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• Woodcock et al TenMenDeep Study EGA Dataset B

  Woodcock et al TenMenDeep EGA Dataset B. These are Illumina based deep sequencing data based on bait capture sequencing. See Woodcock et al methods for more detail. Note: the Amplicon sequencing data type is selected because the EGA Website currently has no option to select Bait Capture Sequencing or similar.

  Dataset EGAD00001005382

• Woodcock et al TenMenDeep Study EGA Dataset A

  Woodcock et al TenMenDeep EGA Dataset A. These are Illumina based deep sequencing data based on bait capture sequencing. See Woodcock et al methods for more detail. Note: the Amplicon sequencing data type is selected because the EGA Website currently has no option to select Bait Capture Sequencing or similar.

  Dataset EGAD00001005381

• AfricanNeo WGS aDNA Dataset

  This dataset includes WGS data of 12 ancient individuals (97–688 years BP) from Zambia and South Africa, presented in Fortes-Lima et al. Nature 2023. Further details like C14-dates and archaeological descriptions were reported elsewhere (Meyer et al. Azania 2021; Steyn et al. African Archaeological Review 2022).

  Dataset EGAD00001011320

• scRNA-seq dataset to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Dataset EGAD00001015770

• National Institute of Neurological Disorders and Stroke (NINDS), Family Study of Essential Tremor (FASET), Identification of Susceptibility Genes for Essential Tremor

  The Familial Study of Essential Tremor (FASET) was designed to identify susceptibility genes for Essential Tremor. ET is among the most common neurological diseases with a prevalence (age > 40 years) estimated to be 4.0% and prevalence in advanced age (> 90 years) exceeding 20%. ET, often referred to as "familial tremor", is generally regarded as a highly genetic disorder with families, with affected members over multiple generations, and twin studies show high concordance among monozygotic twins. Probands (affected with ET) and relatives were enrolled in a family study of ET at Columbia University, New York between 2011 - 2014. The study was approved by the Institutional Review Board at Columbia University and written informed consent was obtained from all enrollees. The criteria for enrollment were: 1) the proband had early-onset ET with age at onset < 50 years, 2) the proband had a diagnosis of definite or probable ET, 3) in addition to the proband, there were at least two affected relatives in the family, 4) additional affected and unaffected family members were willing to participate in the study, and 5) the families contained more than two affected individuals in different generations. Blood samples were also collected for genetic research. For the genetic analyses, we excluded enrollees that we or others had diagnosed with Parkinson's disease (PD) or dystonia. The final sample includes 52 families (52 probands [affected with ET]) and 155 relatives). The number of affected individuals enrolled per family ranged from 3 - 7 (mean = 4.1). Genetic samples from FASET were analyzed with whole genome SNP genotyping (for linkage analyses) and whole exome sequencing. It is hoped that this resource will better help researchers to understand the genetic causes of ET and underlying disease pathogenesis.

  Study phs000966

• GWAS results from Danjou et al, Nature Genetics 2015

  GWAS results in epacts format for Danjou et al, Nature Genetics 2015

  Dataset EGAD00010001722

• International Parkinson's Disease Genomics Consortium (IPDGC), NeuroX Dataset

  Expanded replication set based on Nalls et al. 2014.

  Study phs000918

• Pomalidomide for the Treatment of Bleeding in HHT (PATH-HHT)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To determine efficacy (reduction in severity of epistaxis), tolerability, and improvement in quality of life of pomalidomide compared to placebo after 24 weeks of treatment.Background: This study addresses the efficacy of pomalidomide in the treatment of epistaxis in patients with Hereditary Hemorrhagic Telangiectasia (HHT) who have anemia and/or require blood transfusion or iron infusion for treatment of bleeding-induced anemia and iron deficiency. HHT (also known as Osler-Weber-Rendu disease) is an inherited bleeding disorder. Over 95% of patients develop recurrent epistaxis, which may be severe and result in chronic anemia, need for iron infusions and blood transfusions, substantial psychiatric comorbidity (including depression and post-traumatic stress disorder) and reduction in health-related quality of life (HRQoL). HHT is clinically diagnosed using the Curacao criteria, which consists of 1) spontaneous and recurrent epistaxis, 2) telangiectasias at characteristic sites, 3) visceral arteriovenous malformations (AVMs) or telangiectasias, and 4) a first degree relative with HHT (inheritance is usually autosomal dominant). Patients with three criteria are considered to have definite HHT, and those with 2 criteria probable HHT. HHT affects approximately 1 in 3,800 individuals. Significant manifestations of HHT often do not appear until the third or fourth decades, sometimes later.Participants: 144 patients from 11 clinical centers were enrolled.Design: This is a multi-center, double blind, randomized placebo-controlled trial that investigated the efficacy and safety of pomalidomide in patients with HHT and chronic epistaxis leading to iron-deficiency anemia or requiring intravenous iron infusions or blood transfusion.Screening evaluation included the Epistaxis Severity Score (ESS) with three-month recall, which reflected the patient's history of epistaxis and bleeding over the prior three months, as well as detailed review of iron infusion and red cell transfusion over the preceding six months. Eligible patients were provided a diary to record the duration of each epistaxis event that occurred during the 4 weeks prior to the baseline visit, and then returned for the baseline randomization visit, at which time patients underwent genetic testing, if this had not been previously performed, and completed an ESS with 4-week recall and quality of life assessments. Patients were randomized 2:1, stratified by study site, to either pomalidomide 4 mg/day or matching placebo during each of six 28 day cycles (24 weeks). Patients were seen every four weeks during treatment, and at a 4-week post-treatment follow-up visit to measure the ESS (with 4-week recall), laboratory assessments including iron stores and need for iron infusion, CBC, and metabolic profile. Patients were assessed for adverse events (AE) throughout the study. Treatment dosage could be reduced, or temporarily or permanently discontinued following AE-specific guidelines related to fatigue, cytopenias or other toxicities.Quality of life assessments were completed at baseline, and the 12- and 24-week visits, and the 4-week post-treatment follow-up visit using validated NIH instruments of 1) Neuro-QOL satisfaction with social roles and activities, 2) PROMIS emotional distress – depression, and 3) PROMIS fatigue, and the HHT-specific quality of life instrument developed specifically for this study. The effect of pomalidomide on duration of epistaxis was assessed via diary between weeks 8-12, 20-24 and the 4-week post-treatment period.Conclusions: Among patients with HHT, pomalidomide treatment resulted in a significant, clinically relevant reduction in epistaxis severity. No unexpected safety signals were identified (Al-Samkari et al., 2024; PMID: 39292928)

  Study phs003948

• Supraphysiologic MDM2 Expression Impacts P53-Independent Chromatin Networks and Therapeutic Responses in Sarcoma

  We collected multiple liposarcoma samples from different patients, including different subtypes (DD, WD) and normal adipose tissue as control. This study provides the biggest liposarcoma cohort to date, and examined the molecular regulatory circuits associated with MDM2 overexpression. To this end, we obtained not only RNA-seq data, but also ChIP-seq from Jun, RUNX, MDM2, P53 and H3K27ac, as well as hiChIP from tumor samples and cell lines. We found that MDM2 binds to thousands of genes involved in cellular growth and stress response in a P53-independent manner. Furthermore, we described these active genes engaged in multi-way topological interactions that resemble transcriptional hubs.

  Study phs003272

• Maternal and Developmental Risks from Environmental and Social Stressors (MADRES) Center for Environmental Health Disparities

  MADRES is a prospective pregnancy cohort based in urban Los Angeles, recruiting predominantly low income Hispanic mothers-to-be as part of a children's health study, funded by Environmental Influences on Child Health Outcomes (ECHO). Participants were measured for a number of chemical exposures and biomarkers. Two epigenetic markers will be available through dbGaP: miRNA expression in pregnancy (measured via Nanostring human assay, v3) and DNA methylation from pregnancy and children's cord blood (measured via EPIC array). Principal findings of this research described differences in miRNA expression profiles between early and late pregnancy, as well as miRNA expression affected by psychosocial stress.

  Study phs003194

• Whole exome sequencing of SU- DIPG-XIII from different sites

  Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII)

  Dataset EGAD00001003563

• HTAN Pilot Project: Single-Cell Transcriptomics Toolbox for Fresh and Frozen Human Tumors (Lung, Breast, Ovarian, Melanoma, Neuroblastoma, Sarcoma, Glioblastoma, Glioma, and Leukemia)

  Single cell transcriptomics is a powerful tool to map the complex tumor microenvironment, providing unprecedented resolution into cell types, cell states, cell interactions, and tumor heterogeneity. Depending on their tissue site and whether processing begins from a fresh or frozen sample, different tumors require different optimizations in order to obtain high quality single cell transcriptomic data. In this study, we profiled a range of tumor types, varying in cell-of-origin, solid and non-solid forms, patient ages, and transitions. The tumors also further varied in their tissue site and in their sample collection method. To enable profiling of such diverse samples, we developed a systematic toolbox for single cell RNA-Seq and single nucleus RNA-Seq of fresh and frozen clinical tumor samples. We validated this toolbox for 216,490 cells and nuclei extracted from 39 samples across 23 tumors (some tumors were split into multiple samples). The 23 tumors represented eight unique tumor types. This toolbox comprises both experimental and computational protocols as well as guidelines for comparing and selecting protocols for the biological problem of interest.

  Study phs001983

• Somatic Mutations in Individual Skin Cells

  Ultraviolet (UV) radiation is the primary cause of melanoma through the acquisition of driver mutations in melanocytes. It also plays a significant role in oncogenesis in other skin cells, such as keratinocytes. However, the mutational profiles vary widely among different skin cancers, and the early mutational processes in different cell types from the same skin, is not well understood. Additionally, our preliminary studies also suggest that the mutation burden in different skin cells vary significantly based on risk factors such as the anatomical site and the use of tanning beds. To explore this, we employed innovative Next Generation Sequencing (NGS) tools to perform a site-matched comparison of the genomic landscapes of melanocytes, keratinocytes, and fibroblasts. From 20 biopsies of physiologically normal skin, collected from various anatomical sites across 16 donors, we have performed DNA-sequencing on 106 melanocytes, 78 keratinocytes and 13 fibroblasts. Of these samples, we have also simultaneously performed RNA-sequencing on 78 melanocytes, 46 keratinocytes and 9 fibroblasts. For normal bulk DNA, we also performed targeted (UCSF500; n=9) or exome sequencing (n=8) of skin or saliva samples from the donors.

  Study phs003683

• Veilleux et al. Human Subsistance - chemosensory genes

  BAM files from capture-sequencing dataset described in Veilleux et al.

  Dataset EGAD00001010918

• SCLC study Peifer et al. - WES dataset

  SCLC - Whole genome sequencing data Publication Peifer et al., 2012, Nature Genetics

  Dataset EGAD00001000703

• He et al. WGS data

  This dataset are the bam files of WGS data from the paper by He et al.

  Dataset EGAD00001007133

• SCLC study Peifer et al. - RNAseq dataset

  SCLC - RNA sequencing data Publication Peifer et al., 2012, Nature Genetics

  Dataset EGAD00001001431

• Genetics of Cerebral Hemorrhage with Anticoagulation (GOCHA)

  This is a prospective, longitudinal cohort study of spontaneous ICH. Subjects were recruited from among consecutive patients ≥ 55 years old who presented with primary hemorrhage to the Massachusetts General Hospital or one of our off-site collaborators from 1999 to 2010. Potential subjects were identified by screening lists of all admissions to the neurology and neurosurgery inpatient services. All patients underwent routine clinical evaluation, including history taking and physical examination, laboratory testing, and computed tomography of the brain.

  Study phs000416

• Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program – Sarcomas and other Solid Tumors

  The primary goal of this project involves the comprehensive molecular profiling of patient-derived xenograft (PDX) mouse tumor models. Molecular profiling of each PDX model will include whole exome sequencing (WES), RNAseq, MethylEPIC arrays, CytoSNP array, and DNA fingerprint for quality control. Limited clinical demographic data (e.g. diagnosis, disease site, disease status) will be obtained. This data can be utilized to validate PDX models with matched patient tumors and can be used to guide model selection for downstream preclinical drug testing.

  Study phs003161

• Filtered variants including SLC12A2 in patients with hearing loss

  Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss.

  Study JGAS000379

• scRNAseq of human primary nasal epithelium differentiated at air-liquid interface exposed to SARS-CoV2

  The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we applied single-cell RNA sequencing and proteomics to a primary cell model of human primary nasal epithelium differentiated at air-liquid interface.

  Study EGAS00001005633

• University of Illinois at Chicago (UIC) Autism Centers of Excellence (ACE) Exome Sequencing Analysis

  Autism spectrum disorder (ASD) is highly heritable with recent sibling recurrence risk estimates of 19% overall and 26% in males. The heritable phenotype of hyperserotonemia, or elevated levels of platelet serotonin (5HT), in ~35% of people with ASD is a well-established biomarker. The efficacy of drugs like risperidone and potent serotonin transporter inhibitors at treating behaviors related to Insistence on Sameness, along with evidence of the contribution of hyperserotonemia to autism susceptibility collectively support the hypothesis that dysfunction in the 5HT system is a significant etiological target for investigation of the genetic component to autism. ASD genetic architecture is complex; common variants of large effect do not contribute substantially to overall ASD risk, but there are clearly common variants with small effects and rare genetic/genomic variation of larger effect among ASD genetic risk factors. The NIH ARRA Autism Sequencing Consortium, including Dr. Sutcliffe and Dr. Cook among others, has initiated exome sequencing studies to identify more of the rare variants contributing to ASD. Data from our group and others reveal numerous rare de novo and inherited sequence mutations, and the number of de novo and other functional mutations that are found to affect molecules encoding 5HT signaling and its regulation further reinforces our hypothesis that regulation of serotonin levels is important in autism genetic susceptibility. Integrin receptor signaling pathways were prominently featured among identified de novo mutations, thus defining a set of interrelated gene networks that control 5HT signaling. We propose to extend our findings to date by conducting exome sequencing on ACE subjects, for whom we also have 5HT biochemical data, to identify rare variants (including CNVs) in 5HT-related gene networks. In total we propose to have exome sequencing completed on 523 samples. The purpose of the proposed research is two-fold: 1) we will conduct more extensive investigations to determine the support for the hypothesis that genetic variation at genes regulating platelet serotonin levels affect susceptibility to ASD and 2) we will combine the exome sequence data from these studies with sequence data for autism being accumulated in a variety of other research projects to further the goal of identifying and characterizing the genetic component to ASD.

  Study phs000712

• Low-input PCHi-C data in CD4+ T cells

  Low-input PCHi-C data in CD4+ T cells from Malysheva et al.

  Study EGAS50000001316

• Fine Mapping of Eight Psoriasis Susceptibility Loci

  Psoriasis is a common immune-mediate disease identified through scaly patches of the skin. In this study we collected genotype information on 5,067 samples of European ancestry as a follow-up study of our initial GWAS (Nair et al. 2009). We designed an Illumina iSelect custom genotyping array with 2,269 tagging SNPs in the eight known psoriasis susceptibility regions (MHC, IL12B, IL23R, IL23A, TNFAIP3, IL13, RNF114, and TNIP1). The custom array also included 5,463 SNPs outside the eight known susceptibility regions, which were selected based on their association p-values in a meta-analysis of HapMap-imputed genotypes of two published GWAS-CASP (Nair et al. 2009) and (Ellinghaus et al. 2010). After quality control we analyzed 4,806 samples (2,699 cases and 2,107 controls). Please note: The accession number for this dbGaP study was incorrectly listed in the relevant publication (Das et al., 2015, Eur. J. Hum. Genet 23:844-853) as phs000019.v1.p1.

  Study phs001298

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX038_VOA11267_002

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq

  Dataset EGAD00001005165