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• Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification (H021)

  Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.

  Study EGAS00001006706

• WTCCC case-control study for Multiple Sclerosis

  WTCCC genome-wide case-control association study for Multiple Sclerosis (MS) using the 1958 British Birth Cohort collection as controls.

  Study EGAS00000000022

• WTCCC case-control study for Breast cancer

  WTCCC genome-wide case-control association study for Breast cancer (BC) using the 1958 British Birth Cohort collection as controls.

  Study EGAS00000000024

• WTCCC case-control study for Ankylosing Spondylitis

  WTCCC genome-wide case-control association study for Ankylosing Spondylitis (AS) using the 1958 British Birth Cohort collection as controls.

  Study EGAS00000000018

• Targeted sequencing analysis for MDS with HSCT

  Targeted capture sequencing for cases with MDS who were subjected to unrelated bone marrow transplantation via Japan marrow donor program

  Study EGAS00001001949

• DynaTag for efficient profiling of transcription factors in small samples and single cells

  The dataset included Dynatag data for the occupancy of transcription factors and single nuclei RNA-seq data. Corresponding metadata is provided for both experiments.

  Dataset EGAD50000001562

• cfDNA dataset for cfDNA cohort

  Cell free DNA sequencing data for 233 samples across multiple cancer types for cfDNA cohort

  Dataset EGAD50000000104

• Identifying novel DNA damage response genes in radiosensitive individuals

  Ionizing radiation is an effective therapeutic agent for cancer treatment as well as a potent carcinogen. Sensitivity to the cell-killing effects of radiation can vary across human population with a subset of individuals displaying extreme hypersensitivity. It is usually attributable to inherited defects in DNA damage response pathways. The present study was designed to elucidate the genetic basis of variation in hypersensitivity to radiation exposure through exome sequencing of radiosensitive individuals, with the ultimate goal of identifying genes with the most significant effects on cellular DNA damage responses. The study participants included subjects referred for clinical testing for Ataxia-telangiectasia (A-T), Nijmegen Breakage Syndrome (NBS) or Ligase IV Syndrome. These are rare, recessive genetic disorders and hypersensitivity to radiation exposure is a common phenotype among individuals affected by all the three disorders. The study participants exhibited phenotypic characteristics similar to individuals with A-T, NBS or Ligase IV Syndrome, but lacked the causative mutations in ATM (GeneID:472) or NBN (GeneID:4683) genes. For further validation of the radiation sensitivity phenotype among the enrolled subjects, B-lymphoblastoid cells lines were established for each subject from peripheral blood lymphocytes. Each cell line was evaluated for displaying impaired survival rates relative to normal controls after exposure to ionizing radiation. 53 subjects with validated phenotype were finally included in the study and DNA extracted from their B-lymphoblastoid cell lines was used for exome sequencing. This sequencing data for radiation sensitive subjects is being made available in the dbGaP. It is hoped that this resource will be beneficial for researchers who wish to further investigate components of human cellular DNA damage response pathways and/or genetic architecture underlying radiation hypersensitivity. This data may also aid in the rational design of new radiosensitizing or radioprotective agents.

  Study phs001911

• Optimizing Primary Stroke Prevention in Children with Sickle Cell Anemia (STOP II)

  The STOP II trial evaluated whether prophylactic transfusion in patients with sickle cell disease and high risk of stroke can be safely halted after 30 months of treatment during which patients became low risk for stroke.Stroke causes substantial morbidity in children with sickle cell disease. To prevent first strokes, the Stroke Prevention Trial in Sickle Cell Anemia (STOP) used prophylactic transfusions in children who were identified by transcranial Doppler (TCD) ultrasonography as being at high risk for stroke. This strategy reduced the incidence of stroke among such children from 10% per year to less than 1% per year, leading to recommendations for TCD screening and prophylactic transfusion for children with abnormal velocities on ultrasonography. Despite the reduced risk of stroke, long-term use of transfusions can cause adverse side effects, such as iron overload or alloimmunization. However, cessation of transfusions is associated with recurrence of stroke, and at the time of the STOP II trial, there were no clinical or laboratory indicators to guide the duration of prophylaxis. Therefore the STOP II trial was initiated to determine whether transfusions could be limited by monitoring patients with TCD examinations after transfusions were halted and resuming transfusions if the examination indicated a high risk of stroke.The trial was halted for safety concerns after 79 of a planned 100 children were randomized. Discontinuation of transfusion for the prevention of stroke in children with sickle cell disease resulted in a high rate of reversion to abnormal blood-flow velocities on Doppler studies and stroke incidence.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 phs002386

• DAC for access to anonymised study data for UK and Norwegian AAD families

  Dac EGAC00001000333

• monozygotic twin discordant for schizophrenia

  monozygotic twin discordant for schizophrenia

  Dataset EGAD00001000048

• Biomarkers for Noise-Induced Sleep Disruption

  This project aims to investigate gene expression biomarkers for noise-induced sleep disruption and cognitive changes. The project is a sub-study, part of the larger ASCENT COE project 86 designed to test the ability of broadband pink noise to serve as a countermeasure for sleep loss from simulated aircraft noise. Gene expression research was sponsored by the Federal Aviation Administration.

  Study phs003932

• Patient-derived organoids as predictive models for drug testing and repurposing in glioblastoma therapy

  Glioblastoma multiforme (GBM) remains a highly aggressive brain tumor with limited treatment options and poor prognosis. Temozolomide (TMZ) is the only approved first-line therapy, but frequent resistance limits its efficacy, highlighting the urgent need for alternative treatments. Patient-derived glioblastoma organoids (GBOs) offer a promising preclinical model for personalized drug testing and therapy development.

  Study EGAS50000001221

• RNA004 DRS METTL5 variant of patient sample

  This dataset contains RNA004 DRS data for a single patient sample with heterozygous inactivating SNPs for the methyltransferase METTL5. We provide 1) all reads in a GRCh38 aligned bam file + unaligned reads and 2) filtered reads just for the relevant part of chrR. Both bam files have been called with dorado 0.7.2 to contain the neccessary m6A methylation information. Companion datasets are 1) EGAS50000001201 for DRS of a healthy control with intact METTL5 and 2) PRJEB74238 for IVT 18S rRNA vector data as unmodified control. Please note, that both the companion datasets contain pod5 data, to faciliate re-basecalling.

  Dataset EGAD50000001882

• Capture-based Methods for Transcriptomic Profiling of FFPE material

  This dataset includes all FASTQ files for 11 samples where different capture-based methods for transcriptome profiling have been tested. Specifically, we have the 'traditional' RNA-seq experiment with fresh frozen (FF) material, and 3 different capture methods for the matching formalin-fixed paraffin-embedded samples: Agilent (AGI), IDT, and Twist Biosciences (TBS). In total, there are 43 samples with paired-end FASTQ files (1 sample did not have sufficient material to test all methods). Samples are identified by the R01-R11 IDs with a suffix that indicates the capture method used (or FF for fresh frozen).

  Dataset EGAD00001007655

• RNAseq of baseline tumor tissue obtained during TUR to identify biomarkers for ICB response in MIBC

  RNAseq of baseline tumor tissue obtained during TUR to identify biomarkers for ICB response in MIBC. Constitutes the entire NABUCCO phase 1B clinical trial cohort. The NABUCCO 1 trial contains 18 single-end RNA sequenced samples and 6 paired end RNA sequenced samples. The NABUCCO 2 trial contains 25 paired end RNA sequenced samples. The file type for all of the samples is FASTQ. For single end RNA sequencing, Illumina HiSeq 2500 was used as the sequencing platform. For paired end RNA sequencing, the Illumina NovaSeq 6000 was used as the sequencing platform.

  Dataset EGAD50000002556

• 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

• Neuropsychiatric Genetics of African Populations - Psychosis (NeuroGAP-Psychosis)

  The NeuroGAP-Psychosis study was conducted in South Africa, Kenya, Uganda and Ethiopia as a response to the lack of genetic diversity in large genomic studies of psychiatric disorders. The study aims to expand knowledge of the genetic and environmental risk factors for neuropsychiatric disorders in Africa through large-scale sample collection and analysis. The initial design is a case-control study in which cases are individuals with schizophrenia or bipolar disorder and controls are age, sex and ancestry matched with individuals from the same geographic location. Cases are patients who are recruited from clinical facilities, both inpatient and outpatient. Controls are people who present for treatment for general medical conditions at health facilities. Data on phenotype, mental disorders, history of physical health problems, substance use and history of past traumatic events was collected from all participants. Additionally, a sample of saliva is collected for DNA extraction. DNA samples were sent to the Broad Institute for genotyping using Illumina Infinium Global Screening Array.  

  Study phs002528

• Genome-wide Identification of Variants Affecting Early Human Brain Development

  This is a genome-wide association study (GWAS) of global brain tissue volumes in human infants. The published study for this project includes 561 infants, and 239 parents gave consent for data sharing through dbGaP. An intronic single-nucleotide polymorphism (SNP) in IGFBP7 (rs114518130; GeneID: 3490) met genome-wide significance for gray matter volume (P=4.15x10-10). An intronic SNP in WWOX (rs10514437; GeneID: 51741) neared genome-wide significance for white matter volume (P=1.56x10-8). Additional loci with small P-values include psychiatric GWAS associations and transcription factors expressed in the developing brain. Genetic risk scores for schizophrenia and ASD, and the number of genes affected by rare copy number variants (CNV burden) did not predict global brain tissue volumes. Integrating these results with large-scale GWAS in adolescents [Philadelphia Neurodevelopmental Cohort (PNC)] and adults [Enhancing Neuro Imaging Genetics through Meta-Analysis version 2 (ENIGMA2)] suggested minimal overlap between common variants impacting brain volumes at different ages.

  Study phs001122

• Single-cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation

  GABAergic interneurons are essential for neural circuit function and their loss or dysfunction is implicated in human neuropsychiatric disease. In vitro methods for interneuron generation hold promise for studying human cellular and functional properties and ultimately therapeutic cell replacement. We used a protocol for generating cortical interneurons from hESCs and analyzed the properties and maturation timecourse of cell types using single-cell RNAseq (data available at GEO under: GSE93802 on March 10 2017). Transcriptomic profiles of the hESC-derived interneurons were compared to several different populations of cells from mid-gestation human neocortex that showed differing levels of PAX6 and SOX2 expression. For this study, 104 samples of 100 human neocortical cells each, have been sorted based on SOX2 and PAX6 expression, mRNA recovered from the fixed cells by FRISCR, and transcriptomic profiles generated by SmartSeq2. The RNA-seq data from the 104 100-cell samples is included in this dbGaP study.

  Study phs001276

• CRISPR transduction of iPS cells

  Genome engineering using CRISPR/Cas9 technology enables simple, efficient and precise genomic modifications in human cells. Conventional immortalized cell lines can be easily edited or screened using genome-wide libraries with lentiviral transduction. However, cell types derived from the differentiation of induced Pluripotent Stem Cells (iPSC), which often represent more relevant, patient-derived models for human pathology, are much more difficult to engineer as CRISPR/Cas9 delivery to these differentiated cells can be inefficient and toxic. Here, we present an efficient, lentiviral transduction protocol for delivery of CRISPR/Cas9 to macrophages derived from human iPSC with efficiencies close to 100%. We demonstrate CRISPR/Cas9 knockouts for three non-essential proof-of-concept genes - HPRT1, PPIB and CDK4. We then scale the protocol and validate for a genome-wide pooled CRISPR/Cas9 loss-of-function screen. This methodology enables, for the first time, systematic exploration of macrophage involvement in immune responses, chronic inflammation, neurodegenerative diseases and cancer progression, using efficient genome editing techniques.

  Study EGAS00001005102

• The EVE Asthma Genetics Consortium: Building Upon GWAS

  The EVE Asthma Genetics Consortium comprises U.S. investigators who have conducted genome-wide association studies (GWAS) of asthma; the main objective is to combine results of individual studies to increase the overall power to identify loci for asthma and asthma-associated traits. The consortium includes investigators at 9 U.S. institutions with GWAS results for >10,000 individuals representing European American, African American, African Caribbean, U.S. Hispanic, and Mexican populations and includes the following studies: The Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE) The Genetic Research on Asthma in the African Diaspora (GRAAD) Study The Genetics of Asthma in Latino Americans (GALA 1) Study The Childhood Asthma Management Program (CAMP) The Childhood Asthma Research and Education (CARE) Network The Children's Health Study (CHS) Mexico City Childhood Asthma Study (MCCAS) The Chicago Asthma Genetics Study (CAG)* The National Heart, Lung, and Blood Institute Collaborative Studies of the Genetics of Asthma (CSGA)* The Severe Asthma Research Program (SARP)* (*CAG, CSGA, and SARP are part of the NHLBI-supported SNP Typing for Association with Multiple Phenotypes from Existing Epidemiologic Data (STAMPEED) consortium.) For the GWAS, we developed a common set of >1 million genotyped and imputed SNPs from the EVE Asthma Genetics Consortium to be tested for association with asthma and associated phenotypes in all samples and combined p-values for a grand meta-analysis for asthma gene discovery. A subset of 296 individuals representing African American, European American, and Latino ancestry were selected for whole genome sequencing. The broad goals of this project were to characterize the genetic architecture of asthma and associated quantitative phenotypes (e.g., lung function, total serum IgE) in ethnically diverse populations from the U.S., Mexico, Puerto Rico, and Barbados.

  Study phs001156

• Heart and Vascular Health Study (HVH)

  Objectives The Heart and Vascular Health Study (HVH) is a case-control study of risk factors for the development of myocardial infarction (MI), stroke, venous thrombosis (VT), and atrial fibrillation (AF). The study setting is Group Health, an integrated health care delivery system in Washington State. Background The HVH originated in 1988 with the examination of risk factors for MI. Over the ensuing years, the study has been funded by a series of grants, which have added case subjects with stroke, VT, and AF, and used a common control group. Study aims have focused on the associations of medication use with cardiovascular events. Starting in 1997, the study aims expanded to include genetic associations with cardiovascular disease. Participants recruited in 2009 or later and who provided blood samples for genetic analysis were asked for consent to deposit genetic and phenotype data in dbGaP. Design As part of the HVH study, case subjects were identified by searching for ICD-9 codes consistent with MI, stroke, VT, or AF, and medical records were reviewed to confirm the diagnosis. Control subjects were identified at random from the Group Health enrollment and were matched to MI cases. All subjects have an index date. For cases, the index date was assigned as the date that the cardiovascular event (MI, stroke, VT, or AF) came to clinical attention. For controls, the index date was a random date within the range of the case index dates. For both cases and controls, information was collected from the inpatient and outpatient medical record, by telephone interview with consenting survivors, and from the Group Health pharmacy and laboratory databases. Consenting participants provided a blood specimen. Genetic Research Genetic factors underlying cardiovascular disease are studied using DNA isolated from the blood samples.

  Study phs001013

• Transcriptional Response to Hypoxia in iPSC-Derived Endothelial Cells from a High Altitude Adapted Population

  We established lymphoblastoid cell lines from 10 adult individuals of Tibetan ancestry living in the Chicago area. These lines were reprogrammed to induced pluripotent stem cells (iPSC). We validated genetic ancestry by genome-wide SNP array genotyping and population genetic analyses. After being subjected to standard quality control testing iPSCs were differentiated into endothelial cells. Following differentiation, endothelial cells were isolated via a pull down protocol using beads coated with an antibody for a canonical surface cell marker of the vascular endothelium (CD144). Purified vascular endothelial cells were cultured in parallel in normoxia (20% O2) and hypoxia (1% O2) for 48 hours prior to harvesting and processing for bulk RNA-sequencing. We provide imputed genotype data and bulk RNA-sequencing data in normoxia and in hypoxia for each of the 10 individuals. We also provide multiplexed scRNA-sequencing data for the 10 Tibetan individuals pooled with 10 CHB individuals from the 1000 Genome Project. Additionally, we provide scRNAseq data for the cardiomyocytes derived from the same iPSC lines from the Tibetan individuals pooled together with cardiomyocytes derived from iPSC lines of 10 CHB individuals from the 1000 Genome Project. Lymphoblastoid cell lines from the CHB were reprogrammed to iPSCs and differentiated to cardiomyocytes using the same protocols as used for the Tibetans. The batches of 4 lines were balanced by sex and population. These iPSC-derived cardiomyocytes were cultured in hypoxia (1% O2) for 48 hours and subjected to scRNAseq in pooled batches of 3 or 4 lines. The CHB individuals included in this analysis were: NA18528, NA18531, NA18557, NA18596, NA18606, NA18608, NA18614, NA18619, NA18633, and NA18748.

  Study phs003758

• Accurate detection and classification of pediatric sarcomas based on cell-free DNA fragmentation patterns

  Sequencing of cell-free DNA in the blood of cancer patients (“liquid biopsy”) provides attractive opportunities not only for early diagnosis, but also for minimally invasive monitoring of treatment response and disease courses. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we developed an integrated genetic/epigenetic analysis method and applied it to 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. We achieved sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. We evaluated different metrics for cell-free DNA fragmentation analysis and developed LIQUORICE, a bioinformatic tool for detecting circulating tumor DNA based on tumor-specific chromatin structure. Using machine learning methods, we combined several fragmentation-based metrics into an integrated approach for liquid biopsy analysis tailored to cancers with low mutation rates but widespread epigenetic deregulation. Clinical associations highlighted the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. Additionally, we performed low coverage whole-genome-sequencing on 43 tumor biopsy samples from patients with Ewing sarcoma, in order to compare copy number aberrations detected in cell-free DNA and biopsy samples of the same patients. For validation of the epigenetic signatures inferred from cell-free DNA, we further performed reduced representation bisulfite sequencing (RRBS) on 38 matched biopsy samples from patients with Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent somatic mutations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.

  Study EGAS00001005127