14658 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• WEHI AML Multiome Committee

  This committee oversees access to data generated as part of AML research study at WEHI, ensuring compliance with privacy regulations and ethical standards.

  Dac EGAC50000000912

• Wellcome Trust Sanger Institute

  Access to individual-level genotype data is available by application to the MalariaGEN Independent Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. For further information information on data release policy and data access application form, please follow the link below.

  Dac EGAC00000000002

• PDAC Phenotype and Germline Genotype Data Access Committee

  This Data Access Committee (DAC) is responsible for reviewing and approving requests for access to controlled phenotype metadata and derived germline FUT2/FUT3 genotype data from patients with pancreatic ductal adenocarcinoma (PDAC). Access is granted to bona fide researchers for non-commercial research purposes only, subject to approval by the DAC and in accordance with the original informed consent and applicable ethical regulations.

  Dac EGAC50000000893

• Xeroderma Pigmentosum, Complementation Group C, (XPC) and Non-XPC Cutaneous Squamous Cell Carcinoma (cSCC) Mutation Rate Study

  Base mutations occur at higher frequencies within heterochromatin and late-replicating DNA. In this study, we show that regional differences in mutation frequency are absent in portions of the genome that are not transcribed within cutaneous squamous cell carcinomas (cSCCs) with an XPC-\- genetic background. The XPC-\- genetic background predicates a loss of global genome nucleotide excision repair (GG-NER), thus our data shows that regional differences in mutation frequency are a result of differential access of DNA repair protein. Unexpectedly, we also note that greater transcription reduces mutations on both strands of genes in heterochromatin, and only to those levels observed in euchromatin, in a XPC-dependent fashion. Therefore, transcription likely reduces mutation prevalence by increasing access to DNA repair proteins. This tripartite relationship between DNA repair, transcription, and chromatin state shows a new cancer risk factor in human populations.

  Study phs000830

• mRNA-seq data from ALL patients with NUP214::ABL1 disease

  Dataset contains mRNA-sequencing data (fastq files) from 2 patients with NUP214::ABL1 disease (one T-ALL and one B-ALL patient). Patient samples (peripheral blood or bone marrow) were taken at diagnosis (B-ALL) or relapse (T-ALL). mRNA was extracted from lymphoblasts and underwent paired-end sequencing (75bp) using the Illumina NextSeq platform. Transcriptomic data was used for identification of gene fusions, SNVs and InDels. mRNA-seq data for an additional B-ALL patient with NUP214::ABL1 disease utilised in this study has already been published (EGAS00001006460).

  Dataset EGAD50000001395

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids, aimed at measuring the spontaneous rates of accumulation of new single-nucleotide sequence variations in seven microsatellite stable CRCs and one microsatellite unstable CRC. Mutations accumulated over six+six months were identified via whole genome sequencing of clonal tumoroids.

  Study EGAS50000000284

• Comprehensive genetic analysis of pediatric germ cell tumors

  Germ cell tumors (GCTs) are relatively rare tumors in children. Previous studies showed that adult testicular GCTs had some genomic alterations, but genetic basis of pediatric GCTs is still to be elucidated. We applied DNA methylation array analysis, whole-transcriptome sequencing, targeted capture sequencing, and SNP array analysis to fifty-one GCT samples.

  Study JGAS000204

• Hyperfibrinolysis

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such pedigree, hyperfibrinolysis is associated with increased fibrinolytic activity, resulting in increased bleeding. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000104

• Bleeding

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who exhibit severe bleeding with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000106

• Various_Platelet_Disorders

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who have a platelet disorder with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000107

• Evaluation of capture and amplicon-based targeted sequencing methods on formalin-fixed tumours

  Evaluated performance of three capture (Agilent’s SureSelectXT HS, Illumina’s Nextera Rapid Capture Custom, and New England Biolabs’ Next Direct Custom) and one amplicon-based (Qiagen’s Human Breast Cancer Panel) targeted sequencing methods on paired blood and FFPE, using whole exome sequencing data from matched fresh-frozen tissue as a comparison.

  Study EGAS00001004965

• OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients.

  The OTOF gene, encoding otoferlin, is reported to be one of the major causes of non-syndromic recessive sensorineural hearing loss, and is also reported to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD). In the present study, we performed OTOF mutation analysis using massively parallel DNA sequencing (MPS) to reveal the frequency and clinical characteristics of OTOF-related hearing loss in a large hearing loss population.

  Study JGAS000166

• Sequencing of heritable Bleeding and Platelet Disorders

  The BRIDGE-BPD study aims to discover new causal genes for Bleeding and Platelet Disorders (BPD) by high throughput sequencing using cluster analyses based on improved and standardized deep phenotyping of cases. BPD is one of the 13 Rare Disease projects under the NIHR BioResource Rare Diseases BRIDGE consortium, which is a collaboration aiming to discover the genetic sequence variants underlying unresolved inherited disorders and to improve identification of already identified high penetrance variants.

  Study EGAS00001001172

• Single-cell RNA-seq of human kidney tumors

  The aim of this study is to analyze the transcriptomic information of fresh single cells originating from human clear cell renal cell carcinomas (ccRCC). Samples have been experimentally enriched in malignant cells in order to address specific questions regarding heterogeneity and clonality in ccRCC. Samples include one set of long-term frozen and thawed single cells in order to explore the impact of liquid nitrogen freezing on ccRCC single cells.

  Study EGAS00001006534

• Complex structural variation patterns in pediatric solid tumors

  In this study, we performed systematic characterization of chromoplexy, chromothripsis and extrachromosomal DNA across five types of pediatric solid tumors: neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma. Almost half of all tumors had at least one complex SV and we identified candidate pathogenic events that affect genes or chromosomal alterations known to be relevant in these cancer types. In conclusion, complex SVs are prevalent and highly pathogenic in pediatric solid tumors.

  Study EGAS00001007565

• INdiana GENomics: Implementing an Opportunity for the Under Served (INGENIOUS)

  The INGenious trial planed to enroll a total of 6,000 patients, with 2,000 patients assigned to a pharmacogenetic testing arm and 4,000 to a control arm who will be followed, but not tested. It is randomized between an intervention arm and one that receives no intervention in order that the genotyped group can be compared with one in which undisturbed, routine clinical care is carried out in patients taking the same drugs. Both arms will be followed for a year after being prescribed a targeted medication. Patients randomized into the intervention arm that are prescribed one or more of the 27 targeted index medication will receive pharmacogenomic testing using a custom micro-array measuring 43 Single nucleotide polymorphisms in 14 genes. The study is being conducted by the Indiana University School of Medicine and the Indiana University Institute of Personalized Medicine in collaboration with the Eskenazi and Indiana University Health Systems and will evaluate the economic and clinical outcomes associated with embedding a pharmacogenomics program in a system that serves as the primary health care safety-net in Indianapolis, Indiana. By successfully implementing a pharmacogenomics program and integrating it with the Electronic Health Record and Clinical Decision Support system, physicians will be able to optimize patient care by delivering tailored therapeutic decisions based on the patient's individual genetics.

  Study phs001701

• Pineoblastoma Single-Nuclei RNA-seq Data Access Committee (St. Jude)

  Committee responsible for reviewing and approving external access requests to controlled-access pediatric brain tumor transcriptomic datasets from St. Jude Children's Research Hospital, ensuring alignment with patient consent and institutional ethics policies.

  Dac EGAC50000000839

• Beta-Blocker Evaluation in Survival Trial (BEST-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. Objectives The Beta-Blocker Evaluation of Survival Trial was designed to determine whether bucindolol hydrochloride- a nonselective beta-adrenergic blocker and mild vasodilator- would reduce the rate of death from any cause among patients with advanced heart failure and to assess its effects in various subgroups defined by ethnic background and demographic criteria- specifically women and members of minority groups. Background Although beta-adrenergic-receptor antagonists reduce morbidity and Mortality in participants with mild-to-moderate chronic heart failure, their effort on survival in participants with more advanced heart failure is unknown. Participants There were 2,708 participants. Conclusions Bucindolol resulted in no significant overall survival benefit. (Krause-Steinrauf et al., 2001, PMID: 11386264).

  Study phs003730

• Prospective Investigation of Pulmonary Embolism Diagnosis (PIOPED-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. Objectives: To determine the sensitivities and specificities of ventillation/perfusion (V/Q) lung scans for acute pulmonary embolism (PE).Participants: A total of 1487 participants were enrolled.Conclusions: Almost all participants with pulmonary embolism had abnormal scans of high, intermediate, or low probability, but so did most without pulmonary embolism. Only in a minority of participants did the clinical assessment combined with the V/Q scan interpretation improve the overall chance of reaching a correct diagnosis of acute PE. Although a high probability scan usually indicated the presence of PE, only a small number of participants with PE had a high probability scan. Reference: PIOPED Investigators, 1990, PMID: 2332918.

  Study phs004020

• MUW Data Access Committee

  DAC_for NeoBCCtrial Human Samples metadata access

  Dac EGAC50000000185

• Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT-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. Objectives The Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT) was designed to evaluate the hypothesis that amiodarone or a conservatively programmed shock-only, single-lead implantable cardioverter defibrillator (ICD) would decrease the risk of death from any cause in a broad population of patients with mild-to-moderate heart failure. Background Patients with congestive heart failure (CHF) can die suddenly and unpredictably from arrhythmia despite the use of proven medical therapies, such as beta-blockade. Two approaches have been developed to prevent sudden death among patients with CHF: therapy with amiodarone and therapy with an ICD. However, most of the mortality data on amiodarone and ICD therapy at the time of the study had been obtained in clinical trials performed after myocardial infarction in patients without CHF or those with ventricular arrhythmias. Thus, more data was needed to guide these therapies in patients who did not meet these criteria. Participants There were a total of 2521 participants. 847 were randomly assigned to placebo, 845 to amiodarone, and 829 to ICD therapy. Design Before randomization, participants underwent electrocardiography, a 6-minute walk test, 24-hour ambulatory electrocardiography, liver and thyroid function studies, and chest radiography. Participants were required, if clinically reasonable, to receive treatment with a beta-blocker and an angiotensin-converting-enzyme inhibitor, as well as an aldosterone antagonist, aspirin, and statins, when appropriate. Participants were randomly assigned in equal proportions to receive placebo, amiodarone, or a single-chamber ICD programmed to shock-only mode. Participants assigned to amiodarone or matching placebo began therapy as outpatients immediately after randomization. Placebo and amiodarone were administered as a loading dose of 800 mg/day for one week, 400 mg/day for three weeks, and then as a daily maintenance dosage according to weight and bradycardia status. Participants assigned to ICD therapy received their device a median of three days after randomization. The goal of ICD therapy was to treat only rapid, sustained ventricular tachycardia or ventricular fibrillation. Dual-chamber or biventricular devices, or antitachycardia or rate-response pacing therapies were not permitted. The ICD was uniformly programmed to have a detection rate of 187 beats per minute or more. Antibradycardia pacing was initiated only if the intrinsic rate decreased to less than 34 beats per minute. Median follow-up was 45.5 months. The primary end point was death from any cause. Secondary outcome measures included cardiac mortality, arrhythmic mortality, morbidity, quality of life, and incremental cost-effectiveness of the interventions. Each active treatment arm was compared to the placebo drug arm. Conclusions In participants with NYHA class II or III CHF and LVEF of 35% or less, amiodarone had no favorable effect on survival, whereas single-lead, shock-only ICD therapy reduced overall mortality by 23%.

  Study phs003654

• Paired-end Whole Exome-seq analysis of GBM, additional patient.

  Dataset contains one paired-end Whole Exome sequencing sample. One normal blood sample is also included.

  Dataset EGAD00001011989

• Gene expression-based prediction of pazopanib efficacy in sarcoma (HIPO, H021)

  The multi-receptor tyrosine kinase (RTK) inhibitor pazopanib is approved for the treatment of advanced non-adipocytic soft-tissue sarcoma and has also shown activity in other sarcoma subtypes. However, its clinical efficacy is highly variable, and no reliable predictors exist to date to select patients who are most likely to benefit from this drug. We analyzed the molecular profiles and clinical outcomes of pazopanib-treated sarcoma patients enrolled in a prospective observational study by the German Cancer Consortium, DKTK MASTER, that employs whole-genome/exome sequencing (WGS/WES) and transcriptome sequencing to inform the care of adults with advanced cancer across histologies who are younger than 51 and patients with rare tumors, including rare subtypes of more common entities, regardless of age.​ Among a total of 109 patients with available WGS/WES data, there was no correlation between clinical parameters, specific genetic alterations, or mutational signatures and clinical outcome. In contrast, analysis of a subcohort of 62 patients who underwent molecular analysis before pazopanib treatment and had transcriptome sequencing data available showed that mRNA levels of NTRK3 (hazard ratio [HR]=0.53, p=0.021), IGF1R (HR=1.82, p=0.027), and KDR (HR=0.50, p=0.011) were independently associated with progression-free survival (PFS). Based on the expression of these RTK genes, i.e., the features NTRK3-high, IGF1R-low, and KDR-high, we developed a pazopanib efficacy predictor (PEP) that stratified patients into three groups with significantly different PFS (p<0.0001). Application of the PEP to an independent cohort of pazopanib-treated sarcoma patients from DKTK MASTER (n=43) confirmed its potential to separate patient groups with significantly different PFS (p=0.02), whereas no such association was observed in sarcoma patients from DKTK MASTER (n=77) or The Cancer Genome Atlas sarcoma cohort (n=256) who were not treated with pazopanib. A score based on the combined expression of NTRK3, IGF1R, and KDR allows identification of sarcoma patients with good, intermediate, and poor outcome following pazopanib therapy and warrants investigation as a predictive tool in prospective studies to optimize the use of this drug in the clinic.

  Study EGAS00001005836

• Genomic Characterization CS-MATCH-0007 Arm N

  The CS-MATCH-0007 protocol is part of a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing, RNA sequencing and if possible, whole-genome, methylation and miRNA sequencing using pre-and post-treatment tumor biopsy specimens from patients enrolled on a treatment arm of the NCI-MATCH clinical trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to specific genomic alterations found in their cancers. Arm N is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with PTEN mutation, or deletion with PTEN expression on IHC, are treated with the drug GSK2636771. This subprotocol is one of the treatment arms included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood.

  Study phs002151

• DAC Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma

  Data access requests for the raw data used in publication "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  Dac EGAC50000000016

• Policy Documentation

  Policy Documentation The following policy documentation is required to be prepared and submitted to the EGA, together with your data files and associated metadata. Data Access Agreement (DAA) The Data Access Agreement is a contract made between Data User and Data Access Committee. The agreement should be drafted by the DAC and includes, but is not limited to, details of data use, publication embargoes and storage. Completion of a DAA by the applicant/s should form part of the application process to the DAC. NOTICE The data access agreement template below is provided for guidance only and should be adapted as you see fit to suit your own purpose. In the interest of promoting data sharing, we suggest that if an agreement cannot be met around clause 19 in this example that both parties should agree to remain silent, and that the clause should be removed from the agreement. Example DAA template Alternate (harmonised) DAA template

  Documentation access/data-access-committee/policy-documentation

• DNMT3A microcephalic primordial dwarfism RRBS data

  RRBS sequence data from one control and one patient with de novo DNMT3A mutations resulting in microcephalic primordial dwarfism.

  Dataset EGAD00001004472

• Data access policy

  Investigators who download restricted data from this dataset should: - Not attempt to identify individual human research participants from whom the data were obtained. - Acknowledge in all oral or written presentations, disclosures, or publications the specific dataset(s) or applicable accession number(s) and the repositories through which the investigator accessed any data. Any user requesting access to this data must apply for authorization, which is granted by the Data Access Committee (DAC). The DAC will review and approve or disapprove all requests from the research community for data access. Decisions to grant access are made based on whether the request conforms to the specifications of the Research Ethics Committee approval and program specific requirements or procedures (if any).

  Dac EGAC50000000504

• Human Developmental Biology Resource (HDBR) abnormal fetal samples

  The HDBR (www.hdbr.org) is a human embryonic and fetal tissue bank supplying registered researchers with access to these valuable research materials up to 22 weeks post-conception (PMC4640175). All of the samples collected are analysed for chromosomal abnormalities, and all samples with an abnormal phenotype are either analysed by SNP array, or exome sequenced. This dataset is generated from those abnormal samples that have been analysed by exome sequencing. To request access to this dataset, or if any researcher is interested in obtaining tissue from any of the samples HDBR collect, please email enquiries@hdbr.org.

  Study EGAS00001006300

• Meniere Disease Genomic Data Access Committee

  This Data Access Committee is responsible for reviewing and managing data access requests related to genomic variant files from whole exome sequencing of patients diagnosed with Meniere disease. This includes data from both familial and sporadic forms of the disease.

  Dac EGAC50000000708

• Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals

  Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals. Additional associated phenotype information is available for all individuals included in this study directly from CIBMTR. Data are available under controlled access release upon reasonable request and execution of a data use agreement. Requests should be submitted to CIBMTR at info-request@mcw.edu and include the study reference IB17-04.

  Study EGAS00001006033

• University of Sydney Thyroid Cancer Data Access Committee

  This Data Access Committee (DAC) manages access to genomic data generated by the Thyroid Cancer Research Group at the University of Sydney and Royal North Shore Hospital. The DAC will evaluate data access requests to ensure they align with participant consent and the conditions approved by the Northern Sydney Local Health District Human Research Ethics Committee. Requests will be reviewed for scientific validity, alignment with the original consent, and compliance with institutional and regulatory data governance policies.

  Dac EGAC50000000661

• Ankara Bilkent City Hospital Clinical Research Ethics Committee

  Ankara Bilkent City Hospital Clinical Research Ethics Committee is responsible for the oversight and management of access to genomic and phenotypic data generated by the IDH1 Somatic Mutation Profile in Intrahepatic Cholangiocarcinoma . The committee reviews applications for data access to ensure that the proposed research is consistent with the informed consent provided by participants and meets ethical standards. Access is granted to qualified researchers for non-commercial research purposes upon signing a Data Access Agreement (DAA).

  Dac EGAC50000000940

• A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma

  In this study, we conducted a genome-wide association study (GWAS) of post-bronchodilator (BD) FEV1 (forced expiratory volume in 1 second) and FEV1/FVC (forced vital capacity) in Puerto Rican children with asthma. From September 2003 to June 2010, we recruited 618 Puerto Rican children with asthma, which was defined as physician diagnosed asthma and at least one episode of wheezing in the previous year. The recruited children include 267 from public schools in Hartford, Connecticut and 351 from randomly selected households in San Juan, Puerto Rico.

  Study phs001216

• HPV-associated Cancer Consortium Data Access Committee

  HPV-associated Cancer Consortium Data Access Committee

  Dac EGAC50000000088

• The EMC-HEMA-AML-DNMT3A data access committee controlling the access to DNMT3A-mutated AML

  Dac EGAC00001003511

• Single-cell Transcriptome Profiling of Treatment-naïve and Post-treatment Colorectal Cancer: Insights into Putative Mechanisms of Chemoresistance

  These terms and conditions govern access to the managed access datasets to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions.

  Dac EGAC50000000482

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids, aimed at measuring the spontaneous rates of accumulation of new single-nucleotide sequence variations in seven microsatellite stable CRCs and one microsatellite unstable CRC. Mutations accumulated over six+six months were identified via whole genome sequencing of clonal tumoroids. 150x WGS for 7 samples.

  Study EGAS50000000425

• Personalized Treatment of Sezary Syndrome through a CTLA4:CD28 Fusion

  We sequenced two tumor and one normal whole genome libraries for a Sezary syndrome patient and also sequenced RNA libraries for each tumor. We identified a novel, highly expressed CTLA4:CD28 gene fusion that is predicted to results in a leading to stimulatory T-cell signaling in the presence of an inhibitory signal.

  Study phs000773

• WGS of tissues from members of family with germline POLD1 L474P variant

  The study includes WGS data for DNA extracted from blood, fibroblasts or buccal swabs from sixteen family members, who represent four sub-families, each including two parents and one to three children, comprising a total of eight offspring. In two sub-families POLD1 L474P was carried by the father; in one sub-family, by the mother; and in the other sub-family, both parents had wild-type POLD1.

  Dataset EGAD00001009282

• legitimate academic institutions need to comply with terms of Data Access Agreement to access EGAS00001000323

  Dac EGAC00001000065

• Data access committee handling data access requests for biomarker data from the clinical trial IMmotion150.

  Dac EGAC00001000946

• Data Access Committee for TIX Data

  Data Access Committee for the sequence data for TIX

  Dac EGAC50000000206

• Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study)

  Participants from study sites that recruited during the original study funded by NICHD of pregnant people, called nuMoM2b, participated in this study. The nuMoM2b-HHS1 was a prospective observational follow-up study of the nuMoM2b cohort consisting of interval contacts via phone or web every 6 months to about a year, and an in-person visit 2 to 7 years after the end of the nuMoM2b pregnancy including: Demographics Self-administered questionnaires Clinical measurements Lab results An in-home sleep breathing assessment for the subset of participants with at least one valid sleep breathing assessment during nuMoM2b Abstraction of medical records for pregnancies subsequent to nuMoM2b involving self-reported adverse pregnancy outcomes or multiple births Abstraction of medical records of selected cardiovascular risk-related events or procedures reported by participants. The study capitalized on the rich and unique data prospectively collected during nuMoM2b (biomarkers, uterine artery Doppler studies, fetal growth, psychosocial determinants, sleep, and blood pressure) and rigorous definitions of adverse pregnancy outcomes. These data are stored in the NICHD repository DASH (https://dash.nichd.nih.gov/study/226675). A total of 8,838 nuMoM2b participants were targeted for contact during nuMoM2b-HHS and 7,872 participants were reached, of whom 7,003 completed one or more interval contacts. Of these, 5,206 agreed to the visit, and 4,508 attended an in-person visit.

  Study phs002808

• NTNU Data Access Committee for “ProstOmics: spatial and bulk multi-omics of prostate cancer” datasets archived in Federated EGA Norway

  The ProstOmics project of NTNU contains spatial and bulk multi-omics datasets of prostate cancer, and access request to these datasets are handled by this Data Access Committee on behalf of NTNU.

  Dac EGAC50000000277

• Boyes Lab - DAC policy

  Access to this data is controlled. Upon request from a third party for access to the data, a separate Data Sharing Agreement would be put in place between the University of Leeds and the third party prior to EGA granting access to the data to the third party.

  Dac EGAC50000000283

• Walter and Eliza Hall - Aix-Marseille Université

  Data Access Committee for the Liao et al. 2025 study, D4Z4End2End: complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS and reference cohorts.

  Dac EGAC50000000655

• Data access committee handling data access requests for biomarker data from the clinical trial IMvigor210.

  Dac EGAC00001000945

• Deciphering Developmental Disorders (DDD)

  The Deciphering Developmental Disorders (DDD) study is a research collaboration between the Wellcome Trust Sanger Institute, the NHS clinical genetics services and families across the UK and Ireland. The project aims to improve the diagnosis of children with developmental disorders by using high-resolution microarray and massively parallel sequencing technologies on 12,000 children and their parents. Genetic changes that explain the child's symptoms will be displayed in the DECIPHER database (https://decipher.sanger.ac.uk). Extended datasets generated by the DDD project will be available in the European Genome-Phenome Archive with access carefully managed by a Data Access Committee.

  Study EGAS00001000775

• Demographically Diverse Substance Use Disorder Cohorts of Dr. Stanley H. Weiss

  The Demographically Diverse Substance Use Disorder Cohorts of Dr. Stanley H. Weiss, which constitute the Epidemiology of the Weiss Cohort Projects, consist of a series of inter-connected projects, building upon a set of cohort projects of various groups, mainly drug users from medication-assisted treatment programs, that Dr. Stanley H. Weiss first developed in the 1980’s plus several newer initiatives, each with an array of collaborators. Beginning in the 1980’s, Dr. Stanley H. Weiss started several long-term studies of persons who inject drugs (PWID) across the United States, ultimately enrolling over 10,000 participants through the early 1990’s with an average age then in their 30’s. About a quarter were enrolled from sites in New Jersey (NJ). These studies included the first testing of PWID for the human immunodeficiency virus (HIV) and the human T-cell lymphotropic viruses (HTLV I and HTLV II). Cumulative past support (initiation thru ~ 1999) for these cohort studies included ~ $20 million from intramural resources from the National Cancer Institute (NCI) and the National Institute on Drug Abuse (NIDA), plus multiple grants and in-kind support from the New Jersey Department of Health (NJDOH) totaling ~ $1 million. The Weiss Cohort Projects include the first large AIDS-era cohorts to include women at high risk for HIV. A high percentage of subjects in these studies are black or Latino. Thus, this is an ethnically diverse US cohort, with a high proportion of women included. These subjects are at high risk of parenteral and sexual infection from both drug use and sexual practices. Samples from other studies conducted by Dr. Weiss, in which detailed interviews were conducted, are included as controls (persons documented by us not to have a history of opioid drug use). As one of our groups of subjects have many persons of Haitian ancestry, we specifically included some Haitians who had never used opioids as controls. Our documentation includes such ancestry. These cohorts demonstrated high rates of HIV and HTLV-II infection in PWIDs, including one study initiated in 1981 with confirmation in the later cohorts. In the first two decades of these studies, among numerous publications was the first study showing a very high rate of hepatitis C infection among PWIDs. An example of how the studies’ long-time horizon proved essential was that it first became possible to test whether a person had ever been infected with hepatitis C virus (HCV), as well as how much HCV was in each person’s blood, many years after the specimens were collected. This allowed HCV amounts in blood to be compared for subjects who had died of liver disease early in the study versus those who survived. Then a sequence of published papers culminated in demonstrating, using a nested case-control design, that a high baseline HCV titer was predictive of early progression to death from end-stage liver failure. Outcomes related to HCV (end stage liver disease and hepatocellular carcinoma) remain under study. In the original cohort studies, the mean age at enrollment was ~ 33 years old, so that those still alive in 2022 are mainly now ~ 60 - 75 years old. Many participants have already died. The tincture of time has led to subjects reaching ages when many more are dying from a wide array of outcomes, including from many chronic diseases (including cancer) as well as from infectious agents (especially HIV, HCV) or drug overdose. Renewed collaboration with local drug treatment programs has led to new field-based studies, including examination of some currently evolving problems among drug users. Dr. Weiss joined the National Institute on Drug Abuse (NIDA) Genetics Consortium (NGC) in 2017, and through the NIDA project officer has had access to NGC contract resources (see below). NIH Certificate of Confidentiality, CC-DA-16-214 (attached) protects these studies. Past arrangements related to data on our subjects leads to restrictions on the use of data emanating from our study, such as potential commercialization and restrictions on whom may access and use these data. NIDA Genetics Consortium (NGC) resources further support these endeavors and will be used as part of the NGC analyses studying the genetics of substance use. Study participants signed informed consent for the information collected from them to be used with no time limit and for biologic specimens collected from them to be used without restriction in future research. Serum samples were collected from participants, and from many also plasma, white blood cells and/or urine samples. About 100,000 vials were stored. All specimens have been continuously preserved at sufficiently cold temperatures to prevent deterioration, and many subjects separated white blood cells were processed and frozen in such a way as to maintain viability. Detailed data from the participants has been accumulated over time, and in general, linkage has been retained in each sub-study in accordance with the consent forms and protocols. For some participants, specimens were collected at multiple times (that is, sequential specimens). Multiple specimens from a single person exist in this database, and efforts at de-duplication remain ongoing. Dr. Weiss should be contacted if an investigator requires unique individuals since: • Multiple phases of enrollment occurred, and as our prospective follow-up continues; Dr. Weiss may identify new instances of multiple enrollment. • Some persons are related to each other. • In general, in this dataset for dbGaP, only a single specimen/record form a given person is included. Advances in laboratory testing techniques now permit innovative new uses for our linked research biospecimen repository. The ongoing focus of an interdisciplinary research program based on these cohorts relates subjects’ diseases, behaviors, medical history, and outcomes with biological and exposure markers. Participants’ use of various substances was ascertained on study enrollments, many serially over time. Quantitative frequency of use data, also sometimes sequential over time, were ascertained. Active ascertainment of outcomes is being conducted, including matching to mortality and cancer databases. Investigators interested in collaborations on specific outcomes (which is not part of this dbGaP dataset) or in the use of our stored specimens are encouraged to contact the principal investigator, Dr. Weiss. The processing of the genomic data was done in conjunction with NIDA, and in accordance with some longstanding data cleaning steps used by NIDA in the NIDA Genetics Consortium (NGC), a group to which we shall be contributing these data for collaborative analyses. Since there is the potential for these steps to introduce certain types of potential biases, we summarize these here. Under contract from NIDA, cryopreserved sera or plasma (-80 C) or cells (in liquid nitrogen) were used, with most stored having been stored for 30 to 40 years in our biorepository. In the case of serum or plasma, in which only (largely) cell-free DNA fragments were available, DNA was extracted and restored prior to amplification. Industry standard DNA amplification techniques were done on all samples prior to genotyping in accord with established protocols of the NIDA Genetics Consortium. Our genotype data were run and processed on the Illumina Infinium OmniExpress_v_1.3 array. This array has 714,238 SNPs, and was designed many years ago. There were 628 SNPs on the array that do not correspond to any chromosome position, and these were removed. Genotype data were submitted by NIDA’s contracted genotyping laboratory in six batches over time to NIDA’s contracted dbGaP data management group, which conducted quality control (QC) analyses. QC analysis included an assessment of batch effects on for five of the six batches. (One of the batches, with only 12 samples, was too small for QC analysis of batch effects.) Standard NIDA Genetic Consortium cleaning was performed. Samples with a call rate <.85 were removed. Only one sample per person was retained. When more than one specimen was genotyped from one subject, only the sample with the higher call rate was retained (provided, of course, that that call rate was ≥ 0.85). We have retained some people we know are related, including some found to have been related through genotyping; the pedigree file describes those relationships. In summary, key cleaning steps include: 1. Using PLINK to check gender discrepancy. 2. Using PREST-PLUS and KING (Kinship-based Inference for GWAS) to check relatedness. 3. Using PEDCHECK and PLINK to check/zero-out Mendelian error. 4. Using PLINK to perform sample QC, SNP QC, along with KING to perform chromosome X and chromosome Y QC. 5. SNP-QC: Batch-effect: 5 Batches were compared (one batch, with few samples, was not). These five batches were compared to each other in all ten possible pairs, one batch vs. another batch, examining SNP allele frequency discrepancies by population (from GRAF), Fisher Exact Allelic test, with the criterion of p<5e-8 for removal. 6. SNP-QC: discordant SNPs in QC duplicates. Compared 25 QC duplicated samples with call rate > 0.95, removed SNPs with 3+ discordance. 7. There were 1,056 SNPs that were monomorphic; these have been retained so they can be included in analyses in which our dbGaP data are combined with those from other cohorts (in the latter of which those SNPs may not be monomorphic). The final cleaned dataset submitted has 8,898 samples and 606,793 SNPs.

  Study phs002140