biomarker of homologous recombination deficiency (HRD) and predictive for response to PARP inhibitors. Participants were patients enrolled in clinical trials as 2 independent datasets: (1) high-grade serous ovarian cancer and triple-negative breast cancer (TNBC) from a Phase 1b trial of the PARP inhibitor olaparib in combination with the PI3K inhibitor buparlisib (BKM120) (NCT01623349), and (2) TNBC patients who received neoadjuvant olaparib in the Phase II PETREMAC trial (NCT02624973).

  Study phs003019

• Genomic Analysis of Nucleic Acid Sequences from Pancreatic Cancer

  Our study aims to perform multi-omics analysis of pancreatic ductal adenocarcinoma. We performed dual single-cell RNA sequencing and whole genome sequencing on fresh tumor specimens and dual bulk RNA-sequencing and 16S amplicon sequencing on frozen tumor specimens to identify human and non-human nucleic acid sequences. Additionally, we identified microbial sequences and found that bacterial taxonomic profiles from the same sample strongly correlated across technologies.

  Study phs003035

• Single Cell Genome Variation Induced by Mutational Processes in Cancer - HGSOC Trios Study

  Mutational signatures derived from whole genome sequencing have potential prognostic significance. Identification of high grade serous ovarian cancer patients with deficiency in homologous recombination repair pathways could identify a subset of patients that would benefit from homologous recombination deficiency-specific treatments independent of identification of a pathological BRCA1/2 gene mutation. Clinical protocols rely on a pathologist's assessment of formalin-fixed paraffin-embedded (FFPE) tissues, and thus FFPE tissue samples are readily available. However, the bulk of mutational signature analyses have been performed on fresh frozen tissues. In this study, we aimed to assess the reliability of whole genome sequencing, variant calling, and mutational signature analysis from FFPE tissue samples.

  Study phs003036

• Exploiting New Patterns of Genome Damage in Triple Negative Breast Cancer

  Genomic instability, a feature of triple negative breast cancers (TNBC), represents an opportunity for discovery of biologic and clinically relevant subgroups of patients. Owing to TP53 mutation in the majority of cases, DNA repair deficiency through loss of BRCA1 and BRCA2, and by expression features patterning a basal cell of origin, TNBC represents a molecularly and clinically distinct group of breast cancer patients. Unfortunately, targetable molecular features of TNBC remain elusive and TNBC patients suffer the poorest outcomes amongst clinical subgroups. Within TNBC patients, responses to treatment vary and although gene expression patterns within TNBC have been identified, little progress has been made in developing biomarkers; effective stratification as a route to directing patients to more targeted therapy is lacking. In this study, we exploit mutational processes in TNBC as a new opportunity to stratify patients and to understand the evolutionary progression of TNBC cells harboring specific DNA repair properties.

  Study phs003038

• Metastatic Colorectal Adenocarcinoma Tumor Purity Assessment from Whole Exome Sequencing Data

  As molecular medicine wields greater and greater influence on cancer patient care, including therapeutic selection, it becomes increasingly important to understand the power and deficiencies of computational tools used in decision making processes. Here we use a set of unselected metastatic colorectal tumor samples in a head-to-head comparison between the calculation of stromal content by a board certified pathologist, versus that derived from whole exome sequencing and purity assessment by a variety of common computational methods. We find that in about 1/2 of the samples the computational methods each do a poor job of assessing the percent stromal contamination, and as a result, tumor variant allele frequencies (VAFs) are low or undetected, whereas analysis of organoids derived from the same tumors yielded much higher VAFs in keeping with their lower stromal content. The whole exome sequence of our samples is available via dbGaP, accession phs003059.v1.p1.

  Study phs003059

• De Novo Characterization of Cell-Free DNA Fragmentation Hotspots in Plasma Whole-Genome Sequencing

  The raw sequencing data deposited here are low-coverage (~1X) whole-genome sequencing (WGS) of plasma cell-free DNA (cfDNA). The purpose is to validate the performance of early-stage cancer diagnosis in the Zhou et al. 2020 BioRxiv paper, mainly for two types of cancer: early-stage liver cancer and breast cancer. The cases and controls are matched with age, gender, smoking history, and alcohol usage. We developed a computational method to identify the cfDNA fragmentation hotspots from pooled low-coverage cfDNA WGS data. We found the cfDNA fragmentation hotspots are highly enriched in regulatory regions, such as open chromatin regions. The signals from these regions can help the diagnosis of early-stage cancers and their tissues-of-origin.

  Study phs003062

• Phenotypic Signatures of Circulating Neoantigen-Reactive CD8+ T Cells in Patients with Metastatic Cancers

  Following enrichment of neoantigen-reactive T cells using pHLA tetramers or cell-surface markers, we performed single-cell sequencing (RNA-seq and TCR-seq) of circulating CD8+ T cells from metastatic cancer patient samples (Melanoma, Colorectal, and Breast cancer). In samples from previously studied patients, we identified cells bearing neoantigen-reactive T cell receptors and were able to study their phenotypic program. By studying the circulating neoantigen-reactive T cell program, a gene-signature was derived to identify neoantigen-reactive T cells from blood samples prospectively.

  Study phs003064

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): A Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI). Due to additional sharing restrictions, data from one site can be found in phs003094.

  Study phs003066

• A National Translational Science Network of Precision-Based Immunotherapy for Primary Liver Cancer (PLC)

  The primary objective of the NCI-CLARITY study is to establish a biospecimen repository for genomic, genetic and epigenetic analysis to study the biology of primary liver cancer (PLC) development and progression. Secondary objectives include predicting overall and progression-free survival following immunotherapy. In the retrospective phase, anonymous archival tissue from PLC patients was obtained from five participating sites. Whole exome and transcriptome sequencing was generated and used to predict overall survival in response to immunotherapy.

  Study phs003074

• Retinoblastoma Aqueous Humor Liquid Biopsy Repository

  This study involves the use of the aqueous humor (AH, the clear fluid in the front of the eye) as an organ specific liquid biopsy for retinoblastoma. This relatively new liquid biopsy platform was started at CHLA/USC and was developed to overcome the lack of tumor tissue -- due to contraindication to biopsy -- for this cancer. We have demonstrated that the aqueous humor is an enriched source of tumor DNA. Previously tumoral information was only available after the eye was removed for treatment failure. Due to the AH liquid biopsy, we are now able to assay tumor derived molecular information from these eyes at diagnosis and longitudinally during treatment -- as opposed to only eyes that have failed therapy. We have demonstrated that using the platform we can identify the specific mutations in the RB1 gene that initiate tumorigenesis in this cancer as well as the secondary chromosomal alterations the drive further tumor growth. This database will provide sequencing information as well as associated clinical information and globe salvage outcomes.

  Study phs003077