5735 results for "canc*"

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• 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

• Advancing Precision Oncology in a Humanized, Fully Autologous Mouse Model

  Progress in the early detection and treatment of cancer requires accurate model systems to further evaluate new, promising discoveries. Small animal and, in particular, mouse model systems are attractive to researchers for numerous reasons, including their ease of use and well-described platforms. The ability to grow human tumors in immune-deficient mice (so-called patient-derived xenografts, or PDXs) allows researchers to work directly with human cancer tissue in a controlled setting. However, PDX models are limited by their lack of an intact immune system. Immunotherapy has revolutionized clinical oncology, but lacks pre-clinical models of the human immune system and human cancer to investigate new modalities and limitations/toxicities of treatment regimens. The broad objective of this study is to validate an in vivo model to evaluate human tumors in the context of a complete and intact human immune system in a completely personalized and autologous fashion to study cancer immunotherapy. Herein, we will: (1) validate the ability of our humanized system to serve as a model for cancer immunotherapy treatment response and toxicity in patients with melanoma, including immunotherapy checkpoint blockade and vaccine strategies, and (2) extend our current work in melanoma by validating the ability to establish humanized mice and evaluate tumor growth and leukocyte development in autologous human pancreatic and colorectal tumors established in humanized mice. In each of these areas, we will leverage our multi-institutional team's individual expertise along with our institutional infrastructure to maximize the success of the experimental aims. The results from this project will be widely available to the general research community for future, hypothesis-driven research. Taken together, our study will meet multiple goals and address several unmet needs in cancer immunotherapy, thus significantly enhancing the applicability of a fully autologous and immunocompetent precision model system for use in translational oncology research.

  Study phs003090

• The Genomic Landscape of Interval Colorectal Cancers

  Interval colorectal cancers (CRC), cancers diagnosed after a screening/surveillance exam in which no cancer is detected, and before the date of the next recommended exam, reflect an unprecedented challenge in CRC detection and prevention. To better understand this poorly characterized CRC variant, we examined the clinical and mutational characteristics of interval CRCs in comparison to screen-detected CRCs. We used data from the Prostate, Lung, Colorectal and Ovarian (PLCO) cancer randomized controlled trial (RCT) of flexible sigmoidoscopy (FS) screening, which enrolled 154,900 men and women aged 55 to 74 years between 1993 and 2001. Whole Exome Sequencing (WES) was performed on 323 samples from 168 participants (data available through dbGaP). We found colorectal cancers diagnosed between screening exams (interval cancers) had significantly increased risk of death than screen detected cancers although no significant molecular differences were observed between screen-detected and interval CRC at the whole exome sequencing level.

  Study phs003093

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): a Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study - for Samples Collected at Johns Hopkins

  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).The larger dataset for this study can be found in dbGaP study phs003066.

  Study phs003094

• Integration of Clinical and Molecular Biomarkers for Melanoma Survival (Berwick)

  The long-term goal of the InterMEL Program Project: Integration of Clinical and Molecular Biomarkers for Melanoma Survival is to identify molecular and clinical factors that predict survival of melanoma patients. Our overarching hypothesis is that we can identify factors in the primary melanoma tumor that will lead to more aggressive disease. Melanoma patients diagnosed at American Joint Committee on Cancer (AJCC) tumor, lymph nodes, and metastases (TNM) stages IIA/IIB/IIC/IIIA/IIIB/IIIC/IIID display highly variable clinical outcomes and responses to therapy. We wish to identify robust and reproducible biomarkers or sets of classifiers that distinguish patients likely to have poor prognosis. These biomarkers will help establish targets for adjuvant therapies for this set of patients before the tumors metastasize. Aim 1. Classify actionable somatic mutations, and copy number variations (CNVs) in relationship to melanoma survival. In Project 1, Targeted Sequencing and Clinicopathology to Evaluate Primary Melanoma Molecular Subtypes and Outcomes, we will profile 468 genes using the MSKIMPACT ™ assay and identify somatic mutations and CNVs associated with melanoma-specific survival, as well as their co-occurrence with other mutations, in 1,000 tumors from patients at AJCC TNM stages IIA-IIID: approximately 500 from patients who died with melanoma within five years and approximately 500 from individuals who have lived at least five years. We will also evaluate the joint effects of somatic mutations, CNVs and pathologic characteristics associated with good and poor outcomes. Aim 2. Identify primary melanoma DNA methylation profiles to evaluate subtypes and survival. Although it has been established that melanomas frequently have aberrant DNA methylation, it is unknown if DNA methylation in primary melanomas predicts outcome. In Project 2, Primary Melanoma DNA Methylation Profiling for Evaluating Subtypes and Survival, we will profile the same primary melanomas as in Project 1 with Illumina Infinium 850K methylation arrays. We expect to: identify and characterize DNA methylation-based melanoma subclasses; train, test and validate a CpG signature prognostic for survival from melanoma; determine whether this profile adds information to outcome prediction beyond AJCC TNM staging. This project is based on the hypothesis that DNA methylation in primary melanoma will define subgroups (including a poor-prognosis CIMP – ‘CpG island methylator phenotype' subtype) and that a CpG signature will be prognostic for melanoma survival. Aim 3. Define microRNA expression changes in relation to melanoma survival. MicroRNAs have been associated with poor prognosis in melanoma, as well as in other cancers. In Project 3, Prognostic and Functional Role of a Gene Expression Signature in Melanoma Patients, we hypothesize that altered miRNA expression, captured at the time of diagnosis, may contribute to the aggressive behavior of a subset of early stage primary melanomas. We will profile the same primary melanomas as in Projects 1 and 2 with a Nanostring assay. This project will define and validate a tissue-based microRNA signature in conducted to determine whether the prognostic miRNA signature, as well as other candidate genes emerging from other projects, contribute to melanoma survival. Aim 4. Integrate data from multiple platforms to identify melanoma subtypes and survival. Despite substantial literature on gene tumor mutation-, methylation- and gene expression-based prognostic and predictive signatures for melanoma, few such signatures are used in clinical practice. Project 4, Multiplatform Analysis of Melanoma Molecular Subtypes and Patient Survival Outcome, will use novel integrative clustering methods to identify molecular subtypes of melanoma jointly defined across these platforms.

  Study phs003099

• Childhood Cancer Data Initiative (CCDI): Clonal Evolution During Metastatic Spread in High-Risk Neuroblastoma

  The goal of this study is to deliver a detailed characterization of the patterns of disease dissemination at diagnosis, during progression and in response to therapy in high-risk neuroblastoma. Longitudinal and spatially distinct tumors were collected from patients. Clinical data includes diagnosis and treatment information. Biospecimen data includes whole genome sequencing (WGS) and whole transcriptome sequencing (WTS).

  Study phs003111

• Multiregional Single-Cell Transcriptomic Analysis of Liver Cancer

  In this study, we performed single-cell transcriptomic profiling of human liver tissues collected from hepatocellular carcinoma and intrahepatic cholangiocarcinoma patients. A total of seven primary liver cancer patients enrolled in this study. Samples were collected from multiple regions, including tumor core, tumor border and adjacent non-tumor tissue. The 10x Genomics platform was used to generate single cell 5' libraries. The Illumina NovaSeq 6000 platform was employed for sequencing.

  Study phs003117

• Genetic Epidemiology of Ovarian Cancer Histotypes

  Epithelial ovarian cancer is a highly fatal malignancy with known genetic etiology; however, it is estimated that a substantial portion of narrow sense heritability remains to be discovered. The goal of this research was to use genetic information from distantly related ovarian cancer cases to identify regions of the genome that may harbor rare risk variants for epithelial ovarian cancer. The study was conducted in the setting of the Utah Population Database, a statewide data resource in which extensive ancestry data are linked to Utah Cancer Registry records. Focusing on families with a statistically significant excess risk of epithelial ovarian cancer, we used the Infinium Global Screening Array v.3.0 to generate germline genotyping data for distantly related cases. We then applied Shared Genomic Segment Analysis to each set of related cases to identify genomic regions that may harbor ovarian cancer risk variants. Eleven regions were identified. Genotype data are available through dbGaP for one case from each pedigree. Genotype data from other ovarian cancer cases within the high-risk pedigrees as well as the pedigrees' corresponding structures can be requested and made available with approval from the Utah Resource for Genetic and Epidemiologic Research (RGE).

  Study phs003140

• Integrative Somatic and Germline Computational Biology to Redefine Clinical Actionability in Solid Tumors

  Neuroendocrine tumors (NETs) are rare cancers that arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic NETs (GEP-NETs) growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we performed single-cell RNA-sequencing (scRNA-seq) of fresh resections of GEP-NETs, including four pancreatic NETs, three small intestinal NETs, and one perigastric NET. We used single-cell sequencing to investigate the tumor and immune cellular landscapes of GEP-NET patients. Malignant GEP-NET gene and regulon expression was compared with normal, gastrointestinal endocrine cell differentiation and fate determination stages. We further characterized immune-immune and immune-tumor interaction networks within GEP-NETs, identifying novel therapeutic opportunities in the myeloid compartment of the microenvironment. Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.

  Study phs003141

• Tissue Sampling and Biorepository to improve Cancer Cell Therapy

  This study focuses on the elucidation of determinants of response and resistance to anti-CD19 CAR T-cells in large B-cell lymphoma. Plasma samples were collected prior to treatment and serially post CAR T-cell infusion. Pre-treatment and relapse tumor samples were also obtained as available. Germ-line DNA isolated from Peripheral Blood Mononuclear Cells (PBMCs) was collected for all patients when available. Circulating tumor DNA (ctDNA) and tumor DNA were sequenced using a target hybrid capture oligonucleotide pool. RNA-Seq was also performed on tumor isolated RNA. The authors identified several recurrent genomic alterations associated with relapse, and identified molecular thresholds that were predictive of response.

  Study phs003145

• A Phase II Neoadjuvant Study of Palbociclib in Combination with Letrozole and Trastuzumab as Neoadjuvant Treatment of Stage II-III ER+ HER2+ Breast Cancer (PALTAN)

  Women with early stage ER+/HER2+ breast cancer (BC) are less likely to achieve pathological complete response (pCR) after chemotherapy with standard of care dual HER2 blockade than patients with ER-/HER2+ BC. Additionally, the toxicity burden of standard systemic therapy is high. Thus, this single arm phase 2 clinical trial investigated a novel de-escalation regimen with trastuzumab, letrozole, and palbociclib in those with early stage ER+/HER2+ BC. The aim was to determine if this treatment regimen will achieve similar pCR rates as conventional treatment and spare women the toxicity burden of regular treatments. The primary endpoint was pCR after 16 weeks of treatment with trastuzumab, letrozole, and palbociclib. Patients with newly diagnosed ER+ HER2+ invasive BC with clinical stages II and III were eligible for this protocol. Research biopsies were performed during the treatment course for whole exome and RNA sequencing, PAM50 molecular subtyping, and Ki67 assessment using immunohistochemistry for complete cell cycle arrest (CCCA: Ki67 ≤2.7%). Results showed a pCR of 7.7% and a rate of residual cancer burden at 0 or I of 38.5%. CCCA was observed in 85% at Cycle 1 day 15 post palbociclib, trastuzumab, and letrozole treatment (C1D15), compared to 27% at surgery after palbociclib was discontinued. PAM50 subtyping identified 31.2% HER2-E, 43.8% Luminal B, 25% Luminal A. 161 genes were differentially expressed comparing C1D15 to baseline. Whole exome and RNA sequencing data will be available through dbGaP.

  Study phs003147

• Bladder Cancer Organoids as a Functional System to Model Different Disease Stages and Therapy Response

  The study 'Bladder Cancer Organoids as a Functional System to Model Different Disease Stages and Therapy Response' reports the genomic characterization at the single allele level upon Whole Exome Sequencing of Bladder Cancer (BLCa) Patient Tumor (PT) samples obtained from 18 patients and corresponding Patient Derived Organoids (PDOs), implementing the SPICE pipeline (Ciani Y et al). Our cohort included 21 PTs and 22 PDOs. In this study, we generated a unique biobank resource of BLCa organoids that encompasses a broad spectrum of disease stages. We demonstrated that PDOs retain cancer heterogeneity and mutational burden. Furthermore, we observed that BLCa PDO can have different morphologies which may reflect tumor-specific features. Indeed, a solid morphology may be associated with more advanced tumors, as supported by the high PDO genomic burden and high primary tumor stage. Moreover, with our drug screening pipeline, we demonstrated the clinical relevance and feasibility of using a BLCa PDO-based drug assay for comparing the standard of care (SOC) drugs with compounds not currently in use for BLCa. Response to SOC was highly heterogeneous with approximately 50% of non-muscle invasive bladder cancer and 33% of muscle invasive bladder cancer PDOs showing no or minimal response. The most effective targeted therapy was lapatinib. We used an integrative analysis of drug response profiles with matched PDO genomic analysis to determine enrichment thresholds for candidate markers of therapy resistance and sensitivity. Importantly, by assessing the clinical history of longitudinally sampled cases, the clonal evolution of the disease could be determined and matched with PDO drug response profiles.

  Study phs003149

• International Cancer Proteogenomics Consortium (ICPC): Proteogenomics of East-Asian Breast Cancer

  The incidence of invasive breast cancer is rapidly increasing in East Asia, enriching in younger patients and luminal disease. We presented a deep proteogenomic landscape of a prospectively enrolled early-stage cohort in Taiwan to uncover the etiology, age-related subtype and oncogenic vulnerabilities underlying the heterogeneous disease. Multilayer proteogenomic architecture revealed distinct endogenous and environmental carcinogen-associated mutagenesis, linking APOBEC (apolipoprotein-B mRNA editing enzyme, catalytic polypeptide-like) cytidine deaminase and DBAC (dibenz[a,j] acridine) signatures to significantly elevated hormone biosynthesis and chemical carcinogenesis in younger patients, and identifying a novel subset of high mutation burden and immune escape potentially beneficial from combined epigenetic therapy and immunotherapy. A proteomics-informed classification resolves luminal heterogeneity, defines high-risk recurrent luminal disease and nominates biomarkers and actionable druggable pathways. Furthermore, proteogenomics profile distinguished a young luminal population susceptible to exogenous carcinogen and having DNA repair deficiency. This study illuminates the age-related molecular subtypes and oncogenic vulnerabilities, providing a proteogenomics-transformative guide for patient stratification and precision therapeutics beyond clinical staging.

  Study phs003150

• CPTAC: Proteogenomic Studies of Ovarian Tumor Responses to Agents Targeting the DNA Damage Response

  There is a critical unmet need for predictors of chemo-refractory High-grade serous ovarian cancer (HGSOC). Despite over 3 decades of research on platinum responses in cancer, no predictive biomarker has been translated into clinical use. Predictors of refractory disease could spare these patients the unnecessary toxicity of a platinum-based regimen and provide a means to triage these patients to clinical trials to identify effective therapies for refractory disease. This study has approached the development of a predictor in a novel way enabling detection of a multi-analyte panel biomarker capable of detecting a subset of refractory HGSOCs with high specificity and implicating potential treatment vulnerabilities for refractory disease. We reported the first proteogenomic analysis of platinum refractoriness in HGSOC and made the novel dataset available as a resource to the community, including a ProTrack portal: http://ptrc.cptac-data-view.org/. Detailed proteogenomic profiles were generated for this study from a retrospective cohort of 242 treatment-naive HGSOCs with enriched representation of "exceptional non-responders" (i.e., patients with chemo-refractory disease). Whole genome sequence (WGS) and RNA seq FASTQ files are available through dbGaP. Proteomic data are available through the NCI Proteomic Data Commons (PDC): https://pdc.cancer.gov/pdc/.

  Study phs003152

• Neoantigen-Targeted CD8+ T-Cell Responses 1 With PD-1 Blockade Therapy

  Background: The primary target of T-cell responses induced against cancer cells are peptides derived from non-synonymous mutations presented by HLA (neoantigens). However, the large diversity of HLA alleles and restricted availability of clinical samples have limited the study of the specificity and the evolution over time of the neoantigen-specific T cell responses induced after treatment with immune checkpoint blockade (ICB) immunotherapy. Methods: We applied a newly developed neoepitope-specific T cell isolation technology to perform a longitudinal landscape analysis of the neoepitope-specific T cells in peripheral blood and tumor from 11 patients with metastatic melanoma; 7 with response and 4 with no response to ICB. Briefly, first using computational prediction, the putative neoantigens in each patient were ranked based on affinity for the patient's HLA and expression levels. Then hundreds of barcoded capture reagents consisting of the patient HLA class I subtypes loaded with the corresponding predicted neoantigen were made and used to isolate neoepitope-specific T cells. Once isolated, the TCRs and the barcodes were sequenced. Finally, the tumor reactivity of the isolated neoepitope-specific TCRs (neoTCRs) was assessed upon co-culture of autologous melanoma cell lines from each patient with primary human T cells expressing the neoTCRs generated using a CRISPR-based non-viral gene editing to replace the endogenous TCRs. Results: The tumor mutation burden ranged between 3507 and 177 for patients with response to therapy and 977 to 31 for patients without response to therapy. We screened a median of 172 predicted neoantigen-HLA per patient across their 6 HLA molecules and isolated neoTCRs in all 11 patients. The number of mutations targeted ranged between 13 and 1. We assessed the neoTCR-tumor reactivity in samples from 3 patients with response and 3 patients without response. 39 of the 62 neoTCRs demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Multiple T cell clonotypes recognized a limited number of mutations in 7 patients with response (median of 41 different neoTCR clonotypes per patient), and the T cell specificities were recurrently detected in the blood and the tumor over time. Samples from 4 patients without response to therapy also demonstrated neoepitope-specific T cell responses in blood and tumor to a similarly restricted number of mutations, but lacked TCR polyclonality (median 6.5 neoTCR clonotypes per patient) and were not recurrently detected in sequential samples. Conclusion: Effective ICB therapy is associated with polyclonal neoepitope-specific T-cell responses in the tumor and blood that recognize a limited number of immunodominant mutations and are recurrently detected over time.

  Study phs003153

• An Advanced Molecular Medicine Case Report of a Rare Human Tumor Using Genomics, Pathomics, and Radiomics

  The associated data of this study is derived from a single female patient with pulmonary sclerosing pneumocytoma (PSP). The aim of this study is to provide the most comprehensive, multi-modality sequencing study of a single case of PSP to-date. To this end, the following sequencing experiments were performed: i) RNA-Seq of the primary tumor and adjacent normal tissues (6 replicates for each tissue type), which was intended to analyze RNA-Seq fusions, gene expression, expression mutations, ii) low-pass DNA whole genome sequencing (WGS) from primary tumor tissue and germline, which was intended to analyze copy number aberrations, and iii) DNA targeted panel sequencing of lung cancer associated genes, using primary tumor tissue and germline from white blood cells, which was intended to analyze somatic mutations. Principal findings: i) the PSP hallmark mutation AKT1 (p.E17K) was detected within both the DNA and RNA, and ii) the TP53 signaling pathway was found to be statistically significant by three different pathway analysis tools of analyzing gene expression and pathway ramifications. Among proteins within the TP53 signaling pathway, the p53 inhibitor encoded by MDM2 was found to be overexpressed (by differential gene expression analysis). The original sequencing data (i.e., FastQ files) from each of the aforementioned samples will be accessible through dbGaP.

  Study phs003154

• TCGA WGS Variants Across 18 Cancer Types

  Even though whole genome sequence (WGS) data has been generated and published in many studies, much of this information is not yet processed for use in down-stream analysis. This study's aim is to provide 1342 WGS normal-tumor paired single nucleotide variations (SNP) over 18 different cancer types provided by The Cancer Genome Atlas (TCGA) project. Individual level data for TCGA can be accessed by requesting access for phs000178. This data includes variations within self-reported white and African-American populations. Variations that exist within the tumor tissue but are absent in associated normal organ tissue (as compared to the human reference genome) are reported. Data published includes SNP and small insertions and deletions, which were generated through a pipeline including the VarScan2 variant calling software.

  Study phs003155

• Targeted Long-Read Sequencing of the Ewing Sarcoma 6p25.1 Susceptibility Locus

  Ewing Sarcoma (EwS) is rare but the second most common cancer in children, adolescents and young adults. Recent studies suggest germline variation in or around GGAA microsatellites may interact with fusion oncoprotein binding causing changes in binding affinity and potentially impacting enhancer activity on nearby target genes. This study aims to better understand germline variation around EwS susceptibility regions by performing long-range haplotype sequencing of these regions using PacBio sequencing. Our analysis focused on characterizing variation in GGAA microsatellite length as well as germline variants in or around the microsatellite and their association with EwS risk.

  Study phs003159

• Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases

  This study is a phase I trial combining ado-trastuzumab emtansine (T-DM1) with Temozolomide (TMZ) for the prevention of additional brain metastases after previous occurrence and local treatment in HER2+ breast cancer patients. Twelve patients were enrolled in this study. Data includes whole exome sequencing (WES) from patients' cerebrospinal fluid (CSF) and plasma samples. The CSF was collected from each patient at trial entry and after the initial two treatment cycles of TMZ and T-DM1 treatment. Blood was collected through a standard peripheral venipuncture at the following four time points: 1) upon trial entry, 2) after two treatment cycles, 3) the treatment cycle prior to the last follow-up, and 4) most recent follow-up. Whole exome libraries were captured by the SureSelect Human All Exon V8 Kit (Agilent, Santa Clara, CA, USA) and sequenced by NovaSeq 6000 S2 Sequencer in paired-end sequencing mode (Illumina, San Diego, CA, USA). Gene mutations in DNMT3A, ELP1, NOTCH4, KMT2B, CRLF2, and KCNJ18 were observed in patients' CSF.

  Study phs003165

• Genome-Wide Analysis of Aberrant Position and Sequence of Plasma DNA Fragment Ends in Patients With Cancer

  This study investigated fragmentation characteristics in plasma cell-free DNA and evaluated the relevance of such analysis for cancer diagnostics. Specifically, we performed whole genome sequencing (WGS) of healthy individuals and cancer patients, and evaluated genome-wide coverage and sequences surrounding fragment ends. This was a retrospective study of archived plasma samples. The WGS data are available through this submission. Detailed study design and findings were published in Budhraja et al. Science Translational Medicine 2023.

  Study phs003170

• Molecular Subtyping Reveals Immune Alterations Associated with Progression of Bronchial Premalignant Lesions

  Exposure to cigarette smoke creates a field of injury throughout the entire respiratory tract inducing genomic alterations that lead to an "at-risk" airway where lung cancers develop. Lung squamous cell carcinoma (SCC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions (PMLs). Effective tools to identify and treat premalignant lesions at highest risk of progression to invasive carcinoma are not available. Endobronchial biopsies and brushings were obtained from high-risk subjects undergoing lung cancer screening at approximately 1-year intervals by white light and auto-fluorescence bronchoscopy and computed tomography at the Roswell Park Cancer Institute in Buffalo, NY. Subjects were selected that had biopsies collected in repeat locations via serial bronchoscopies. mRNA sequencing was performed on a discovery cohort (DC) of samples comprising endobronchial biopsies and brushes collected between 2010 and 2012 (n=30 subjects, n=197 biopsies, and n=91 brushings). mRNA sequencing was subsequently performed on a validation cohort (VC) of samples comprising endobronchial biopsies and brushes collected between 2010 and 2015 (n=20 subjects, n=111 biopsies, and n=49 brushings). Data analysis identified four distinct molecular subtypes (Proliferative, Inflammatory, Secretory, and Normal) in the bronchial biopsies that correspond to a spectrum of biological and morphological alterations. The Proliferative subtype was enriched with dysplastic PMLs from current smokers that exhibit up-regulation of metabolic and cell cycle pathways and down-regulation of cilium-associated processes. Molecular subtype classification in the validation cohort biopsies replicated these significant clinical and biological associations. Airway brushes from normal fluorescing areas of the large airway classified as the Proliferative subtype specifically predict the presence of biopsies of this same subtype. Within the Proliferative subtype, genes associated with interferon signaling and antigen processing and presentation were observed to be down-regulated among dysplastic biopsies that persist or progress in the future. Innate and adaptive immune cells were computationally predicted to be depleted in these biopsies and this was confirmed via immunofluorescence staining of adjacent biopsies. These findings provide a proof of concept that molecular biomarkers of endobronchial biopsies can enhance histopathological grading and that immunoprevention strategies are an important future direction in intercepting the progression of PMLs to lung cancer.FASTQ files from the RNA sequencing of these biopsies and brushings will be available via dbGaP.

  Study phs003185

• Temporal Evolution Reveals Bifurcated Lineages in Aggressive Neuroendocrine Small Cell Prostate Cancer Trans-Differentiation

  Trans-differentiation from adenocarcinoma to small cell neuroendocrine (SCN) cancer is an adverse consequence of treatment escape in various cancers, including prostate, lung, and bladder cancers (Balanis and Sheu et al., 2019 Cancer Cell). Expression of dominant negative p53 (TP53DN), myrAkt1, RB1-shRNA, c-Myc, and Bcl2(PARCB forward transformation) using human naïve prostate basal epithelial cells recapitulated both transcriptional and histological characteristics of small cell neuroendocrine prostate cancer (NEPC) (Park et al., 2018 Science). To study the temporal transcriptional landscape during this trans-differentiation process, we conducted a time course study using a PARCB model by integrating multi-omics sequencing, including bulk RNA-sequencing and ATAC-sequencing on samples taken at different time point, as well as single cell RNA sequencing on serial xenograft tumors. We found a common SCN pathway that resulted in two distinct end states defined by mutually exclusive expression of ASCL1 and ASCL2. Further investigation using CUT&RUN sequencing identified TFAP4 as a potential epigenetic regulator of both proteins. Our study reveals temporal and transcriptional changes from prostate adenocarcinoma to NEPC trans-differentiation.

  Study phs003230

• Tamoxifen Response at Single Cell Resolution in Estrogen Receptor Positive Primary Human Breast Tumors

  Primary breast tissue, normal and cancerous, was collected immediately after resection. The tissue was dissociated and treated with 10uM tamoxifen or control media for 12 hours in suspension. Single cell libraries were then created using a 10x Genomics gel bead droplet-based kit and sequenced via Illumina sequencing platforms. Differences in cell response to tamoxifen was observed between cell types and distinct responsive and unresponsive cell populations were determined.

  Study phs003186

• Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy

  Essential epigenetic dependencies have become evident in many cancers. Based on functional antagonism between BAF/SWI/SNF and PRC2 in SMARCB1-deficient sarcomas, we and colleagues recently completed the clinical trial of the EZH2 inhibitor tazemetostat, leading to its FDA approval. However, the principles of tumor response to epigenetic therapy in general and tazemetostat in particular remain unknown. Using functional genomics of patient tumors and diverse experimental models, we defined molecular mechanisms of tazemetostat resistance. We found distinct classes of acquired mutations that converge on the RB1/E2F axis, decoupling EZH2-dependent differentiation and cell cycle control. This allows tumor cells to escape tazemetostat-induced G1 arrest despite EZH2 inhibition and suggests a general mechanism for effective EZH2 therapy. Using RNA-sequencing of patient tumor specimens, we identified specific genes as markers of a deficient RB1/E2F axis, which we propose as prospective biomarkers for therapy stratification. This offers a paradigm for rational epigenetic combination therapy suitable for immediate translation to clinical trials.This study was performed on archived tumor tissue collected as part of the above clinical trial at Memorial Sloan Kettering Cancer Center. Patient tumors were classified into "Response" or "Progression" groups based on RECIST 1.1 criteria. "Response" included tumors exhibiting a complete response, partial response, or stable disease. All other tumors were classified under the "Progression" group. Archived frozen tumor samples were weighed and up to 20-30mg were homogenized in RLT buffer, followed by extraction using the AllPrep DNA/RNA Mini Kit (QIAGEN catalog 80204) according to the manufacturer's instructions. RNA was eluted in 13 μL nuclease-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1 μg of total RNA with DV200 percentages varying from 78% to 100% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and sequenced using NovaSeq 6000 in a PE150 mode, with the NovaSeq 6000 S4 Reagent Kit (Illumina). On average, 84 million paired reads were generated per sample and 70% of the data mapped to mRNA. For analysis, read adaptors were trimmed and quality filtered using 'trim_galore' and mapped to GRCh38/hg19 reference genome using STAR v2.7.9 with default parameters.

  Study phs003188

• Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and is Associated with Worse Outcomes

  Small-cell lung cancer (SCLC) is a very aggressive neuroendocrine lung cancer often associated with oncogenic MYC amplifications, which are known to drive SCLC heterogeneity marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states. The genetic mechanisms of MYC amplification and phenotypic plasticity between cell states is not known. Using data from cell-lines and a few patient-derived samples along with integrated whole-genome sequencing, long-range optical mapping, single-cell DNA sequencing, and fluorescence in situ hybridization, we have attempted to successfully characterize extrachromosomal DNA (ecDNA) as the primary source of MYC amplifications and driver fusions in SCLC.

  Study phs003190

• RNA Splicing Dysregulation in the Pathogenesis of Chronic Lymphocytic Leukemia

  RNA splicing dysregulation is a hallmark of cancers, promoting the onset and progression of disease. In chronic lymphocytic leukemia (CLL), spliceosome mutations leading to aberrant splicing occurs in approximately 20% of patients. However, the underlying mechanism for splicing defects in spliceosome unmutated CLL cases remains elusive. To discover posttranscriptional regulation of RNA splicing, we performed RNA sequencing using RNA derived from B cells from 6 healthy donors and 36 CLL patients, along with MAZTER sequencing from 9 CLL patients (8 matched with RNA sequencing cohort) and B cells from 5 healthy donors. We found that CLL cells have dysregulated m6A modification sites on transcripts from splicing factors, suggesting a critical role of m6A modification in RNA splicing dysregulation.

  Study phs003191

• Genomic Analysis of Prostate Tumor Heterogeneity in Metastasis

  To investigate the molecular changes, mutations, and signaling pathways that characterize the initial steps of prostate cancer metastasis to the lymph nodes, we analyzed 19 discrete lymph node (LN) metastases, 97 primary tumor foci, 39 benign lymph nodes, and 10 normal adjacent prostate tissue samples from 43 patients enrolled in a clinical trial (NCT01808222) of extended lymphadenectomy and metastasis excision guided by [18F]-fluciclovine PET imaging for high risk, newly diagnosed prostate cancer conducted at Emory University. These patients fell within high or very high-risk groups (T3a, Gleason score 8-10, or PSA greater than 20 ng/ml). Of these patients, 16 had LN metastases at least 4 mm in diameter, and 20 patients had no metastases. For metastatic patients, we performed RNA and Whole Exome Sequencing (WES) on three primary tumor foci, one benign LN, and all LN metastases greater than 4mm in diameter. For non-metastatic patients, we sequenced two primary tumor foci and one benign LN. In total, RNAseq was performed on 165 tissue samples from 43 patients, and WES was performed on 137 samples from 35 patients.

  Study phs003404

• Genomic Analyses of Germline and Somatic Variation in High-Grade Serous Ovarian Cancer

  The goal of this study was to identify and characterize germline and somatic genetic variation in women with high grade serous ovarian cancers treated at a single cancer center and their associations with relapse-free and overall survival. We conducted paired tumor/normal targeted next-generation sequencing of 577 genes in pathways of DNA repair, response to DNA damage, cell-cycle regulation, programmed cell death, MAPK, and P13K/AKT/MTOR signaling in 114 tumors from 71 women. In addition, we investigated single copy number alterations (SCNAs) and loss of heterozygosity in a subset of 61 tumors. We validated our results with data from ovarian tumors in TCGA. Our results were similar to other studies of high-grade serous carcinomas. As an example, we found that approximately one third of the tumors harbored loss of function variants in homologous recombination genes and that >90% had TP53 somatic mutations. Through GISTIC analysis of the OncoScan data on tumor DNA from 61 cases, we identified several regions of high copy number alterations including including NOTCH3 and PIK3R2 that were significantly associated with an increase in cancer recurrence and a reduction in overall survival. We identified few changes in mutation profiles where we had multiple tissues, either from multiple surgeries or from the primary site to metastatic sites within the same surgery. However, we did not investigate copy number alterations in multiple tissues from the same individuals, and so it may be that copy number alterations are more important. Data available through dbGAP will be the BAM files and the phenotypic data on the tumor samples, the age, race, ethnicity of the participants and their outcomes, and the Oncoscan OSCHP files.

  Study phs003198

• RNA-Seq Data From Early Stage Triple Negative Breast Cancer Tumors Treated With TVEC and Chemotherapy (MCC18621)

  This study is a phase 1/phase 2 trial testing the combination of talimogene laherparepvec (TVEC) and neoadjuvant chemotherapy for the treatment of stage II-III triple negative breast cancer. The trial demonstrated that the addition of TVEC to neoadjuvant chemotherapy was feasible, and resulted in a pathological complete response (pCR) rate of 45.9%, residual cancer burden (RCB) 0-1 rate of 65%, and event free survival of 89%. The macrodissected formalin-fixed paraffin-embedded (FFPE) samples were from 50 patients treated across two phases at different timepoints (pre-treatment, 6th week of treatment, and surgical resection). RNA-Seq data is provided along with clinical classifiers.

  Study phs003199

• E5103 Correlative Studies

  ECOG-ACRIN E5103 (E5103) was a phase III adjuvant breast cancer trial that randomized 4994 patients with node-positive or high-risk node-negative breast cancer to intravenous doxorubicin and cyclophosphamide every 2 or 3 weeks (at the discretion of treating physician), for four cycles of adriamycin and cyclophosphamide (AC) followed by 12 weeks of weekly paclitaxel (80 mg/m2) alone (Arm A), or to the same chemotherapy with either concurrent bevacizumab (Arm B), or concurrent plus sequential bevacizumab (Arm C). To develop predictive genetic biomarkers for chemotherapy efficacy and toxicities, we have successfully performed genome-wide genotyping and whole exome sequencing in the germline (blood) DNA of 3215 and 672 patients, respectively, from the E5103 trial to investigate the association of genetic variants with chemotherapy efficacy and toxicities. Case and control studies were performed with genome-wide analyses (GWAS) and whole exome analyses (WES) across all arms of E5103 to identify genotypes at single-nucleotide polymorphisms (SNPs) and deleterious gene mutations that were associated with paclitaxel-induced peripheral neuropathy (TIPN). Through GWAS, we have identified a SNP, rs3125923, and through WES, Cytochrome P450 oxidoreductase (POR), that was significantly associated with grade 3-4 TIPN.

  Study phs003201

• Melbourne Collaborative Cohort Study DNA Methylation Studies

  This dataset contains raw Illumina 450K blood DNA methylation data from a subset of participants in the Melbourne Cohort Study (MCCS), a prospective study of 41,513 healthy adult volunteers (24,469 women) aged between 27 and 76 years when recruited between 1990 and 1994. Nested case-control studies: DNA methylation data were generated as part of cancer case-control studies nested in the MCCS. Participants were cancer-free at blood draw; blood samples were taken at baseline (1990-1994) for 97% of participants; and for 3% of participants at the second wave of follow-up (2003-2007). Eight separate studies were conducted of breast, prostate, colorectal, lung, kidney, urothelial and gastric cancer and B-cell lymphoma, for a total of > 3,500 cancer cases. Controls were individually matched to cases on age, sex, and country of birth using incidence density sampling. Additional matching on smoking history was made for the study of lung cancer. Longitudinal study: For a subset of 1,100 participants with baseline DNA methylation measures (from dried blood spots) who were selected as controls in the nested case-control studies, repeated methylation measures were made using wave 2 follow-up samples (also from dried blood spots) to study longitudinal DNA methylation changes. Project aims: 1. Nested case-control studies: To assess prospective associations between peripheral blood DNA methylation and risk of eight cancer types (breast, prostate, colorectal, lung, kidney, urothelial cell and gastric cancer, and mature B-cell neoplasms). 2. Longitudinal study: To assess associations between lifestyle changes and changes in peripheral blood DNA methylation.

  Study phs003213

• Molecular Determinants of Esophageal Cancer in Tanzania

  We describe the genomic profiles of 61 esophageal squamous cell carcinoma (ESCC) cases from Tanzania and compare them to profiles from an existing cohort of ESCC cases from Malawi. We also provide a comparison to ESCC tumors in The Cancer Genome Atlas Program (TCGA). Despite a high burden of ESCC in Eastern Africa, investigations into the genomics in this region are nascent. This represents the largest comprehensive genomic analysis of ESCC from sub-Saharan Africa to date. We observed substantial transcriptional overlap with other squamous histologies via comparison with TCGA PanCan dataset. DNA analysis revealed known mutational patterns, both genome-wide as well as in genes known to be commonly mutated in ESCC. TP53 mutations were the most common somatic mutation in tumors from both Tanzania and Malawi but were detected at lower frequencies than previously reported in ESCC cases from other settings. In a combined analysis, two unique transcriptional clusters were identified: a proliferative/epithelial cluster and an invasive/migrative/mesenchymal cluster. Mutational signature analysis of the Tanzanian cohort revealed common signatures associated with aging and cytidine deaminase activity and an absence of signature 29, which was previously reported in the Malawi cohort.

  Study phs003217

• Whole Exome Sequencing and RNA-Seq to Characterize the Somatic Breast Cancer Landscape Among Latinas in California

  Somatic mutational profiles are increasingly being used to guide treatment. However, there is a dearth of data from non-European populations. To address this gap, we conducted paired tumor/normal whole exome paired-end sequencing and tumor RNA-Seq on 146 breast tumors from 140 Hispanic/Latina (H/L) women with breast cancer. We characterized somatic mutations, copy number alterations, tumor subtypes [Prediction Analysis of Microarray 50 (PAM50)], Catalogue Of Somatic Mutations In Cancer (COSMIC) mutation signatures and expression profiles, and compared them to breast tumors from non-Hispanic White (White) women in The Cancer Genome Atlas (TCGA). Using MutSigCV, we found that the most commonly mutated genes, including TP53, RUNX1, PTEN, PIK3CA, MAP3K1, GATA3, CDH1 and CBFB, were similar to those in breast tumors from non-Hispanic white women. Novel findings were that outliers of BLTP2 (aka KIAA0100) over-expression and COSMIC mutational signature 16 were more common in tumors from H/L women than White women. We also identified that the known germline APOBEC3A/B deletion variant was significantly more common in H/L women and was associated with indigenous American ancestry. Data available through dbGaP will be whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data, as well as phenotypic data, including estrogen receptor, progesterone receptor, and HER2 receptor status, tumor histology, stage, and grade, and age at diagnosis.

  Study phs003218

• Hi-C Profiling of Solid Tumor Samples

  Structural variants, such as translocations, inversions, duplications, and deletions, have long been recognized as mutations that can contribute to the initiation and progression of cancer. This can occur through a variety of mechanisms, including changes in gene dosage and the generation of fusion genes. In recent years, it is becoming increasingly clear that these events also can alter how genomes are organized in 3D space in the nucleus and contribute to changes in enhancer-promoter regulation. However, it remains poorly understand how often 3D genome structural changes occur in cancers, what genes are affected by these events, and in which tumor types. This study is part of ongoing work to better characterize 3D genome structural changes across a variety of tumor types to better understand where and when 3D genome structure changes as the result of structural variation in cancer genomes and to characterize the genes and tumor types affected.

  Study phs003227

• Single Cell Genotypic and Phenotypic Analysis of Measurable Residual Disease in Acute Myeloid Leukemia

  Acute myeloid leukemia (AML) is a group of blood cancers with high mortality. Even though complete remission is often achieved, majority of the AML patients still relapse. Measurable residual disease (MRD), defined as the population of cancer cells which persists following chemotherapy, is responsible for AML relapse. Understanding the biology enabling MRD clones to resist therapy is necessary to guide the development of curative treatments more effectively. Discriminating residual leukemic clones, preleukemic clones, and normal precursors remains a challenge with current MRD tools. We developed a single cell MRD (scMRD) assay by combining flow cytometric enrichment of the targeted precursor/blast population with integrated single cell DNA sequencing (scDNA-seq) and immunophenotyping (Tapestri, Missionbio). The platform utilizes a custom amplicon panel covering 109 amplicons across 31 genes frequently mutated in AML and a panel of 42 oligo-conjugated antibodies against surface makers. We applied our scMRD assay to sequence 30 MRD samples (multiplexed into 6) from 29 AML patients to study the clonal architecture and protein correlation. In addition, 2 MRD samples were sequenced with scDNA+protein sequencing technology without enrichment or multiplexing. Five patients with AML at diagnosis were also sequenced with scDNA+protein sequencing technology without enrichment or multiplexing. In order to establish the sensitivity of our scMRD assay, we spiked AML cells into normal bone marrow cells. We sequenced 12 such spiked samples after multiplexing.

  Study phs003233

• Deterministic Evolution and Stringent Selection During Pre-Neoplasia

  The earliest events during human tumor initiation are poorly characterized but may hold clues as to how to detect and prevent malignancy. Here we model this occult process by engineering TP53 deficiency in primary human gastric organoids and performing experimental evolution in multiple clonally derived cultures over two years, thereby defining causal relationships between this common initiating genetic lesion and resulting phenotypes. TP53 loss induced progressive aneuploidy, including copy number alterations and complex structural variants that are common in established gastric cancers, and which accrued along a defined temporal order. Longitudinal single cell sequencing of TP53 deficient gastric organoids similarly indicates progression towards malignant transcriptional programs. Moreover, lineage tracing with expressed cellular barcodes revealed highly reproducible dynamics whereby initially rare subclones with shared transcriptional programs repeatedly attain clonal dominance. This powerful platform for experimental evolution reveals stringent selection and convergence at the genotypic and phenotypic levels in pre-malignant epithelial organoids, illuminating evolutionary constraints and barriers to malignant transformation.

  Study phs003249

• Genetic Analysis of Skin Cells

  Cutaneous squamous cell carcinoma (cSCC) is a form of skin cancer originating from keratinocytes in the skin. They have high mutation burdens, primarily driven by UV-radiation-induced DNA damage. The order in which mutations undergo selection during the evolution of cSCC is not known. A subset of cSCCs grow out of benign neoplasms called actinic keratoses. To better understand the evolution of cSCC, we identified cases of cSCCs adjacent to actinic keratoses. From these cases, we separately microdissected the surrounding normal skin, the actinic keratosis, and the cSCC, and we performed targeted DNA-sequencing on the tissue from each area. We reconstructed tumor phylogenies and performed spatial transcriptomics on the 10X FFPE Visium platform on a subset of cases. Collectively, these studies revealed the mutational and gene expression changes that arise during the evolution of cSCC.

  Study phs003282

• Investigating the Role of Neddylation in the Repair of Topoisomerase I-Mediated DNA Damage in Colorectal Cancer

  Colorectal cancer is one of the most lethal cancers worldwide. First-line chemotherapy for metastatic CRC (mCRC) entails a combination of irinotecan with 5-fluorouracil and leucovorin (FOLFIRI). Irinotecan is a prodrug that is converted within the cell to its active metabolite SN38, a potent TOP1 inhibitor. TOP1 relieves DNA torsional strain arising from DNA metabolism by cleaving one strand of the DNA duplex and forming an enzyme-DNA covalent intermediate that can be trapped by inhibitors. The resulting TOP1 DNA-protein crosslinks (TOP1-DPCs) interfere with replication and transcription and induce cell death if left unrepaired. I have established the role of the ubiquitin-proteasome pathway in TOP1-DPC repair, but it remains unknown how ubiquitylation is activated. One possibility is that collision between advancing replication forks and the DPCs triggers a specific ubiquitin ligase to target DPCs for degradation. The DDB1-CUL4 (Cullin 4)-RBX1 (CRL4) ubiquitin ligase complex performs a salient role in both replication and DNA repair upon its activation by auto-NEDD8 modification (neddylation), but it is unknown whether it plays a role for TOP1-DPC repair. We plan to define the role of neddylation for TOP1-DPC repair during replication and examine irinotecan plus pevonedistat (PEV), a NEDD8-activating enzyme inhibitor in multiple clinical trials, in CRC patient-derived preclinical models including 3D organoids. The three in-house organoids, from which samples have been submitted to dbGaP, were sequenced as a means of verifying their identity as colon cancer organoids, to allow us to investigate the combination of TOP1 inhibitors and PEV and the molecular mechanisms underlying this drug combination in these organoids.

  Study phs003257

• MAITS in HCC

  Hepatocellular Carcinoma (HCC) is a leading cause of cancer-related death and can be considered a prototype of inflammation-derived cancer arising from chronic liver injury. The cell composition of the HCC tumor immune microenvironment (TiME) has a major impact on cancer biology as the TiME can have divergent capacities on tumor initiation, progress, and response to therapy. Recent development of multi-omics and single-cell technologies help us to comprehensively quantify the cellular heterogeneity and spatial organization of the TiME and to further our understanding of antitumor immunity. We investigated the cellular composition of liver cancer patient samples (n=8) using single-cell RNA-seq. For this purpose, mononuclear cells were isolated from human liver cancer samples. Three locations within the tumor-bearing liver were used: adjacent liver, rim and tumor core. Then, cells were FACS sorted (either CD45+ cells or MAIT cells) and subjected to 10X Chromium-based scRNA-seq. We investigated immune cell changes and the cellular heterogeneity of the HCC TiME with a focus on MAIT cells. Annotated H5 files are provided. Clinical metadata including TMN stage, sex, gender, ethnicity, pretreatment, and histopathological reports are available for all patient samples. Further details on the study can be obtained in our paper once it’s published.A complementary dataset derived from ultrahighplex CO-Detection by indEXing (CODEX) from paired patient samples can be accessed through The Cancer Imaging Archives (TCIA) under DOI: https://doi.org/10.7937/bh0r-y074.

  Study phs003279

• Immune-Related Adverse Events after Immune Checkpoint Blockade-Based Therapy are Associated with Improved Survival in Advanced Sarcoma

  Immune activation after immune checkpoint blockade (ICB) can lead to a unique group of adverse events (AEs), which have been associated with improved outcome in many carcinomas. The association between immune-related AEs (irAEs) and outcome in patients with sarcoma is not well studied. This study has two components: (1) a retrospective clinical study of irAEs among 131 patients treated with ICB at Memorial Sloan Kettering Cancer Center and (2) an analysis of a subset of these patients who have whole transcriptome sequencing available for analysis. In the clinical study portion, we reviewed a cohort of patients with advanced sarcoma treated on prospective clinical trials utilizing ICB-based therapy between April 2017 and January 2020. The objectives were to pool the safety data from each trial, identify irAEs, and correlate them with best overall response by RECIST 1.1, progression-free survival (PFS) and overall survival (OS). Association of irAEs with response and survival was assessed using a Cox regression model. A total of 131 patients were included. Forty-two (32%) had at least one irAE of any grade and 16 (12%) had at least one Grade ≥ 3 irAE. On Cox analysis adjusting for clinical covariates that were significant in the univariate setting, the hazard ratio (HR) for an irAE (HR 0.662, 95% CI 0.421 - 1.041) approached, but did not reach statistical significance for PFS (P = 0.074), while patients had a significantly lower HR for OS (HR 0.443, 95% CI 0.246 – 0.798; P = 0.007) compared to those without or before an irAE. Tumor samples with available RNA sequencing data were stratified by presence of an irAE to identify patterns of differential gene expression. In total, 71 unique patients had RNA sequencing available for analysis. The transcriptomes of 31 of these patients have been previously uploaded to dbGaP (phs002852), leaving 36 unique transcriptomes that have not been previously publicly shared. Three patients did not agree for their sequencing to be publicly shared. Therefore, 33 unique patient samples will be uploaded to this dbGaP study. Overall, this study found that gene expression profiling on baseline tumor samples from patients who had an irAE had higher numbers of tumor-infiltrating dendritic cells, CD8+ T cells, and regulatory T cells as well as upregulation of immune and inflammatory pathways.

  Study phs003284

• FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-Free DNA

  Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from existing datasets, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues of origin directly from plasma whole genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow coverage WGS and whole genome bisulfite sequencing (WGBS) data from both cancer patients and healthy controls.

  Study phs003287

• Cell-Free, Methylated DNA in Blood Samples Reveals Tissue-Specific, Cellular Damage from Radiation Treatment

  Radiation therapy is an effective cancer treatment, although damage to surrounding healthy tissues can also occur. Cell-type specific DNA methylation patterns can be used to decode the cellular origins of cell-free DNA fragments, allowing for minimally-invasive monitoring of tissue damage. To evaluate whether changes in cell-free DNA methylation can indicate damages to tissues in patients treated with radiation, we collected serum samples from 15 breast cancer patients at three timepoints during their standard-of-care radiation therapy after surgery. A baseline sample was taken for each patient before onset of radiation therapy and a second End-Of-Treatment (EOT) sample was taken 30 minutes after the last treatment fraction. Finally, a recovery sample was taken one month after completion of radiation therapy. From serum samples, cell-free DNA was isolated and bisulfite capture-sequencing DNA methylation data were generated. Bisulfite capture-sequencing DNA methylation data were also generated from buffy coat and tissue-specific endothelial gDNA samples as well as from serum/plasma samples of healthy controls. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct tissue-specific epithelial and endothelial responses to radiation across multiple organs. In conclusion, as a proof of concept we show that cell-type specific methylation signatures can be applied to detect cellular injury from radiation treatment using minimally invasive cell-free DNA in blood samples.

  Study phs003290

• Whole Exome Sequencing Analysis of Carfilzomib-Related Cardiotoxicity in Multiple Myeloma Patients

  This study investigated the contribution of germline genetic variants in protein-coding genes in carfilzomib-related cardiovascular adverse events among patients with multiple myeloma using whole-exome sequencing (WES) analysis. We analyzed 247 patients with multiple myeloma who had been treated with carfilzomib at the Moffitt Cancer Center. We identified a missense mutation in the TMSB10/TRABD2A locus that appeared to be associated with a higher risk for cardiovascular adverse events in these patients. In this submission, we will provide all the genotype data along with the phenotype data of whether or not a patient developed cardiovascular adverse events after carfilzomib treatment and all the covariates used in this analysis.

  Study phs003308

• PD-1 Instructs a Tumor Suppressive Metabolic Program to Restrain AP-1 Activity in T Cell Lymphoma

  T cell non-Hodgkin lymphomas (T-NHLs) represent a heterogeneous group of aggressive cancers of mature CD4+ T cells, for which therapeutic options are limited. Recent work uncovered that the PDCD1 encoded immune checkpoint receptor PD-1 is a key tumor suppressor in T cells. PD-1 is recurrently inactivated in T-NHL and the highest frequencies of PDCD1 deletions are detected in advanced disease, predicting worse prognosis. The tumor-suppressive mechanisms of PD-1 signaling remain unknown. In the present study, we identify transcriptional and epigenetic mechanisms underlying PD-1 tumor suppression in T-NHL.Some subjects included in this study overlap with the subjects from phs002456. To establish the link between the overlapping subjects, the Subject Consent datasets will be utilized.

  Study phs003312

• Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer

  Bladder preservation with trimodality therapy (TMT), consisting of transurethral tumor resection followed by chemoradiation, is an alternative to radical cystectomy for muscle-invasive bladder cancer (MIBC), but molecular determinants of response are poorly understood. Patients with cT2-T4aN0M0 MIBC treated with definitive-intent chemoradiation as part of TMT were retrospectively identified from a single institution between 1986-2015. Pre-treatment Formalin Fixed Paraffin Embedded (FFPE) tumors from 76 MIBC patients were subjected to whole exome sequencing (WES). Our integrated analysis yielded insights into molecular features associated with favorable long-term response to TMT, including alterations in DNA damage response genes. Of these, mutations in ERCC2, a DNA helicase in the nucleotide excision repair pathway, were significantly associated with improved long-term outcomes after TMT, particularly in patients who received concurrent cisplatin-based chemotherapy.

  Study phs003402

• A Pilot Study of Neoadjuvant Nivolumab, Ipilimumab and Intralesional Oncolytic Virotherapy for HER2-Negative Breast Cancer

  This study was a single arm phase 1 trial that assessed the regimen safety and feasibility as well as tumor response in patients with localized HER2-negative breast cancer treated with talimogene laherparepvec (T-VEC) in combination with nivolumab and ipilimumab. The primary objective was to evaluate the safety and adverse event profile of this treatment combination. Six patients were enrolled, four having relapses after prior neoadjuvant chemotherapy, and two who were previously untreated. One patient had a pathological complete response, three patients had pathological partial responses, one showed no significant response, and one had disease progression. Biopsies demonstrated increased immune cell infiltration in samples from patients who responded to therapy. In this study, the checkpoint blockade immunotherapy combined with T-VEC provided responses in patients with advanced or relapsed HER2-negative breast cancer at the expense of long-term toxicities.

  Study phs003316

• Integrative Age-Related Changes in Genome and Epigenome in Human Lung in Relation to Smoking

  The Integrative Age-Related Changes in Genome and Epigenome in Human Lung in Relation to Smoking study was designed to assess DNA methylation and gene expression profiles in cytologically normal bronchial progenitor "basal" cells. The cells were collected from 54 consented bronchoscopy specimen donors at standard airway locations during clinically indicated bronchoscopy, and then outgrown in primary cultures. DNA methylation profiles were assessed using Enzymatic-Methyl sequencing (EM-seq: 96% genomic coverage, 7.5x depth) in all 54 donors' samples. The gene expression profile was evaluated by bulk RNA-Seq in 39 donors' samples. The study participants were at the ages of 33 - 81 years old at enrollment. Of the 54 donors, 31 were newly diagnosed with lung cancer. As for tobacco smoke exposure, there were 19 current, 18, former, and 17 never smokers. There are 26 subjects whose specimens were used for single cell whole-genome sequencing study phs002758.

  Study phs003317

• RNA Sequencing of ECOG-E1308

  This study reports the RNA sequencing of HPV positive oropharyngeal squamous cell carcinoma samples from patients with HPV-associated stage III or stage IV cancer of the oropharynx that was surgically resectible. These patients participated in the ECOG-E1308 trial, a phase II trial that studied paclitaxel, cisplatin, and cetuximab followed by cetuximab and two different doses of intensity-modulated radiation therapy.

  Study phs003320

• BarcUVa-Seq (Biology of Colorectal Cancer Risk Enhancers)

  This study was designed to generate a cohort of normal colon mucosal biopsies from the "average risk" population. Its primary aims included the development of an RNA-seq dataset of normal colon mucosal biopsies across three colon regions (ascending, transverse and descending). Further, we aimed to provide plausible prioritization to genetic components of colorectal cancer risk by employing methods such as expression quantitative trait loci analysis. In doing so, we provide a novel reference dataset for the study of colon cancer risk in the healthy colon epithelium. RNA-seq was performed in batches on an Illumina HiSeq 2500 (batch 1-7) or NovaSeq 6000 (batch 8) on a total of 463 samples. Matched genotyping data was generated on the Illumina OncoArray BeadChip. Phasing was carried out using Minimac 3 and imputation was performed using The Haplotype Reference Consortium panel on the Michigan Imputation Server.Genotype and RNA-seq data will be made available in dbGaP.

  Study phs003338

• Meta-Analysis of Genome-Wide Association Studies of Bladder Cancer Risk

  This meta-analysis consists of genome-wide genotype for 13,447 cases and 342,580 controls of European ancestry to identify novel susceptibility loci for bladder cancer. Cases were defined as histologically confirmed primary carcinoma of the urinary bladder of all stages, including carcinoma in situ (International Classification of Diseases for Oncology, C670-C679, 188). All histologic subtypes were included. Summary-level results for the association between genotyped/imputed variants and risk of bladder cancer are included.

  Study phs003342

• Targeted Linked-Read DNA-seq Analysis of Castration-Resistant Prostate Cancers

  Androgen receptor (AR) inhibition is standard of care for advanced prostate cancer (PC). However, its efficacy is limited by progression to castration-resistant PC (CRPC), usually due to AR re-activation via mechanisms that include AR amplification and structural rearrangement. These two classes of AR alterations often co-occur in CRPC tumors, but it is unclear whether this reflects intercellular or intracellular heterogeneity of AR. It is important to resolve the mechanisms of AR genomic rearrangements to develop new therapies and predictive biomarkers for PC. We developed a targeted linked-read DNA sequencing assay to interrogate alterations in AR and a panel of genes known to be amplified or mutated in CRPC. Linked-read DNA-sequencing libraries were generated using the 10X Genomics Chromium platform and subjected to hybridization enrichment using a custom-designed Agilent SureSelect bait panel. Post-capture DNA-seq libraries were pooled and sequenced on an Illumina HiSeq 2500 using 2x150 bp settings. This targeted linked-read DNA-seq assay was used to interrogate a set of 6 benchmarking samples harboring known AR gene rearrangements and other alterations in AR, as well a panel of 6 patient-derived xenograft CRPC tumors and 23 clinical CRPC tumors. In this cohort, we identified a subset of samples that developed complex, multiply-rearranged AR gene structures in conjunction with very high AR copy number. The data that will be made available through dbGaP are raw FASTQ files.

  Study phs003343

• Low-Dose Carboplatin Modifies the Tumor Microenvironment to Augment CAR T Cell Efficacy in Human Prostate Cancer Models

  Single-cell RNA sequencing (scRNA-seq) was performed to analyze the transcriptional modifications in the tumor microenvironment of prostate cancer patient-derived xenografts (PDX). The analyzed PDX tumor was PDX-287R from the MURAL collection of PDXs (PMID: 34413304). Mice harboring PDX tumors were treated with the carboplatin chemotherapy, and tumors were harvested 3 weeks later. RNA sequencing (RNA-Seq) was used to define immune and non-immune cell populations and anti-tumor innate immune signaling within the tumor microenvironment. To investigate the response of tumor cells to carboplatin treatment in more detail, RNA-Seq was performed on FACs-isolated tumor cells from PDX-287R at one week post-treatment. Gene set enrichment analysis showed an enrichment for apoptotic pathways, with significantly increased expression of the pro-apoptotic genes FAS, BAX, BBC3, IFI6, and JUN. Previously, carboplatin has been shown to activate the cGAS/STING pathway, and here we also found an increase in STING signaling, with an enrichment for the cytosolic DNA sensing pathway and increased expression of STING1, STAT1 and STAT2. There was also a significant increase in the expression of genes involved in T cell chemotaxis, CXCL10, CXCL11, and CCL20. Collectively, carboplatin-induced cell death in tumor cells likely initiated a pro-inflammatory phenotype in prostate cancer PDXs.

  Study phs003369

• Cryptic Splice Mutation in the Fumarate Hydratase Gene in Patients With Clinical Manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC)

  Four patients with hysterectomy were evaluated for biochemical and molecular evidence of autosomal dominant Fumarate Hydratase (FH) alterations causing Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC). HLRCC is an autosomal dominant condition characterized by the development of cutaneous and uterine leiomyomas, and risk for development of an aggressive form of papillary renal cell cancer. Enzyme assay, western blot analyses, direct nanopore RNA sequencing, and whole genome sequencing (WGS) were utilized. The study identified a cryptic splice mutation in intron 9 of the FH gene that results in retention of 57 base pairs of intronic sequence in the affected allele of the mature FH mRNA.

  Study phs003381

• Adipose Tissue Omics In Obesity

  This project used a multi-omics approach to study the adipose tissue transcriptome in humans with and without obesity. Our human cohort included males and females between the ages of 18-80 who underwent elective abdominal surgery at the University of Michigan and the Ann Arbor Veterans Affairs Healthcare System.Patients with advanced cancer or immuncompromised status were excluded. Visceral adipose tissue (VAT/omental) and subcutaneous adipose tissue (SAT/abdominal wall) were collected from subjects with obesity (BMI>=35) at the beginning of elective surgical procedures, placed on ice, and transported back to the laboratory for immediate processing. For adipose tissue stromal cells (ASC) isolation, adipose tissue was digested with Type II collagenase (2 mg/mL in PBS/2% BSA) at 37oC, 60min, centrifuged at 250 rcf, and the stromal-vascular cell pellet was retrieved, plated overnight, and the adherent cells passaged three times to enrich for ASC, which were then frozen in DMEM/F12, 15% fetal calf serum, and 10% DMSO in liquid nitrogen until use. Single nuclear sequencing was performed on preparations from intact adipose tissue. Bulk RNA sequencing and single cell sequencing were performed on ASC isolated from intact adipose tissue and cultured in 2D and 3D culture systems. We currently apply bulk, single cell, and single nuclear sequencing analyses to these tissues. One component of this project studies single nuclear sequencing in nuclei isolated from intact adipose tissues from human subjects with obesity, focusing on depot comparisons (VAT vs. SAT). This cohort also permits comparisons of adipose tissue transcriptomes between male and female subjects, controlling for age and BMI. Primary findings to date include identification of multiple ASC, adipocyte, and endothelial cell (EC) subpopulations, T-cell, and macrophage (MAC) populations that are in concordance with and expand upon other published datasets. Of two dominant ASC subpopulations, one (inflammatory-mesothelial, IM- ASC) is present in VAT, but absent in SAT, while the other (fibroadipogenic, FA-ASC) is present in both VAT and SAT. We identified multiple EC subtypes with features of lymphatic, venous, and arterial EC, and a PRDM16 expressing population with features of an EC progenitor. Immune cell populations match recent experimental validation of lipid-activated macrophage (LAM) phenotypes, TIM4 macrophages, and a prominent population of MRC1/CD206+ resident AT macrophages with expression signatures related to glucocorticoid activation. These data support depot-specific differences in ASC subpopulations and previously unrecognized EC heterogeneity within human AT, with the potential to shed light on functional differences in AT depot and disease state. Planned future studies include ATAC-Seq and other omics analyses. Another component of this project studies transcriptional responses of ASC in vitro to various stimuli, including different matrix environments. Current data includes bulk RNA Sequencing of human ASC from VAT and SAT differentiated into mature adipocytes in hydrogels of differing stiffness (3%, 5%, 10%) to define transcriptional responses to matrix environments of different stiffness. Primary findings to date include enrichment of adipogenesis and lipid and oxidative metabolic gene pathways in adipocytes in 5% relative to 3% hydrogels, while fibrotic gene pathways have been enriched in 3% hydrogels. These data demonstrate that intermediate density matrix promotes a more adipogenic, less fibrotic adipocyte phenotype geared towards increased lipid and aerobic metabolism. Planned future studies include expansion of intact tissues from our cohort studied with single nuclear sequencing, as well as further study of ASC responses in vitro to different biologic stimuli, including different matrix environments.

  Study phs003390

• A Phase III Randomized Study of Nivolumab Plus Ipilimumab Versus Nivolumab in Stage IV Squamous Cell Lung Cancer

  Lung-MAP (S1400, NCT02785952) was a multicenter, open-label, phase III randomized clinical trial. The Lung-MAP-I substudy (S1400I) was conducted from December 2015 to April 2018, through the National Clinical Trials Network and led by the SWOG Cancer Research Network. The trial compared nivolumab plus ipilimumab (nivo+ipi) with nivolumab monotherapy (nivo) in patients with chemotherapy-pretreated, immunotherapy-naïve, advanced squamous non-small cell lung carcinoma (sqNSCLC). Two hundred fifty-two patients were randomly assigned to receive nivo+ipi (n = 125) or nivo (n = 127). The clinical efficacy endpoints were overall survival, progression free survival, duration of response, and best objective response by RECIST 1.1. Multi-omic translational analysis was performed in collaboration with the the CIMAC–Cancer Immunologic Data Commons (CIDC) Network using available tumor tissue samples and blood samples (n = 160) submitted for Lung-MAP screening and provided by the SWOG tissue bank.

  Study phs003412

• Transcriptomic and Epigenetic Profiling of SCLC Patient Samples

  Small cell lung cancer (SCLC) is an aggressive disease with poor outcomes and limited treatment options. Recent studies have identified transcriptionally defined subsets of SCLC that may allow for the personalization of treatment. Here we use transcriptomic sequencing and methylation profiling (RRBS) of biopsy and cfDNA to develop a highly accurate DNA methylation-based classifier to distinguish SCLC subtypes. These results demonstrate the clinical feasibility of molecular subtyping of SCLC.

  Study phs003416

• Hereditary Gastric Cancer Syndromes: An Integrated Genomic and Clinicopathologic Study of the Predisposition to Gastric Cancer

  Gastric cancers are cancers of the stomach. Hereditary cancers are passed from parent to child. Researchers want to gather data about hereditary gastric cancers. Bulk RNA sequencing (RNA-seq) of signet ring cells (SRCs) and adjacent non-SRC epithelium (NEP) was performed on laser-capture microdissected (LCM) regions of interest found in risk-reducing total gastrectomy specimens from hereditary diffuse gastric cancer (HDGC) patients (Clinicaltrials.gov ID: NCT03030404). Twenty patients (6 male, 14 female) with confirmed HDGC were identified. Analysis of differentially expressed genes (DEGs) demonstrated upregulation of certain individual epithelial–mesenchymal transition (EMT) and proliferation genes. SRC regions had significant enrichment in pathways involved in T cell signaling. CIBERSORTx predicted significant increases in the presence of regulatory T cells (Tregs) specific to SRC regions.

  Study phs003422

• CALGB/SWOG 80405: Genome-Wide Association Study of Patients with Advanced or Metastatic Colorectal Cancer Treated with First-Line Chemotherapy Combined with Cetuximab and/or Bevacizumab

  CALGB/SWOG 80405 (NCT00265850) was a randomized phase III study of bevacizumab, cetuximab, or the combination of these two monoclonal antibodies, in addition to systemic chemotherapy for patients with untreated metastatic adenocarcinoma of the colon or rectum. We prospectively collected germline DNA and conducted genome-wide association studies using clinical outcomes and molecular features.

  Study phs003428

• Circulating Genomic Determinants of Treatment Failure in Hodgkin Lymphoma

  In this study, we show that the plasma representation of mutations exceeds the bulk tumor representation in most cases, making classic Hodgkin Lymphoma (cHL) particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumors, we demonstrate hazard ratios (HRs) circulating tumor DNA (ctDNA) shedding to be shaped by DNASE1L3, whose increased tumor microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R-mutations that are dependent on IL13 signaling and therapeutically targetable with IL4R blocking antibodies. Finally, we demonstrate the clinical value of pre- and on-treatment ctDNA levels for longitudinally refining cHL risk prediction, and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL as well as capturing molecularly distinct subtypes with diagnostic, prognostic, and therapeutic potential.Methods utilized include a) targeted genotyping of baseline plasma samples, b) whole exome sequencing (WES) of baseline plasma samples, c) epigenetic expression inference from cell-free DNA-sequencing (EPIC-Seq) to infer gene expression from cell-free DNA (cfDNA) fragmentation profiles, d) ctDNA tracking in on-treatment samples, e) RNA-Sequencing, and f) Phased variant Enrichment and Detection Sequencing (PhasED-Seq).All patients were treated at cancer centers across Europe and North America between 2011 and 2020. The following 3 cancer centers, Stanford (CA, USA), Bellinzona [Confoederatio Helvetica (CH) or Switzerland], and Leuven (Belgium), were included. The 6 clinical trial collectives included in this study are the Phase III trial AHOD1331 trial (NCT02166463) and the Phase II cHOD17 study (NCT03755804) for enrolled pediatric patients, the Phase III AHL2011 (NCT01358747), the Phase II BREACH trial (NCT02292979), a pilot study evaluating concurrent Pembrolizumab with AVD (Doxorubicin, also known as Adriamycin, Vinblastine, and Dacarbazine; NCT03331341), and a Phase II study evaluating PVAB (Prednisone, Vinblastine, Doxorubicin and Bendamustine; NCT02414568) in older patients (61 years and older). In addition, lymph node specimens from a biorepository at St. Jude Children's Research Hospital (TN, USA) were included.

  Study phs003435

• KRT17High/CXCL8+ Tumor Cells Display Both Classical and Basal Features and Regulate Myeloid Infiltration in the Pancreatic Cancer Microenvironment

  Recent studies have uncovered the co-existence of basal and classical subtypes within pancreatic ductal adenocarcinoma (PDAC). We sought to characterize these intermediary cells using single-cell RNA sequencing of PDAC. We performed subtyping on 18 single-cell RNA sequencing human PDAC samples to identify multiple intermediary subtypes. We compared single-cell profiling of patient-matched blood and tumor samples to measure changes in the local and systemic immune microenvironments in CXCL8-high tumors vs. CXCL8-low tumors. Finally, we leveraged longitudinally patient-matched blood over the course of chemotherapy. In our studies we identified a cluster of KRT17high intermediary cancer cells that uniquely express high levels of CXCL8 and other cytokines which in turn influence the myeloid compartment both locally and systemically. We utilized sequencing data from dbGaP study accession phs002070. In addition to that, we included sequencing from new specimens which are deposited to this submission, consisting of one additional tumor specimen and 5 PBMC samples, sequenced after chemotherapy (longitudinally matched to PBMC samples in phs002071.v1.p1). FASTQ files of these sequencing runs are available through this dbGaP submission.

  Study phs003436

• Profiling RNA Translation in Pediatric Medulloblastoma

  This study provides RNA-sequencing and ribosome profiling data for patient-derived cell lines and patient tissue samples for children with medulloblastoma. Ribosome profiling is a variant protocol of RNA-sequencing that directly sequences ribosome-bound RNA fragments only. Associated RNA-seq and Ribo-seq data obtained separately for some cancer cell lines can be found on the NCBI SRA as PRJNA957428. Samples were processed for poly-A mRNA sequencing using the Roche Kapa Kit. Ribosome profiling was performed as described in the manuscript referenced below (Hofman et al.) and based on the article by McGlincy et al., Methods (2017). Ribo-seq data were analyzed for sample quality using RiboseQC (Calviello, Nat Struct Mol Biol, 2020). These data were used to quantify P-sites of open reading frames. RNAseq and ribo-seq data were integrated and compared to determine translational efficiency values using TPM (Ribo-seq) over TPM (RNA-seq) as the metric. Ribo-seq data on 14 samples and RNAseq data on 21 samples derived from 16 fresh-frozen surgical samples for medulloblastoma and 5 autopsy samples are available through dbGaP. A second cohort of 4 medulloblastoma samples (RNAseq, Ribo-seq) related to this study can be found on the EGA at EGAS00001007426.

  Study phs003446

• BPH Tissues for Cell Culture and Analysis - Spatial Transcriptomics Identifies Candidate Stromal Drivers of Benign Prostatic Hyperplasia

  The study goal was to apply spatial transcriptomics to identify candidate stromal drivers of benign prostatic hyperplasia (BPH). Laser microdissection (LCM) with RNA-seq of the stroma adjacent to hyperplastic and budding BPH ducts identified secreted factors including IGF1 and CXCL13. Single‐cell RNA sequencing (scRNA‐seq) revealed their co-expression from BPH fibroblasts. Additional studies sought to define similarities to embryonic prostate development, as well as therapeutic applications. Subjects were those who underwent prostatectomy for prostate or bladder cancer, with concurrent BPH, and who consented to use of surplus tissue for research studies. LCM/RNA-seq studies included 5 patients, and scRNA-seq studies included 1 patient. Phenotypic data submitted to this study include patient age, sex, prostate size, and international prostate symptom score (IPSS). Sequencing was done on an Illumina NovaSeq 6000 (LCM/RNAseq) and Illumina HiSeq X-Ten (scRNA-seq). The data processing pipeline utilized Kallisto (LCM/RNA-seq) and Cell Ranger (scRNA-seq). Data submitted are raw sequencing (Fastq) files.

  Study phs003477

• Breast Cancer in Blacks: Impact of Genomics, Healthcare Use and Lifestyle on Outcomes (BRIGHT)

  Young Black females bear a disproportionate burden of breast cancer (BC) mortality compared to White females and are underrepresented in clinical studies. It remains critical to understand factors that contribute to the high mortality from BC among young Black females in order to improve outcomes. The higher BC mortality rate among young Black females with breast cancer is partially attributed to the disproportionately higher proportions who develop the aggressive triple-negative breast cancer (TNBC). In addition to biologic factors, timely access to care, and lifestyle factors contribute to this disparity. Consequently, we sought to evaluate the interplay between biologic and non-biologic contributors to BC outcomes (i.e., BC disease-free survival (DFS)), and to better characterize the highly aggressive TNBC among young Black females based on distinct molecular subtypes. Ultimately, it is critical to assess both biologic and non-biologic factors to fully understand and address existing health disparities in this population. Through prior and subsequent recruitment of a population-based study of young Black females diagnosed with invasive breast cancer spanning 2009-2016, we: 1) assessed the contribution of biologic and non-biologic factors on BC-DFS observed among young Black females with BC, and 2) investigated molecular features of the subgroup with TNBC. Through this study, consented participants were asked to provide a saliva sample from which DNA was extracted for germline analyses, including germline inherited cancer genetic testing and Infinium Expanded Multi-Ethnic Genotyping Array. Breast cancer tumor specimens were also collected, and tumor RNA was extracted from viable FFPE tumor samples. Tumor RNA analyses included gene expression profiling through NanoString PAM50.Data that will be available through dbGaP for this study include SNP array data and PAM50 data.

  Study phs003466

• A Missense SNP in the Tumor Suppressor SETD2 Reduces H3K36me3 and Mitotic Spindle Integrity in Drosophila

  While examining DNA from renal cell carcinoma (RCC) patients we observed a single nucleotide polymorphism (SNP; rs58906143,chr3:47163422 C→G (hg19); E902Q*) within SETD2 that was overrepresented in kidney cancer patients compared to control patients. This original study utilized directed sequencing of 14 genes. In an expanded study using a Taqman assay to study the specific SNP, a G allele was found in 72/493 cases (14.6%) and 24/356 (6.7%) controls. Analysis by ancestry revealed that there was there was a G allele in 50/119 (42.0%) cases and 21/71 (29.6%) controls in patients with African Ancestry while there was a G allele in 19/335 cases (5.7%) and 3/269 (1.1%) controls in patients with European Ancestry. These differences did not reach statistical significance. Concurrently, we studied the functional effect of this SNP in a Drosophila model. The homologous amino acid substitution at E741Q reduces H3K36me3 levels which could be rescued by wild type Set2. Additionally, the mutation resulted in significant defects in spindle morphogenesis, consistent with a role for SETD2 in alpha-tubulin methylation during mitosis. Data available through dbGAP include the 14 gene sequence files of 52 control and 128 RCC patients, the results of Taqman SNP (rs58906143) analysis in text files for 221 controls and 357 RCC patients, and compiled phenotype data including age and assigned race. Due to data use limitations, genotyping data for 8 RCC patients and 83 controls as well as GWAS data for ancestry determination will not be available on dbGaP, but will be made available on request.

  Study phs003474

• Germline Genome Sequencing from Patients with Early-Onset Merkel Cell Carcinoma

  Merkel cell carcinoma (MCC) is a rare neuroendocrine skin cancer associated with advanced age. Approximately 5% of cases are early-onset MCC, occurring in individuals younger than 50 years. This study used genome sequencing to identify germline risk factors among patients with early-onset MCC. The available data in the database of Genotypes and Phenotypes (dbGaP) includes genome sequencing of peripheral blood mononuclear cell (PBMC) DNA from 37 patients with early-onset MCC (age ATM = 2, BRCA1 = 2, BRCA2 = 1, TP53 = 1, and MAGT1 = 1).

  Study phs003485

• Acquired Cross-Resistance in Small Cell Lung Cancer Patient-Derived Xenografts

  Here we present whole genome sequencing and RNA sequencing of patient-derived xenograft (PDX) models of small cell lung cancer (SCLC). These models were derived at a variety of clinical time points from either biopsy/resection samples, malignant effusions, or circulating tumor cells (CTCs), and grown in the subcutaneous flank of NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl /SzJ) mice. The first analysis published with these data was to determine the genomic and transcriptomic features of PDX models derived after relapse that demonstrated in vivo resistance to multiple chemotherapy regimens (cross-resistance).

  Study phs003486

• Integrating Genomic and Transcriptomic Data to Identify Breast Cancer Susceptibility Genes

  Genetic factors play an important role in the etiology of both sporadic and familial breast cancer. Since 2007, common genetic variants in ~200 loci have been identified in genome-wide association studies (GWAS) in relation to breast cancer risk. However, it is often difficult to translate GWAS findings to disease prevention and treatment since causal genes in the large majority of GWAS-identified loci are unknown. Furthermore, a large fraction of breast cancer heritability remains unexplained. Recent studies suggest that nearly 80% of disease heritability can be explained by genetic variants regulating gene expression. Herein, we propose three well-powered transcriptome-wide association studies (TWAS) to systematically investigate the association of breast cancer risk with gene expression across the transcriptome of African, Asian and European descendants. In Aim 1, we will perform RNA sequencing and high-density genotyping assays using normal breast tissue samples, and build race-specific gene expression prediction models using data from 1000 women of African, Asian and European descent. These models will be applied to the GWAS data generated from approximately 320,000 breast cancer patients and controls to impute gene expression for association analyses of predicted gene expression with risk of breast cancer overall, and by estrogen receptor and HER2 status. In Aim 2, we will select the top 50 genes identified in Aim 1 for in vitro functional assays to assess their influence on major cell functions related to cancer biology. In Aim 3, we will evaluate whether TWAS-identified genes may express differently in normal breast tissues and breast cancer tissues collected from African, Asian, and European descendants to assess whether these genes may contribute to racial differences in breast cancer risk by molecular subtypes. With strong methodology and a large sample size, we believe that this proposed study should be able to identify and characterize a large number of novel genes related to breast cancer risk. Uncovering breast cancer susceptibility genes will greatly improve the understanding of the genetic and biological basis for breast cancer and accelerate the translation of genetic findings to disease prevention and patient care.

  Study phs003535

• Spatial Transcriptomics Reveals Discrete Tumor Microenvironments and Autocrine Loops Within Ovarian Cancer Subclones

  Ovarian masses from patients with high grade serous ovarian carcinoma undergoing debulking surgery were subjected to spatial transcriptomics profiling using the 10x Genomics Visium (fresh frozen) platform. Copy number inference using inferCNV predicted the presence of subclones with mutually exclusive copy number alterations (CNAs) in 5 of the 8 patient samples studied. In one patient, 3 subclones were predicted. For this patient sample, a serial section of the same tumor was used to microdissect regions corresponding to each of these subclones, and a 'normal' region predicted to contain only fibroblasts and no tumor cells. These microdissected regions were processed for low pass whole genome sequencing (WGS) and CNAs recorded using ichorCNA. An oral biopsy lacking tumor cells from an unrelated donor was used as a negative control for CNA inference. The CNAs predicted by inferCNV for the three subclones were validated by the low pass WGS and no CNAs were observed in the normal region containing fibroblasts.

  Study phs003561

• Submission 5 - study_title 1

  Submission 5 - description 1

  Study EGAS50000000284

• The tissue origin of highly elevated cell-free DNA in patients with and without cancer

  Forty years ago, the first measurements of cell free DNA (cfDNA) from cancer patients revealed that its total concentration was often elevated compared to healthy controls. The basis for this increase, and in particular the source of the extra cfDNA in such patients, has never been determined. To address this issue, we assessed methylation patterns of cfDNA from 57 individuals, 34 of whom had unequivocally elevated cfDNA concentrations (i.e., >15 ng/mL of plasma). We found that the excess cfDNA in cancer patients did not come from either neoplastic cells or surrounding cells from the tumor's tissue of origin. Instead, 80% of the cfDNA was derived from neutrophils, B cells or T cells, with neutrophils accounting for ~2/3. B cells contributed more than T cells despite the great excess of T cells over B cells in the blood. To see if this result was generalizable to other clinical situations in which elevated cfDNA concentrations have been described, we evaluated nine patients before and one day following surgery. After surgical resection, cfDNA concentration increased by an average of 16.1-fold, as expected. The majority of this increase (55%) was contributed by leukocytes, though damaged hepatocytes contributed a substantial minority (31% of increase). These data suggest that the elevated concentrations of cfDNA in cancer patients, as with patients after surgery, arises largely from dying leukocytes—not from the neoplastic cells or the tissue of origin of the cancer.

  Study EGAS00001005400

• Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk

  Study EGAS00001006137

• DAC for Castleman. National Cancer Centre Singapore.

  Dac EGAC00001003328