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• The Nephrotic Syndrome Study Network (NEPTUNE)

  The Nephrotic Syndrome Study Network (NEPTUNE) is a collaborative investigational infrastructure of 40 North American sites for conducting clinical and translational research in Focal Segmental Glomerulosclerosis (FSGS), Membranous Nephropathy (MN), and Minimal Change Disease (MCD). NEPTUNE provides prospective, un-blinded, standardized evaluation of clinical and molecular outcomes in two cohorts: A) adults and children with incident or prevalent, biopsy-proven FSGS, MN, or MCD, recruited at the time of first biopsy, and B) children with incident Nephrotic Syndrome without a diagnostic kidney biopsy.

  Study phs003210

• A Phenotypic and Genomics Approach in a Multi-Ethnic Cohort to Subtype Systemic Lupus Erythematosus

  Systemic lupus erythematosus (SLE) is a complex autoimmune disease that affects multiple organ systems and varies in severity across different populations. To examine the clinical heterogeneity of SLE, we sought to identify different lupus subtypes within our multi-ethnic cohort using a clustering approach. Additionally, with genome-wide methylation and genotype data generated for our cohort, we applied integrative methods to investigate genetic and epigenetic risk factors. This integrative and computational approach revealed molecular differences associated with phenotypic clusters.

  Study phs001850

• A Pilot Study to Evaluate Tissue- and Plasma-based DNA Driver Mutations in a Cohort of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasms

  This is a retrospective study aimed at evaluating concordance between intraductal papillary mucinous neoplasm (IPMN) tissue and patient-matched plasma circulating tumor DNA (ctDNA) using a targeted sequencing approach. Archival solid tissue genomic DNA was available for 46 patient FFPE blocks patient-matched plasma ctDNA was available from 15 of those patients. All tissues were obtained pre-treatment from patients with an IPMN diagnosis and subjected to Qiagen custom next generation sequencing panel.

  Study phs003043

• Patient-Derived Breast Cancer Organoid Study

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

  Study phs002722

• Deep RNA sequencing in CLL

  Chronic lymphocytic leukemia (CLL) is a B-cell neoplasm with a heterogeneous clinical and biological behavior. We have performed deep RNA sequencing in different subpopulations of B-lymphocytes from healthy individuals and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. The transcriptomic architecture of CLL uncovered here refines the biological characterization of the disease and opens new perspectives for the clinical management of patients.

  Study EGAS00001000374

• Aneurysmal Subarachnoid Hemorrhage patients with or without vasospasm

  Cerebellar vasospasm is a severe complication of aneurysmal subarachnoid hemorrhage (aSAH) occurring for 30% of aSAH patients. To date, no biomarker of vasospasm occurrence exists and thus all aSAH patients undergo a preventive and dangerous treatment. In this study, we explored the miRNome of aSAH patients to detect potential expression differences between the patients developing a vasospasm (VSP+) or not (VSP-). The shared data include raw and normalized count miRNA data in aneurysmal subarachnoid hemorrhage patients with or without vasospasm.

  Study EGAS00001003092

• PETAL Network: Outcomes Related to COVID-19 Treated With Hydroxychloroquine Among Inpatients With Symptomatic Disease (ORCHID) Trial

  ORCHID was a multicenter, blinded, placebo-controlled randomized trial conducted at 34 hospitals in the US between April 2 and June 19, 2020. Adults hospitalized with respiratory symptoms from severe acute respiratory syndrome coronavirus 2 infection were enrolled, with the last outcome assessment on July 17, 2020. The planned sample size was 510 patients with five interim analyses; however, the trial was stopped at the fourth interim analysis for futility with a sample size of 479 patients.The distribution of the day 14 clinical status score (measured using a 7-category ordinal scale) was not significantly different for patients randomized to receive hydroxychloroquine compared with placebo.Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002299

• RRBS data of 48 individuals of the Dutch Hunger Winter Families Study

  The dataset entails 48 RRBS libraries of 24 siblings. 24 individuals are conceived during the Dutch Famine, a severe 6 month famine at the end of World War 2. A same sex sibling was added as a control, allowing partial matching for (early) familial environment and genetics.

  Dataset EGAD00001000733

• RNA-seq of Toxoplasma gondii response in human macrophages

  Toxoplasmosis is a zoonotic disease caused by a ubiquitous protozoan parasite called Toxoplasma gondii, which can infect all mammal and bird species throughout the world. seroprevalence varies widely between countries. Studies have estimated that between 7-34% of people in the UK have been infected with T. gondii. The vast majority of these people will not have noticed any symptoms, however about 10% of people develop a mild to moderate self limiting flu-like illness. Following the acute active stage of the infection the parasite persists in the body in the form of cysts, particularly in heart and skeletal muscle and nervous system tissues, for many years, and usually for life. In immunocompetent persons these cysts do not pose a health risk. We will use RNA-seq to quantify the transcriptional response of macrophages to T gondii infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001003241

• Ongoing Replication Stress Tolerance and Clonal T Cell Responses Distinguish Liver and Lung Recurrence and Patient Outcomes in Pancreatic Ductal Adenocarcinoma

  Patients with metastatic pancreatic ductal adenocarcinoma (PDAC) survive longer when disease spreads to the lung but not to the liver. We generated overlapping, multi-omic datasets to identify molecular and cellular features that distinguish patients whose disease develops liver metastasis (liver cohort) from those whose disease progression results in lung metastasis without liver metastases (lung cohort). Lung cohort patients generally survived longer than liver cohort patients, independent of tumor subtype. We developed a pORG gene signature that distinguishes primary tumors in the liver and lung cohorts. We identified ongoing replication stress (RS) response pathways in high pORG/liver cohort tumors, while low pORG/lung cohort tumors had greater densities of lymphocytes and shared T cell clonal responses. Our study demonstrates that liver-avid PDAC is associated with tolerance to ongoing RS, limited tumor immunity, and less favorable outcomes; whereas low RS, lung-avid/liver-averse tumors are associated with active tumor immunity that may account for favorable outcomes. As expected, we found high frequencies of KRAS, TP53, CDKN2A, and SMAD4 gene alterations in our tumor samples. High pORG activity (GSVA scores) in our primary tumors appear to be positively correlated with alteration frequencies in both TP53 and CDKN2A. We did not see a correlation with alterations in KRAS as almost all the tumor samples have KRAS alterations. From a de-identified dataset of 1,873 patients diagnosed with and/or treated for PDAC at our institution between 2004 and 2020, we identified 422 patients for which we had specimens with sequencing data (N=374) and/or specific evidence of disease metastasis site(s) from the OHSU cancer registry or disease-relevant computed tomography (CT) scans to allow cohort classification. Note that our study includes RNA-Seq, DNA-Seq panel, and TCR-Seq (T-cell Receptor Sequencing) data, but that this dbGaP submission just includes the patients/samples with RNA-Seq and/or DNA-Seq panel data. Therefore, this submission includes 290 samples from 278 patients. TCR sequence data is available on the Adaptive Biotechnologies platform. Clinical course timepoints, patient demographics, stage, grade, nodal involvement, resection margins, and angiolymphatic invasion were provided as deidentified data by the OHSU cancer registry with quality control data verification in a subset by pathologists (BB and TM). We reviewed all available computed tomography (CT) scans for all patients with primary tumor resection dates recorded by the cancer registrar, with tumor samples analyzed by RNA-seq, DNA-seq, or TCR-seq, and/or with additional information indicating metastatic spread (e.g., metastatic samples received for related studies). We abstracted the site of all lesions proven to be metastatic by biopsy and/or that clearly increased in size during progression or decreased in size during treatment as long as a radiologist described the lesion as “likely”, “suspicious for”, “concerning for”, or “favor” metastasis. Clinical imaging was reviewed by a radiologist (AG) to validate patient assignments to the liver, lung, and neither liver nor lung (other recurrence site) cohorts. Time to recurrence was calculated from the earliest of either the recurrence date provided by the OHSU cancer registry, or the date of earliest lesion abstracted from CT reports. The subject attributes reported in this submission were up to date at the time of our data freeze, which occurred July 2021.

  Study phs003597

• Combined Tumor and Immune Signals From Genomes or Transcriptomes Predict Outcomes of Checkpoint Inhibition in Melanoma

  Cancer immunotherapy with checkpoint blockade (CPB) leads to improved outcomes in melanoma and other tumor types, but a majority of patients do not respond. High tumor mutation burden (TMB) and high levels of tumor-infiltrating T cells have been associated with response to immunotherapy, and integrative models using DNA and RNA have improved predictions of clinical benefit. However, identification of immune and tumor-intrinsic features in models using DNA or RNA alone have not been comprehensively explored in melanoma. In this study, we sequenced DNA and RNA of tumors from 67 melanoma patients receiving CPB, and aggregated this cohort with previously published data, yielding whole exome sequencing (WES) data for 189 patients and bulk RNA sequencing data for 178 patients. Using these datasets, we derived genomic and transcriptomic factors that predict overall survival (OS) and response to immunotherapy. Using whole exome DNA data alone, we calculated T cell burden (TCB) and B cell burden (BCB) based on rearranged TCR/Ig DNA sequences, and found that melanoma patients with high TMB and either high TCB or high BCB survived longer and had higher response rates, as compared to patients with low TMB and either low TCB or low BCB. Next, using bulk RNA-Seq data, differential expression analysis identified 83 genes which are associated with high or low OS. By combining pairs of immune-expressed genes with tumor-expressed genes, we identified three gene pairs which are associated with response and survival (Bonferroni P<0.05). All three gene pair models were validated in an independent cohort (n=180) (Bonferroni P<0.05). The best performing gene pair model included the lymphocyte-expressed MAP4K1 (Gene ID: 11184) and the transcription factor TBX3 (Gene ID: 6926) which is overexpressed in poorly differentiated melanomas. We concluded that RNA-based (MAP4K1 and TBX3) or DNA-based (TCB and TMB) models combining with immune and tumor measures improve predictions of outcome after checkpoint blockade in melanoma.

  Study phs002683

• Predicting Chemotherapy-Induced Mucositis with Genetic and Clinical Factors

  We hypothesized that genetic variability in the enzymes/proteins involved in drug metabolism, inflammation, and immune function is a major underlying contributor to mucositis incidence and progression and that, based on this variability we can identify variants that influence risk, and develop a mucositis progression prediction model that improves on existing models by incorporating genetic variability along with clinical factors. Using genome wide association study (GWAS) combined with a pathway candidate gene approach and a modified case-control study method, we investigated the hypothesis in a sample of 1092 patients who received a myeloablative dose of melphalan (MEL) followed by autologous hematopoietic stem cell (ASCT) transplantation as treatment for multiple myeloma and for whom banked blood stem cell samples and clinical data were available.

  Study phs000545

• Integrated genomic analysis for HCC

  Liver cancer is a common malignancy and is the third cause of cancer-related death in the world and hepatocellular carcinoma (HCC) is the major type of liver cancer, accounting for ~90% of cases. Only 20 ~ 30% of patients can benefit from combined immunotherapy and targeted therapy due to the high inter-tumor heterogeneity of HCC. This work aims to identify homogeneous and robust molecular subtypes in HCC based on a large, homogenous and well-annotated cohort. We performed whole genome/exome sequencing (WGS/WES) and/or RNA sequencing (RNA-seq) on 529 HCC from 461 patients collected mainly in France. Based on the great consistence between genomic and transcriptomic data, we identified 9 robust HCC subtypes mainly based on driver mutations. And we further characterized HCC subtypes using genomic, transcriptomic and clinicopathological features. Among 9 subtypes, 5 subtypes belonged to chromosome instable tumors, while 3 subtypes belonged to chromosome stable tumors. In addition, our subtypes were associated with prognosis and we also found different distributions of subtypes across various features, such as etiology and gender. Our study provided a robust molecular classification based on a large HCC dataset from Western country, it improves our understanding of the mechanisms of carcinogenesis and will facilitate development of genome-based precision medicine in HCC.

  Study EGAS00001007957

• UK10K_RARE_THYROID

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches.Two cohorts of subjects are being analysed: Individuals with Congenital Hypothyroidism (CH) due either to dysgenesis or dyshormonogenesis; Patients with Resistance to Thyroid hormone (RTH), a disorder characterized by elevated thyroid hormones and variable tissue refractoriness to hormone action. The CH cohort has been enriched for genetic aetiologies by recruiting cases that are familial, on a consanguineous background or syndromic. The RTH cohort consists of cases in which candidate gene analyses have been negative.For further information with regard to this cohort please contact Krishna Chatterjee (kkc1@medschl.cam.ac.uk).

  Study EGAS00001000131

• 5- FU treated organoids

  5-Fluorouracil (5-FU) is a chemotherapeutic drug component that is commonly used for the treatment of solid cancers. The anticancer properties of 5-FU have been attributed to interference with nucleotide synthesis and through direct incorporation into the DNA as being a pyrimidine analog. As both mechanisms of action may have a mutational impact on surviving tumor cells, we performed three independent analyses to characterize the genomic consequences of 5-FU treatment: i) in vitro treatment of intestinal organoids with 5-FU followed by whole genome sequencing, ii) genome-wide mutation analyses in tumor samples from 5-FU treated patients with breast or colorectal cancer, and iii) analysis of paired biopsies from patients treated with 5-FU between biopsies. Our results demonstrate that both in vitro and in vivo 5-FU causes a mutational pattern that is dominated by T>G substitutions in a CTT context and with strong resemblance to COSMIC signature 17. Interestingly, this signature is also found in non 5-FU treated patients, most prominently in esophageal tumors, indicating that distinct endogenous and exogenous triggers can converge into highly similar mutational signatures. Furthermore, our results suggest that 5-FU may have adverse mutagenic effects on healthy cells and contributes to genetic variability in surviving cancer cells thereby contributing to tumor evolution.

  Study EGAS00001003592

• Digital tEchnology For Lung Cancer Treatment

  The aim of the DEFLeCT project (Digital tEchnology For Lung Cancer Treatment) is to generate a technological platform for precision medicine in order to set predictive personalised algorithms for patient diagnosis and therapy. All resectable patients having histologically confirmed stage IB-IIIA non-small cell lung cancer(NSCLC) will be enrolled in the PROMOLE study, a related and ongoing observational prospective clinical study, for tissue sampling. A large biobank of lung cancer samples and the corresponding healthy tissues and biological components (ie, blood, stools, etc.) with complete clinical, pathological and molecular information will be collected. The project will lay the basis of a knowledge hub and qualified technology aimed not only at answering the medical and scientific community's questions, but also meant to be useful to individual patients by predicting the response to adjuvant and second-line drugs in case of relapse of the disease.

  Study EGAS00001007219

• National Children's Study Vanguard Study Formative Research Study (NCS)

  The National Children's Study (NCS) is a multi-year prospective epidemiological study tasked with identifying a nationally representative sample of 100,000 children and following them from pregnancy through age 21 to study environmental impacts on growth, development, and health. Determination of NCS enrollee ancestry is important for assessing the diversity of study enrollees and for examining the effect of ancestry on various health outcomes. We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites by analyzing 29,972 markers on exome arrays, using the participants of the 1000 Genomes Project (1KG) super populations (e.g. European, East Asian) as reference populations, and compared this to self-reported ethnicity and race. Self-reported ethnicity and race agreed with predicted super population in 98.9% of individuals. NCS individuals identified as Asian by self-report had genetic ancestry of either South Asian or Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 11 (33%) matched the South Asian and Asian groups, while these groups were less represented in the other reported categories (27/609, 4.4%). Our data suggest that self-reported ethnicity and race categories have some limitations in accurately capturing this information for Hispanic and South Asian populations. Overall, our data indicate that despite the complexity of the U.S. population, individuals know their ancestral origins and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.

  Study phs000662

• CNCD Recall by Genotypes

  This is a DAC to handle recall by genotype studies by the conducted by the Center for Non-Communicable Disease Karachi, Pakistan.

  Dac EGAC50000000937

• Profiling heterogeneity in Human derived IPSC-neurons (2020-05-18)

  The impact of genetic variants on molecular pathways that give rise to neurodegenerative diseases such as Alzheimer's and Parkinson's is best elucidated in the appropriate cell types and molecular contexts. Existing studies have focused on bulk profiling of mixed cell types, but have ignored assaying genetic effects across development and cell differentiation. At the core of this proposal is the idea to use single-cell assays to study genetic effects during differentiation of dopaminergic and cortical neurons to identify the sequence of molecular events from variants to healthy and diseased cell states in a cell-specific manner. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-18.

  Dataset EGAD00001006157

• 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

• The role of gut microbiota in metabolic diseases

  Diabetes is a major disease in the elderly and is responsible for increased risk of myocardial infarction and stroke. Recently, the relationship between microbiota and diabetes has been reported in animals and humans. In this study, blood, stool, and saliva samples were collected from examinees at the University of Tokyo Health Screening Center, and 16S rRNA and metagenomic analyses were performed to determine the variation of microbiota. Furthermore, metabolome analysis and transcriptome analysis (CAGE analysis) using blood were performed to reveal changes in host metabolites and gene expression. By comparing the host- and bacteria- derived information with the metabolic parameters, we analyzed whether microbiota can be a predictor of metabolic diseases.

  Study JGAS000569

• Transcriptomic profiling of proximal and distal regions of human long head biceps tendon

  Tendinopathy is a prevalent musculoskeletal disorder marked by extracellular matrix disorganization, collagen remodeling, vascular ingrowth, and pain, yet its underlying molecular mechanisms remain insufficiently defined. The long head of the biceps tendon (LHBT) is particularly prone to mechanical overload and early degenerative changes, making it a relevant model for studying tendon pathology. In this study, we aimed to characterize region-specific gene expression changes along the LHBT to better understand the molecular basis of degeneration. We collected paired proximal and distal LHBT tissue from patients undergoing rotator cuff repair surgery and performed bulk RNA sequencing. This approach enables the identification of degeneration-associated transcriptional signatures while minimizing inter-patient variability.

  Study EGAS50000001454

• Chip_seq_oesophageal_adenocarcinoma_

  There is complex interplay between underlying genetic sequence and epigenetic factors, however this interplay is still illusive. Massively reconstructed cancer genomes can be used in order to better understand this relationship. Six oesophageal adenocarcinoma organoids will be sequenced using long read sequencing technologies and will be profiled for a range of epigenetic marks. Combination of genetic and epigenetic data will allow the thorough characterisation of reference cancer genomes and will provide novel insights into mechanisms of gene regulation. Description: Chip-seq Sequencing of 5 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical rescetion of the tumour. All model derivations took place with the CGaP facility in Sanger.

  Study EGAS00001007180

• The aim of this project is to identify, on 15 French Caucasian and 10 African-Caribbean men, through an integrative approach of DNA sequencing and transciptomic analyses, relevant genomic events that characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer.

  Every year about 70,000 new cases of prostate cancer are diagnosed in France and 8,700 men died from this disease. But the incidence and the rate of mortality per 100,000 men in the French West Indies are respectively 1.5x and 2x upper than the rates observed in the metropolitan France. The aim of this project is to identify, on 15 French Caucasian and 10 African-Caribbean men, through an integrative approach of DNA sequencing and transciptomic analyses, relevant genomic events that characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer.

  Study EGAS00001002176

• Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes

  Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neo-antigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma (UM) generate such immunogenic neo-antigens. Memory CD8+ T cells specific for these neo-antigens are preferentially found in 20% of UM patients bearing SF3B1 mutated tumors. Single cell analyses of neo-epitope specific T cells from the blood identified large clonal T cell expansions, with distinct effector transcription patterns. Some of these expanded TCRs are also present in the corresponding tumors. CD8+ T cell clones specific for the neo-epitopes specifically recognize and kill SF3B1-mutated tumor cells, supporting the use of this new family of neo-antigens as therapeutic targets.

  Study EGAS00001005226