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• An integrated single-cell reference atlas of the human endometrium

  This dataset includes both the anchor scRNA-seq and snRNA-seq datasets used to build the Human Endometrial Cell Atlas (HECA). HECA provides a comprehensive definition of endometrial cell types and states throughout the menstrual cycle in donor with and without endometriosis. It identifies consensus cell types across datasets generated by teams worldwide, as well as previously unreported cell types, all of which are validated and mapped in situ using spatial transcriptomics. Processed data is available from ArrayExpress with accession number E-MTAB-14039. See Marečková, M., Garcia-Alonso, L., Moullet, M. et al. An integrated single-cell reference atlas of the human endometrium. Nat Genet 56, 1925–1937 (2024) https://doi.org/10.1038/s41588-024-01873-w for more information.

  Dataset EGAD00001015446

• Single-cell RNA sequencing of human kidney transplant nephrectomies with chronic rejection or non-alloimmune graft injury

  This dataset contains raw single-cell RNA sequencing (scRNA-seq) data for five new kidney allograft nephrectomy samples used to construct the described in the following study: https://www.biorxiv.org/content/10.1101/2022.10.28.514222v2.full. The full description of processing is described in the manuscript. Briefly, samples were digested into a single cell suspension and run according to the 10X Genomics Chromium 5’ single cell kit (v2). Sequencing was performed using an Illumina Novaseq instrument. Samples were designated as TXN2 (EGAN00002519570, mycotic pseudoaneurysm, control dataset), TXN3 (EGAN00002235628, renal vein thrombus, control dataset), TXN5 (EGAN00002519573, chronic transplant rejection), TXN6 (EGAN00002519572, chronic pyelonephritis and renal artery stenosis, non-alloimmune graft injury dataset), TXN7 (EGAN00002519576, recurrent focal segmental glomerulosclerosis, non-alloimmune graft injury dataset).

  Dataset EGAD00001015631

• Targeted sequencing of 72 prostate cancer driver in 712 plasma cell free DNA samples

  Dataset contains targeted sequencing data of 712 plasma cell free DNA samples and 428 white blood cell samples collected from 428 men with metastatic prostate cancer. Target capture was performed using a hydridization-based custom Roche SeqCap EZ Choice kit, designed to capture all exons of 72 prostate cancer driver genes. Cell free DNA was extracted from 10 mL blood samples. Libraries were sequenced using Illumina HiSeq 2500 or Illumina MiSeq instruments to a median coverage of 750x. 62% of samples had ctDNA fraction above 2% of total cfDNA. Note that "Dataset type" is erroneously listed as "Amplicon sequencing", because "Captured-based targeted sequencing" or "Hybridization-based targeted sequencing" were not available options in EGA at the time of submission.

  Dataset EGAD00001004208

• Pilot experiment on functional genomics in osteoarthritis_RNA

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.

  Dataset EGAD00001001331

• Whole Genome Sequencing of Liver Cancers

  Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers.

  Dataset EGAD00001003281

• Identification of rare variants associated with cardiovascular traits in Cilento isolates

  The aim of this project is to identify rare genetic variants of large effect implicated in complex diseases by focusing on the study of cardiovascular diseases and related quantitative traits in a well characterized isolated population in Cilento area, Italy. The reference panel has been selected carefully in order to maximize the imputation coverage and quality on the all population samples. The selected individuals should meet three criteria: selected individuals should be chip-genotyped and closely related to the maximum number of chip-genotyped individuals so as to maximize imputation coverage; relatedness between selected individuals should be minimal, so as to minimize redundancy in genetic information of the reference panel. We perform exome sequencing on samples from 250 individuals from the Campora and Gioi-Cardile populations.

  Dataset EGAD00001002195

• Targeted Validation Samples

  The dataset consists of targeted sequencing data obtained from an independent cohort of 11 patients to validate discriminative DMRs (differentially methylated regions) for Acute coronary syndrome (ACS) subtypes. The cohort includes 2 healthy subjects, 4 STEMI (ST-segment elevation myocardial infarction), 3 NSTEMI (non-ST-segment elevation myocardial infarction), and 2 UA (unstable angina) patients. The sequencing panel targeted 18,831 CpGs for analysis, reaching at least 5 reads coverage for 75% of the targeted CpGs in each sample. The sequencing was performed using the NEBNext Enzymatic Methyl-seq Module and the Nonacus Cell3TMTarget: Library Preparation kit, followed by probe hybridization, capture enrichment, and sequencing on the Novaseq 6000 platform, generating 400 million reads. The dataset is in raw fastq format.

  Dataset EGAD00001010934

• The Haemgen RBC study

  Anaemia is a major determinant of global ill-health. To refine our understanding of the genetic factors influencing red blood cell formation and function, we carried out a meta-analysis of genome-wide association studies (GWAS) for six red blood cell traits: haemoglobin (HB), mean cell haemoglobin (MCH), mean cell haemoglobin concentration (MCHC), mean cell volume (MCV), packed cell volume (PCV) and red blood cell count (RBC). We provide genome-wide association results for 62,553 people of European ancestry using up to 2,644,161 autosomal SNPs. Participants with extreme measurements (>+/-3SD from mean) were excluded on a per phenotype basis. Imputation was done using haplotypes from HapMap Phase 2. SNP associations with each phenotype were tested by linear regression using an additive genetic model. Associations were tested separately in each cohort, with principal components and other study specific factors as covariates to account of population substructure. We then carried out meta-analysis of results from the individual cohorts using z-scores weighted by square root of sample size. SNPs with MAF<1% (weighted average across cohorts) were removed, as were SNPs with weight <50% of phenotype sample size. Anaemia is a major determinant of global ill-health. To refine our understanding of the genetic factors influencing red blood cell formation and function, we carried out a meta-analysis of genome-wide association studies (GWAS) for six red blood cell traits: haemoglobin (HB), mean cell haemoglobin (MCH), mean cell haemoglobin concentration (MCHC), mean cell volume (MCV), packed cell volume (PCV) and red blood cell count (RBC). We provide genome-wide association results for 62,553 people of European ancestry using up to 2,644,161 autosomal SNPs. Participants with extreme measurements (>+/-3SD from mean) were excluded on a per phenotype basis. Imputation was done using haplotypes from HapMap Phase 2. SNP associations with each phenotype were tested by linear regression using an additive genetic model. Associations were tested separately in each cohort, with principal components and other study specific factors as covariates to account of population substructure. We then carried out meta-analysis of results from the individual cohorts using z-scores weighted by square root of sample size. SNPs with MAF<1% (weighted average across cohorts) were removed, as were SNPs with weight <50% of phenotype sample size.

  Study EGAS00000000132

• Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort

  CARDIA is a study examining the etiology and natural history of cardiovascular disease beginning in young adulthood. In 1985-1986, a cohort of 5115 healthy black and white men and women aged 18-30 years were selected to have approximately the same number of people in subgroups of age (18-24 and 25-30), sex, race, and education (high school or less and more than high school) within each of four US Field Centers. These same participants were asked to participate in follow-up examinations during 1987-1988 (Year 2), 1990-1991 (Year 5), 1992-1993 (Year 7), 1995-1996 (Year 10), 2000-2001 (Year 15), 2005-2006 (Year 20), and 2010-2011 (Year 25); the proportions of the surviving cohort that have returned for the seven follow-up examinations were 90%, 86%, 81%, 79%, 74%, 72%, and 72%, respectively. In addition to the follow-up examinations, participants are contacted regularly for the ascertainment of information on out-patient procedures and hospitalizations experienced between contacts. Within the past five years, 95% of the original surviving cohort has been contacted. While the specifics of each examination has differed somewhat, data have been collected on a variety of factors believed to be related to heart disease. These include conditions with clear links to heart disease such as blood pressure, cholesterol and other lipids. Data have also been collected on physical measurements such as weight and skinfold fat as well as lifestyle factors such as substance use (tobacco and alcohol), dietary and exercise patterns, behavioral and psychological variables, medical and family history, and other chemistries (e.g., insulin and glucose). In addition, subclinical atherosclerosis was measured via echocardiography during Years 5, 10, and 25, computed tomography during Years 15 and 20, and carotid ultrasound during Year 20. The CARDIA Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs000285 CARDIA Cohort. phs000236 PAGE_CALiCo_CARDIA phs000309 GENEVA_CARDIA phs000399 GO-ESP HeartGO_CARDIA phs000613 CARDIA_CARe

  Study phs000285

• Sleep Abnormalities in Rare Genetic Disorders: Angelman Syndrome, Rett Syndrome, and Prader-Willi Syndrome

  This research study will investigate sleep behavior in the rare neurological disorders Angelman Syndrome (AS), Rett Syndrome (RTT), Prader-Willi Syndrome (PWS) and Early-onset Morbid Obesity (EMO). Sleep is very important to proper health and plays a critical role in learning, memory, brain development and brain function. Sleep disturbances can have negative effects on health and the quality of life of children and their families. Sleep disorders are common in individuals with AS, RTT, PWS and EMO. As a result, individuals with AS, RTT, PWS and EMO are at risk for sleep-related health problems that can worsen existing daytime behaviors and lead to additional problems with learning and memory. The principal objectives of the study are to: Characterize sleep behavior in individuals with Angelman Syndrome, Rett Syndrome, Prader-Willi Syndrome and Early-onset Morbid Obesity. Compare sleep behavior in these individuals with sleep behavior in normal controls Assess the natural history of sleep behavior in individuals with Angelman Syndrome, Rett Syndrome, Prader-Willi Syndrome and Early-onset Morbid Obesity About this Study This is a questionnaire study that will evaluate the sleep behavior of individuals with AS, RTT or PWS (participants), or unaffected siblings of individuals with AS, RTT or PWS (controls). Those participating in the study will already be registered with the Rare Disease Clinical Research Network (RDCRN) and have a confirmed diagnosis of AS, RTT or PWS or be an unaffected sibling. We will look at the medical records on file with the RDCRN to confirm diagnosis of AS, RTT or PWS. Study participants will participate in the study at their regularly scheduled RDCRN clinic visits. Participants will be asked to complete questionnaires at the study visits that will document their sleep behaviors. The questionnaires are not difficult and participants should be able to complete them in approximately 15-30 minutes. Parents and legal guardians are allowed to assist participants or answer on their behalf. Questionnaires will be administered at the initial study visit and at a 12 month follow-up visit to document any changes in sleep behavior. We hope to enroll approximately 1400 individuals with either AS, RTT or PWS or their unaffected siblings.

  Study phs001292