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• Nanopore medulloblastoma data

  Nanopore data from 3 medulloblastoma samples of which 2 are tumor-normal pairs sequenced with the MinIon and one is tumor only data sequenced on the PromethIon. The data consists of BAM files aligned using minimap2

  Dataset EGAD00001010851

• Colon adenomas and adenocarcinomas and matched mucosae

  Whole exome sequencing of neoplastic colorectal lesions, matched normal mucosa and peripheral blood leucocytes from 7 individuals. Data is contained within FASTQ files.

  Dataset EGAD00001010875

• The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

  Here we aimed to contribute to the description of the genetic architecture of Congenital heart defect (CHD) in Down syndrome (DS), and report the results of a genome-wide association study using samples from DS individuals with and without CHD. CHD is a common developmental defect of DS occurring in 40% of cases. This case-control GWAS includes 187 DS with CHD as cases, and 151 DS without CHD as controls.

  Study EGAS00000000129

• Differential gene expression in the colon mucosa of irritable bowel syndrome patients with diarrhea-predominant symptoms

  The aim of this study is to characterize the pathophysiology of the irritable bowel syndrome (IBS) on the functional level and in parallel on the gene expression level. For this purpose RNAseq of mucosal biopsies was performed. The data from the differential expression analysis will be further processed by Ingenuity Pathway Analysis (IPA) software to gather Information on activated or inhibited signaling pathways in the disease.

  Study EGAS50000000046

• Arcagen – thoracic malignancies

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from rare thoracic malignancies (n=102)

  Study EGAS50000000123

• Gene Expression of Small Cell Carcinoma of the Ovary-Hypercalcemic Type (SCCOHT)

  Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer afflicting young women at a median age of 24 years. SCCOHTs are characterized by loss of protein expression of SWI/SNF chromatin remodeling ATPases SMARCA4 and SMARCA2 through mutation and epigenetic silencing, respectively. This study aims to establish gene expression profiles of this cancer through RNA-Seq of fourteen pathologically confirmed cases of SCCOHT tumors.

  Study phs001528

• Genetics of Schizophrenia in an Ashkenazi Jewish Case-Control Cohort

  Schizophrenia is characterized by high heritability (~80%), yet the identification of susceptibility genes has proven extremely challenging. The Ashkenazi Jewish population, derived from a limited number of founders, may be enriched for a subset of susceptibility alleles, which may also have higher odds ratios than those detected by previous studies. GWAS was conducted in a large Ashkenazi case-control cohort, derived from the Hebrew University Genetic Resource, using the Illumina HumanOmni1-Quad BeadChip.

  Study phs000448

• Stand Up 2 Cancer (SU2C) Genomics-Enabled Medicine for Melanoma (GEMM) Trial

  The goal of the GEMM Trial is to ascertain if comprehensive and systematic interrogation of a patient's tumor molecular profile improves outcomes compared to the current practice of physician's choice for metastatic melanoma patients who have progressed following first line therapy. The data shared here includes tumor/normal exome and tumor RNAseq data for the trial patients, as well as archival data for a subset of patients.

  Study phs001786

• OICR: Molecular Pathological Epidemiology of Colorectal Cancer

  Colorectal cancer, the second most commonly diagnosed cancer, is a biologically heterogeneous disease. To characterize the molecular attributes of colorectal tumors, we conducted targeted sequencing at the Ontario Cancer Research Institution (OICR) of tumor and matched normal DNA samples from 2,542 colorectal cancer cases in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) [phs001078] and the Colon Cancer Family Registry (CCFR). These consortia are based on cohort and population-based case-control studies.

  Study phs002050

• Reference Profiles of ExRNAs in Normal Human Pregnancy

  In this study, we did a comprehensive exRNA profiling of plasma and serum specimens from healthy pregnant women, sampled at different gestational time points, and including subjects with diverse geographical and ethnic backgrounds. This study also contains samples from male and female healthy donors to provide a baseline. The aim of this study is to identify miRNAs that can predict the gestation age and to build a miRNA profile across gestation using small RNA-seq data.

  Study phs003182

• Mobile Technology to Identify Mechanisms Linking Genetic Variation and Depression in Intern Health Study (IHS)

  The Intern Health Study is an NIH-funded longitudinal cohort study that assesses stress and mood in medical interns at institutions around the US, enrolling over 3000 new interns each year. We are hopeful that data collected in this study will further understanding of the psychological, genetic, and program factors involved in the development of depression under stress, and make a real change in the residency experience.

  Study phs001826

• Germline Sequencing for Aggressive Prostate Carcinoma

  This study aims to elucidate the genetic determinants of susceptibility to aggressive prostate carcinoma. To this end, germ line whole exome sequence has been generated from patients with aggressive prostate cancer. Whole genome sequence for a representative subset of tumors from patients whose cancer was resistant to primary therapy is included as well. This deep genomic interrogation will allow the identification of rare, functionally disruptive variants that may play a role in disease progession and response to treatment.

  Study phs000661

• Correlates of Human Nerve Repair

  This is a longitudinal prospective cohort study in patients with carpal tunnel syndrome undergoing decompression surgery. Phenotypic data and skin biopsies were collected before and 6 months after surgery to determine molecular and cellular correlates associated with neural regeneration and neuropathic pain. RNA sequencing was performed in the skin samples and differential gene expression was determined post compared to pre surgery. The molecular changes identified in skin were correlated with the clinical phenotype representing neural regeneration.

  Study phs001796

• Extracellular microRNA Biomarkers for Diagnostic and Prognostic Assessment of Preeclampsia at Triage

  This study is comprised of samples from 123 donors (71 cases and 52 controls) undergoing evaluation for preeclampsia. All samples were collected between 20 and 40 weeks of gestation. Small RNA sequencing was done on serum RNA obtained from donors. We were able to identify 3 bivariate extracellular miRNA biomarkers that can enable early diagnosis of preeclampsia. The raw fastq small-RNA sequencing fastq files will be submitted to dbGaP.

  Study phs003169

• Ataxia Gene Identification by Integrated Genomic Analysis

  Ataxias are a group of diseases that result in a lack of coordinated muscle movement. Hereditary ataxias are genetically heterogeneous and it is reported that 40% of suspected genetic ataxias currently have an unknown cause. We used exome sequencing to detect mutations responsible for ataxia. We sequenced, when available, multiple individuals per family to identify family specific mutations and further confirmed segregation of variants using samples from available affected and unaffected family members.

  Study phs000757

• Genetics and Pathophysiology of Autoinflammatory Disorders

  In this study, patients with suspected disorders of inflammation and innate immune system dysregulation will undergo whole exome sequencing. This will involve both family studies (often trios or multiplex families including affected and unaffected individuals) and sporadic cases. The overall objective is to discover rare/novel high-penetrance mutations in genes that have not yet been implicated as the cause of monogenic autoinflammatory diseases. The aim also includes discovery of variants associated with inflammatory disease susceptibility.

  Study phs001860

• Airway Epithelial Cell Culture RNA Expression

  This study seeks to characterize airway epithelial mRNA and miRNA expression under a variety of experimental conditions. Samples are available from primary human cell cultures as well as cell lines grown under a variety of experimental conditions as documented in the phenotype and conditions associated with each individual sample. For some experiments, cells on plastic were exposed to cigarette smoke condensate to evaluate the effects of smoking. FOSL1 is a target gene for regulation by MIR34A family microRNAs.

  Study phs002472

• Genetic Analysis of Syndromic Orofacial Clefting

  The goal of this study is to identify previously unknown genetic causes of human syndromic cleft lip/palate by using genome sequencing. Many previous studies have shown that isolated cleft lip and/or palate are not often likely to be monogenic or Mendelian diseases. We hope that by focusing on syndromic presentations, we will find novel causes of disorders which include orofacial clefting among their phenotype(s). Data provided will be fastq files from sequencing partners.

  Study phs002997

• 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

• Panel sequencing of endocrine-resistant breast cancer

  Patients with endocrine-resistant breast cancer in Stockholm Sweden. DNA obtained from patients primary and relapse tumors, and tumor-free lymph nodes used as germline control. DNA was extracted from formalin-fixed paraffin-embedded tissue and sequenced by 370-gene panel-based sequencing with Kapa HyperPlus library preparation and Twist Bioscience hybrid capture. Custom bait sets (panels) from Twist Bioscience. Paired end 2x150 bp using NovaSeq X. The data is presented as fastq-files.

  Study EGAS50000000236

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  Colorectal cancer (CRC) is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. To understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary CRCs in a population-based cohort with long-term follow-up. This study constitutes the largest integrated genome and transcriptome analysis of CRC to date, and links mutations, gene expressions and patient outcomes.

  Study EGAS50000000124

• Systematic Identification of Minor Histocompatibility Antigens Informs Outcomes after Allogeneic Stem Cell Transplantation

  This study cohort is composed of 287 patients affected by myeloid disease (AML/MDS) who were subjected to allogeneic hematopoietic cell transplantation (allo-HCT) from an HLA-matched related donor. For each study subject, we have collected genomic DNA from both donor and recipient (D-R). Resulting germline whole exome sequencing from D-R pairs has formed the basis for applying an analytical pipeline to systematically predict minor histocompatibility antigens (mHAgs)

  Study phs003394

• CIDR: Molecular Pathological Epidemiology of Colorectal Cancer

  Colorectal cancer, the second most commonly diagnosed cancer is a biologically heterogeneous disease. To characterize the molecular attributes of colorectal tumors, we conducted targeted sequencing at the Center for Inherited Disease Research (CIDR) on 4,518 tumor and matched normal DNA samples from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colon Cancer Family Registry (CCFR). These consortia are based on cohort and population-based case-control studies.

  Study phs001905

• Circulating tumour DNA (ctDNA) data of High Grade Serous Ovarian Cancer Patients

  This study contains circulating tumour DNA (ctDNA) data derived from longitudinal plasma samples of High Grade Serous Ovarian Cancer (HGSC) patients belonging to the DECIDER study (NCT04846933). Ovarian cancer kills more than 40 000 women in Europe each year, and HGSC is the most common and most difficult to treat subtype of this disease. This study contains different sequencing datasets with samples from different stages during the treatment of the patients.

  Study EGAS50000000674

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

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

  Study phs003648