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• scEC&T-seq manuscript data

  This dataset includes all data produced in the study describing "scEC&T-seq", a method for parallel sequencing of extrachromosomal circular DNA and transcriptome in single cells. This dataset includes: - Illumina scEC&T-seq Circle-seq data (scCircle-seq) for a total of 626 single cells / nuclei - bam files - Illumina scEC&T-seq RNA-seq data (scRNA-seq-Illumina) for the same single cells / nuclei - bam files - Nanopore scCircle-seq data for 18 single cells - bam files - Nanopore bulk WGS for 2 cell lines and 2 primary tumor samples - bam files - Illumina bulk WGS for 2 cell lines - bam files - Illumina bulk Circle-seq data from 1 cell line - bam file - Illumina ChIP-seq H3K27me3 data from 1 cell line - fasta files + peaks bed file + coverage bw file

  Dataset EGAD00001010071

• 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

• Genomics and Methylation of Neuroendocrine Prostate Cancer from cfDNA (Cornell/Trento 2019)

  A subset of castration resistant prostate cancers develop small cell neuroendocrine prostate cancer (NEPC) as a mechanism of treatment resistance. Metastatic tissue biopsies to evaluate for NEPC transformation are invasive and challenging to perform serially. We performed whole exome and whole genome bisulfite sequencing of plasma cfDNA and matched tumor biopsy samples from 62 patients with metastatic prostate cancer along the disease spectrum to evaluate for NEPC associated genomic and epigenomic features. Multiple tissue biopsies and/or plasma time points were included for a subset of patients to characterize disease heterogeneity and dynamic changes. Computational analysis of clonality and allele specific quantification allowed for detailed comparison of matched tumor tissue and cfDNA data (CLONET v2). Methylation profiles detected from tissue and plasma data were compared and NEPC specific alterations were evaluated in cfDNA. The study supports the feasibility of a plasma based assay for the detection of NEPC.

  Study phs001752

• 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

• 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

• Data access committee for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer

  Dac EGAC00001001435

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000162

• WGS DATA FILES FOR SJCBF

  DATA FILES FOR SJCBF

  Dataset EGAD00001000268

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000853

• CGMH data access committee for the CGMH-OCCC-WES data

  CGMH data access committee for the CGMH-OCCC-WES data

  Dac EGAC50000000028

• The data access committee for Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

  Dac EGAC50000000588

• DAC for pediatric AML genomic sequences

  DAC for dataset containing matched tumor-healthy genomic sequences from patients with pediatric AML

  Dac EGAC50000000666

• DAC for DLBCL dataset

  Data Access Committee for cfDNA sequencing dataset from 290 samples from patients with DLBCL and HGBL.

  Dac EGAC50000000257

• DAC for the access to IMMUcan data

  This DAC will assess the requests for the access to IMMUcan data

  Dac EGAC50000000829

• Metastatic_Prostate_Follow_Up_2

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000756

• Metastatic_Prostate_Follow_Up

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000730

• Nrf2 transcript alterations

  WGS and RNA-seq data for Nrf2 study

  Study EGAS00001001740

• Targeted Gene Panel for 171 PTCLs

  Targeted Gene Panel for 171 PTCLs

  Dataset EGAD00001003967

• DATA FILES FOR PCGP SJMEL WXS

  DATA FILES FOR PCGP SJMEL WXS

  Dataset EGAD00001001246

• DATA FILES FOR PCGP SJMEL RNASEQ

  DATA FILES FOR PCGP SJMEL RNASEQ

  Dataset EGAD00001001247

• WGS data for NRF2 study

  WGS data for cell lines and clinical samples

  Dataset EGAD00001002244

• 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

• 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

• The data access committee for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

  Dac EGAC00001003253

• Screening for human epigenetic variation at CpG islands

  Screening for human epigenetic variation at CpG islands

  Dataset EGAD00001000059

• DATA FILES FOR SJACT (WGS)

  DATA FILES FOR SJACT

  Dataset EGAD00001000160

• DATA FILES FOR SJINF

  DATA FILES FOR SJINF

  Dataset EGAD00001000165

• Fastq files for SAIF genome

  This dataset contain the raw files generated for SAIF genome project

  Dataset EGAD00001000254

• Engineering Immune Cells for Therapy, Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich

  CRISPR engineering of human T cells

  Dac EGAC50000000405

• DATA FILES FOR SJEWS-WGS

  DATA FILES FOR SJEWS-WGS

  Dataset EGAD00001001020

• DATA FILES FOR Histone Capture bams

  DATA FILES FOR Histone Capture bams

  Dataset EGAD00001000657

• SNP data for Ovarian cancer PRS

  SNP data for Ovarian cancer PRS (cases)

  Dataset EGAD00001008143

• Elucidating Mechanisms of the Graft versus Leukemia Effect of Hematopoietic Stem Cell Transplant for Acute Myeloid Leukemia

  Donor lymphocyte infusion (DLI) is an established mode of adoptive cellular therapy for treatment of relapsed disease after allogeneic hematopoietic stem cell transplantation (HSCT). For patients with acute myeloid leukemia (AML), the response rate to DLI is only 20%. Here we use next generation sequencing technologies to understand the transcriptomic and immunologic features associated with response or resistance to therapy.

  Study phs003630

• Single-cell transcriptome analysis of B-cell development in the ABO platform

  The dataset includes samples from four individual donors, pooled at each cell-harvesting time point (days 21, 28, and 35). Single-cell RNA sequencing was performed on the 10x Genomics Chromium platform using GEM-X Single Cell 5′ v3 and GEM-X Single Cell V(D)J v3 for BCR profiling. For each timepoint, paired libraries were constructed: a 5′ GEX library and a V(D)J-B library. Per reaction 350,000-400,000 cells were loaded, aiming for 60,000 cells per reaction. Pooled libraries were sequenced on an Illumina NovaSeq X sequencer. 50,000 read pairs per cell for GEX and 5,000 read pairs per cell for V(D)J were targeted.

  Dataset EGAD50000002433

• Normal brain controls for ICGC PedBrain DNA methylation sequencing

  DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) used, for example, for the following studies: Mack, Witt, et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature 506(7489):445-450, 2014 (see EGAS00001000443) Hovestadt, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. 510(7506):537-541, 2014 (see EGAS00001000561)

  Study EGAS00001000909

• CATHeterization GENetics (CATHGEN)

  The CATHGEN biorepository consists of biological samples collected on 9334 sequential consenting individuals undergoing cardiac catheterization at Duke University Medical Center between 2001 and 2010 inclusive. The Institutional Review Board informed consent allowed for 50 mL of blood to be collected from fasting patients through the femoral arterial sheath during the catheterization procedure. Three 7.5 mL EDTA tubes for DNA extraction are stored at -80°C. The Duke Database for Cardiovascular Disease (DDCD) provides the bulk of the clinical data used for analysis. Follow-up includes mortality information gleaned from the National Death Index and Social Security Death Index plus follow-up phone calls and written questionnaires regarding MI, stroke, re-hospitalization, coronary re-vascularization procedures, smoking, exercise, and medication use.

  Study phs000703

• Exploring germline and somatic mutagenesis in the extended family with germline pathogenic variant in POLD1

  This study aimed to estimate the influence of POLD1 L474P on somatic and germline mutagenesis. We studied the mutation rate and spectra in germline and soma in an extended family harboring the POLD1 c.1421T>C p.(Leu474Pro) pathogenic variant. The study includes WGS data for DNA extracted from blood, fibroblasts or buccal swabs from the 16 family members, from DNA obtained single-cell derived colonies obtained from immortalized fibroblasts for 8 of 16 family members and from the same single-cell derived immortalized fibroblasts after approximately 40 passages for 6 out of 8 family members. Additionaly, study includes WXS sequencing for 1 tumor FFPE sample and adjacent normal tissue from the individual from one family member.

  Study EGAS00001006434

• Fixation effects on variant-calling in a clinical resequencing panel

  Formalin fixation is the standard method for preservation of tissue for diagnostic purposes, including pathological review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic tests. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade laboratory-developed targeted resequencing assay. We examined and quantified several parameters relating to sequencing quality and variant-calling from tumor and normal colon epithelial tissues. We identify one alterative fixative, Sakura Universal Molecular Fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathological review.

  Study EGAS00001003507

• single-cell RNA-seq Case-Control study of children progressing to Type1 diabetes

  Single-cell RNA sequencing was carried out on four selected PBMC samples of Finnish children at risk of developing Type 1 diabetes and their gender age and HLA matched control children using 10X genomic platform. All four Case children were positive for multiple islet specific autoantibodies and two of them also progressed to clinical disease during the follow up whereas the control children remain negative for all autoantibodies. Age at seroconversion for Case 2, 3, 5, and 9 children is 12, 18, 24, and 18 months, respectively. Age at sampling, in months, for the pairs was as follows (Case/Control): pair 2:24/24; pair 3: 12/18; pair 5: 12/12; pair 9:24/18.

  Study EGAS00001004070

• Surgical Treatment for Ischemic Heart Failure (STICH-BioLINCC)

  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. ObjectiveTo compare medical therapy with coronary bypass surgery and/or surgical ventricular reconstruction for patients with congestive heart failure and coronary artery disease.BackgroundCoronary artery disease (CAD) is the most common cause of heart failure, which in turn is a major cause of death and disability globally. Evidence from previous clinical trials supports the use of coronary-artery bypass grafting (CABG) to relieve disabling symptoms of angina, particularly among high-risk subgroups with extensive CAD. However, the studies did not include patients with severe left ventricular dysfunction, and developments in medical therapy have since led to updated guidelines. In addition, the benefits of CABG in patients with ischemic cardiomyopathy had still not been clearly established at the time of this study. STICH sought to evaluate the role of CABG in the treatment of patients with CAD and left ventricular systolic dysfunction.Reduced left ventricular function may occur after myocardial infarction, often in conjunction with left ventricular remodeling, including left ventricular enlargement and changes in chamber geometry. Left ventricular remodeling is correlated with progression of heart failure and a poor prognosis. Therefore, a surgical approach to remodeling through left ventricular volume reduction could improve outcomes for patients with CAD and heart failure. Surgical ventricular reconstruction (SVR) has been shown to reduce the left ventricular volume, increase the ejection fraction, and improve ventricular function. There is also evidence that SVR performed with CABG may reduce the rate of hospitalization and improve ventricular function, as compared to CABG alone. As part of a second hypothesis, STICH additionally investigated whether SVR when added to CABG would improve outcomes in patients with heart failure and CAD.ParticipantsA total of 2,136 participants were enrolled in STICH. 1,212 were enrolled in the hypothesis 1 component of the trial, with 602 participants assigned to receive medical therapy alone, and 610 participants assigned to receive medical therapy plus CABG. 1,000 were enrolled in the hypothesis 2 component, with 499 participants assigned to receive medical therapy plus CABG, and 501 participants assigned to receive medical therapy plus CABG and SVR. 76 participants that were assigned to the CABG with medical therapy treatment were enrolled in both hypothesis components.DesignAfter initial determination of overall eligibility, participants were evaluated to determine which component of the STICH program was appropriate for them on the basis of suitable therapeutic options. All participants underwent cardiac imaging for assessment of left ventricular function and wall motion. Participants in the hypothesis 1 component were randomly assigned to receive either medical therapy alone or medical therapy plus CABG. Participants in the hypothesis 2 component were randomly assigned to receive either medical therapy plus CABG or medical therapy plus CABG and SVR.At baseline, demographic factors and clinical characteristics were assessed, including current medications and prior diagnostic and other cardiovascular procedures, and a physical examination was performed. Guideline-based recommendations for drug and device use were emphasized for all participants. All participants underwent follow-up evaluations at the time of discharge or at 30 days for participants still hospitalized, every 4 months for the first year, and every 6 months thereafter. The median length of follow-up was 56 months for hypothesis 1 and 48 months for hypothesis 2.For participants receiving CABG, arterial grafting for stenosis of the left anterior descending coronary artery was required for all participants without specific contraindications. The use of additional arterial conduits supplemented by vein grafts was recommended for revascularization of all major vessels with clinically significant stenoses. Concurrent mitral-valve surgery for regurgitation was performed at the discretion of the surgeon. For participants receiving SVR, the operation was most commonly performed during a single period of cardioplegic arrest after construction of bypass grafts. However, the procedure could also be performed with the heart beating in order to facilitate identification of the noncontractile zone of scarring. After an anterior left ventriculotomy was centered in the zone of anterior asynergy, a suture was placed in the interior of the ventricle to encircle the scar at the boundary between the akinetic and viable tissue. Visual inspection and palpation facilitated the judgment of whether a patch was needed to optimize the chamber size without deforming the left ventricle during closure of the ventriculotomy.The primary outcome for hypothesis 1 was the rate of death from any cause. The primary outcome for hypothesis two was a composite of death from any cause and hospitalization for cardiac causes.ConclusionsThere was no significant difference between medical therapy alone and medical therapy plus CABG for death from any cause, though participants that underwent CABG had lower rates of death from cardiovascular causes, death from any cause, or hospitalization for cardiovascular causes. Adding SVR to CABG reduced the left ventricular volume, as compared with CABG alone. However, this anatomical change was not associated with a greater improvement in symptoms or exercise tolerance, or with a reduction in the rate of death or hospitalization for cardiac causes.

  Study phs003493

• Identifying causative mutations for Thrombocytopenia with Absent Radii

  Identifying causative mutations for Thrombocytopenia with Absent Radii

  Dataset EGAD00001000018

• DAC for hepatoblastoma sequencing data

  Data Access Committee for sequencing data of hepatoblastoma PDX cell models sequenced under University of Helsinki.

  Dac EGAC50000000548

• TTN gene targeted sequencing for AMC cohort

  TTN gene targeted sequencing for AMC cohort (n=24)

  Dataset EGAD00001005497