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• Nanopore whole genome sequencing data of human PGT samples

  Data generated from embryo trophectoderm biopsies and corresponding parental blood samples

  Study EGAS50000000553

• Nouscom Data Access Committee

  The Data Access Committee reviews and approves data access requests for "WES Analysis of precancerous lesions in Lynch Syndrome" study, ensuring compliance with participants’ consent and institutional ethical regulations.

  Dac EGAC50000000784

• JAK and STAT alterations in CD30 positive LPD

  JAK and STAT alterations in CD30 positive LPD, panel sequencing, 12 cutaneous lymphoma patients, 40 samples

  Dataset EGAD00001005801

• Additional Sanger Sequencing and qPCR data to PSCNL samples

  Sanger sequencing and RT-qPCR data for validation used in Primary lymphomas of the central nervous system (PCNSL).

  Dataset EGAD00001008583

• Organoid Derivation Project WGS: Release 2

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

  Dataset EGAD00001005955

• Organoid Derivation Project TGS: Release 2

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

  Dataset EGAD00001004999

• Organoid Derivation Project WGS: Release 1

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

  Dataset EGAD00001005000

• Organoid Derivation Project TGS: Release 3

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

  Dataset EGAD00001005958

• MIBS MGS

  Metagenomic sequencing of the human gut in Maastricht IBS studies, cases and controls.

  Study EGAS00001001924

• UK10K COHORT IMPUTATION

  Imputation panel created from UK10K_COHORT_ALSPAC (EGAD00001000740) and UK10K_COHORT_TWINSUK (EGAD00001000741) datasets.

  Study EGAS00001000713

• Ulcerative colitis study - WES data

  Whole Exome Sequencing data of Single crypts, bulk crypt samples, and colitis-associated cancer.

  Study EGAS00001003801

• scRNAsequencing of in vitro expanded limbal stem cells of aniridia donors

  Identifying potential heterogeneity and expression differences within Aniridia limbal stem cells.

  Study EGAS00001007397

• Parkinson's Families Project

  SNP array data of 698 individuals with early onset and/or familial Parkinson's disease.

  Study EGAS00001007906

• An isoform quantitative trait locus in SBNO2 links genetic susceptibility to Crohn’s disease with defective antimicrobial activity

  Despite major advances in linking single genetic variants to single causal genes, the significance of genetic variation on transcript-level regulation of expression, transcript-specific functions, and relevance to human disease has been poorly investigated. Strawberry notch homolog 2 (SBNO2) is a candidate gene in a susceptibility locus with different variants associated with Crohn’s disease and bone mineral density. The SBNO2 locus is also differentially methylated in Crohn’s disease but the functional mechanisms are unknown. Here we show that the isoforms of SBNO2 are differentially regulated by lipopolysaccharide and IL-10. We identify Crohn’s disease associated isoform quantitative trait loci that negatively regulate the expression of the noncanonical isoform 2 corresponding with the methylation signals at the isoform 2 promoter in IBD and CD. The two isoforms of SBNO2 drive differential gene networks with isoform 2 dominantly impacting antimicrobial activity in macrophages. Our data highlight the role of isoform quantitative trait loci to understand disease susceptibility and resolve underlying mechanisms of disease. This dataset contains RNAseq raw data from CD14+ monocyte-derived macrophages and siRNA-mediated knockdown experiments, as well as RNAseq raw data from THP-1 monocytes-derived macrophages following ectopic expression of SBNO2 isoforms.

  Dataset EGAD50000000264

• Gene Expression in an African American Schizophrenia Dataset

  Schizophrenia is a common and severe psychotic disorder. While some common SNPs and rare copy number variants have been identified as being significantly associated with disease risk, the biological mechanisms remain largely undefined. To identify gene expression abnormalities in schizophrenia, we generated whole-genome gene expression profiles using RNAseq on lymphoblastoid cell lines from schizophrenia cases and controls of African American ancestry. Genes related to immune processes were enriched in the genes differentially expressed in the schizophrenia cases. Approximately half of the differentially expressed genes in this African American dataset were also differentially expressed by affection status in our previously studied European ancestry dataset (PMID: 28418402).

  Study phs002842

• FaceBase Study of Facial Shape in Tanzania: CIDR

  The goals of this project are to identify loci that underlie major genetic determinants of orofacial shape, by means of a GWAS in a cohort of normal African children (from Tanzania) from whom we have collected 3D digitized facial morphometric scans, and a subsequent replication study of normal children from the same population. These studies are part of the NIDCR FaceBase initiative (https://www.facebase.org/). In addition to dbGaP, all study genotype and phenotype data (including primary facial scans and landmarks) will be available for data-sharing with qualified investigators via the NIDCR FaceBase Hub (www.facebase.org/), following approval by the NIDCR FaceBase Data Access Committee.

  Study phs000622

• Single-Cell RNA-Sequencing Analysis of Responses to Pembrolizumab in Sezary Syndrome

  This phase 2 single arm clinical trial assessed the efficacy of pembrolizumab in patients with previously treated mycosis fungoides or Sezary syndrome. Pembrolizumab was found to have a 38% overall response rate, and a 27% overall response rate in subjects with Sezary syndrome. We performed single-cell RNA-sequencing on samples collected before the first treatment and after 3 weeks of pembrolizumab treatment. Sequencing was performed on cryopreserved peripheral blood T-lymphocytes isolated from 6 trial participants, including 3 patients who responded to pembrolizumab treatment and 3 patients who did not respond. A total of 118,961 peripheral blood T-cells are included in this data set.

  Study phs002933

• GWAS in Fibrosing Interstitial Lung Disease

  This study was a case-control genome-wide association study of 1616 non-Hispanic white cases and 4683 controls. Under an additive model for the minor allele at each SNP, we identified 19 SNPs, representing 7 chromosomal locations (5p15, 6p24, 7q22, 11p15, 15q14-15, 17q21, and 19p13), with genome-wide significant (P < 5x10-8) associations using the discovery samples included in this submission. We genotyped the 19 genome-wide significant SNPs in addition to 178 SNPs with 5x10-8 < P-value <.0001 and found 4 additional loci (3q26, 4q22, 10q24, and13q34) with genome-wide significant SNPs in the meta-analysis.

  Study phs000751

• Massachusetts General Hospital/Eisai National Institute of Mental Health (NIMH) Genetics Initiative Alzheimer's Disease GWAS - Affymetrix GeneChip Human Mapping 500K Array Set

  This study cohort was collected as part of the National Institute of Mental Health (NIMH) Alzheimer's disease Genetics Initiative Study. Recruitment of families, predominantly sibling, for the cohort was focused on local memory disorder clinics, nursing homes, and the surrounding community. Clinical evaluation was performed at the University of Alabama at Birmingham, Johns Hopkins University, and Massachusetts General Hospital/Harvard Medical School. Informed consent was obtained from all study participants, for participants with extensive cognitive impairment, a legal guardian or caregiver with power of attorney provided consent. To determine age of onset, a creditable informer was interviewed and medical records were evaluated.

  Study phs000483

• Genetics of Male Infertility Initiative (GEMINI)

  The Genetics of Male Infertility Initiative (GEMINI) project is a multi-center study designed to discover and characterize genetic variants conferring risk for male infertility. Patients enrolled in GEMINI have been clinically diagnosed with male infertility. Patients are recruited from multiple medical centers and are primarily of European ancestry. DNA from each patient is extracted from peripheral blood or saliva and used for exome sequencing. Genetic data generated by the GEMINI project has contributed to the discovery of over a dozen genes involved in human infertility. A VCF file of genetic data from GEMINI patients that have been appropriately consented will be available through dbGaP.

  Study phs003115

• Lysosomal Disease Network (LDN6719) Immune Response to Intrathecal Enzyme Therapy in Mucopolysaccharidosis 1 Patients

  In this study we characterized the immune response to intrathecal (IT) recombinant human alpha-L-iduronidase (rhIDU) in mucopolysaccharidosis I (MPS I) subjects with spinal cord compression who had been previously treated with intravenous rhIDU. Concentrations of specific antibodies and cytokines were measured in serum and cerebrospinal fluid (CSF) collected before monthly IT rhIDU infusions. These serologic findings were compared with clinical adverse event (AE) reports to establish temporal correlations with clinical symptoms. We found that IT rhIDU was generally well tolerated in the subjects studied although one subject had moderate to severe clinical symptoms and serologic abnormalities consistent with an immune response.

  Study phs000862

• Genomics of Relapsed Small Cell Lung Cancer Progression

  Small cell lung cancer (SCLC) accounts for nearly 15% of all patients with lung cancer. Though the response to initial therapy is favorable in many patients, a majority of patients go on to develop recurrent disease which is very difficult to treat. The response rates to chemotherapy are very low and most patients succumb to relapsed SCLC within a few months. Virtually no progress has been made in the treatment of SCLC in the last three decades. In order to better understand the molecular alterations in relapsed SCLC, we have generated exome and RNA sequence from normal, primary tumor and relapse tissues of SCLC patients.

  Study phs001049

• Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

  Patients with metastatic urothelial cancer (n=29) were treated with atezolizumab (anti-PD-L1). All 29 patients had T-cell receptor sequencing (TCR-seq) of the pre-treatment blood; 24 also had TCR-seq on at least one post-treatment blood sample. 24 patients had TCR-seq of their pre-treatment tumors. TCR-seq data can be found at http://doi.org/10.5281/zenodo.546110. 26 patients also had RNAseq of their tumors and whole exome sequencing (WES) of their tumors and matched normal blood. WES results for one sample were excluded from our analysis after failing to meet coverage requirements.

  Study phs001743

• PAX4 loss of function increases diabetes risk by altering human pancreatic endocrine cell development

  The coding variant (p.Arg192His) in the transcription factor PAX4 is associated with an altered risk for type 2 diabetes (T2D) in East Asian populations. In mice, Pax4 is essential for beta cell formation but its role on human beta cell development and/or function is unknown. Participants carrying the PAX4 p.His192 allele exhibited decreased pancreatic beta cell function compared to homozygotes for the p.192Arg allele in a cross-sectional study in which we carried out an intravenous glucose tolerance test and an oral glucose tolerance test. In a pedigree of a patient with young onset diabetes, several members carry a newly identified p.Tyr186X allele. In the human beta cell model, EndoC-βH1, PAX4 knockdown led to impaired insulin secretion, reduced total insulin content, and altered hormone gene expression. Deletion of PAX4 in human induced pluripotent stem cell (hiPSC)-derived islet-like cells resulted in derepression of alpha cell gene expression. In vitro differentiation of hiPSCs carrying PAX4 p.His192 and p.X186 risk alleles exhibited increased polyhormonal endocrine cell formation and reduced insulin content that can be reversed with gene correction. Together, we demonstrate the role of PAX4 in human endocrine cell development, beta cell function, and its contribution to T2D-risk.

  Dataset EGAD50000000516

• WES in muscle-invasive bladder cancer (MIBC) treated with durvalumab plus olaparib in the neoadjuvant setting: NEODURVARIB trial

  This submission contains the metadata derived from the whole exome sequencing of 70 samples from 26 patients who developed advanced urothelial carcinomas. The patients were enrolled in the Neodurvarib clinical trial, which compares the molecular profiles at diagnosis and after neoadjuvant treatment with Durvalumab and Olaparib. In this regard, the analyzed samples include: normal tissue and tumoral tissue obtained from the transurethral resection of the bladder (TURBT, a procedure performed prior to neoadjuvant therapy) from the 26 patients (52 samples), as well as tissue obtained from the radical cystectomy (a procedure performed after treatment with the aforementioned drugs; 18 samples).

  Study EGAS50000000791