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• WGS data of XPC-ko human small intestinal organoid cultures

  Whole genome sequencing (WGS) data of human small intestinal organoid cultures, which were deleted for the XPC gene using CRISPR-Cas9. Contains WGS data of 1 clone and 1 subclone.

  Dataset EGAD00001003779

• DEEP-IHEC-release-2017

  Raw data files for the German Epigenome Project (DEEP), IHEC/EpiRR submission of 2017. metadata available at: http://deep.dkfz.de/#/experiments

  Dataset EGAD00001003974

• Meso RNA-seq data (SSA cell line study)

  RNA-seq data for mesothelioma cell lines after spliceostatin (SSA) or control (DMSO) treatment.

  Dataset EGAD00001001914

• Multiomic Dissection of Movement and Neurocognitive Toxicity Following BCMA-Targeting CAR T Cell Therapy

  Raw sequencing data (GEX, TCR, adn CSP libraries) for longitudinal cerebrospinal fluid and PBMC samples from a multiple myeloma patient treated with cilta-cel who developed MNT.

  Dataset EGAD50000002339

• National Eye Institute (NEI) Age-Related Eye Disease Study 2 (AREDS2)

  The Age-Related Eye Disease Study 2 (AREDS2) was a multi-center, randomized Phase III clinical trial designed to assess the effects of oral supplementation of high doses of lutein, zeaxanthin, and omega-3 fatty acids (docosahexaenoic acid [DHA] and eicosapentaenoic acid [EPA]) in reducing the risk of progression to late age-related macular degeneration (AMD), progression to cataract surgery, and/or progression to moderate vision loss in high-risk participants. The effect of the study supplements on cardiovascular outcomes and cognitive function were also examined. Other study goals included evaluation of eliminating beta-carotene and/or reducing zinc in the original AREDS formulation on the progression and development of late AMD. AREDS2 sought to validate the AREDS AMD scale developed from the photographic data obtained from AREDS, (Study Accession: phs000001).Eighty-two clinical sites across the United States enrolled 4,203 participants aged 50 to 85 (mean age 74 years) between October 2006 and September 2008. Enrollment was restricted to people at high risk of progression to late AMD with either bilateral large drusen or large drusen in 1 eye and late AMD in the fellow eye. Follow-up assessments in the clinic occurred on an annual basis for an average of 5 years, with telephone calls every six months during each year. Blood or saliva samples were also collected from 2,000+ AREDS2 participants for genetic research. Of these, samples from 1,800+ AREDS2 participants were included in the International Age-Related Macular Degeneration Genomics Consortium - Exome Chip Experiment, and have exome chip data available in the dbGaP (Study Accession: phs001039). In addition, samples from 1300+ AREDS2 participants were included in the International Age-Related Macular Degeneration Genomics Consortium - Whole Genome Sequencing Study in the dbGaP (Study Accession: TBD). Of 1363 AREDS2 participants with whole genome sequencing, 488 previously participated in AREDS.Please see "The Age-Related Eye Disease Study 2 (AREDS2) Research Group" document for a full list of AREDS2 study contributors.

  Study phs002015

• Genome_Diversity_in_Africa_Project__Uganda

  Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into the evolutionary processes that shape both human adaptation and variation in disease. Populations from SSA have the highest levels of genetic diversity. This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene–disease association signals. A systematic assessment of genetic diversity within SSA would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) aims to produce a comprehensive catalogue of human genetic variation in SSA, including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. This resource will make a substantial contribution to understanding patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies in SSA populations and studies comprising globally diverse populations, complementing existing genomic resources. Specifically, we plan to carry out high depth whole genome sequencing of up to 2000 individuals across Africa (25 individuals from each ethnolinguistic group). Our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from SSA accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across SSA; 3) develop a cost-efficient, next-generation genotype array for diverse populations across SSA; and 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics

  Study EGAS00001002523

• Population Structure and Genetic Diversity in Argentinean populations

  Argentina was one of the last places peopled when humans entered the Americas. Its earliest archeological sites are dated from 13,000 years BP, and throughout its history the region has exhibited broad cultural diversity, involving both hunter-gatherer and agro-pastoral societies, different linguistic families, the Southern expansion of the Inca Empire, the arrival of the Spanish conquistadors and slave trade from Africa. More recently, Argentina has had the highest proportion of influx of transoceanic migration between 1850 and 1940 of any Latin American country. Furthermore, the geographical distribution of immigrants was oriented towards the Pampa region of central-eastern Argentina and the Northeast, so different patterns of mixed ancestry throughout the country are expected. In this present work we aim to describe the history and structure of the Argentinean population. Thus far, we have collected DNA samples from 2904 participants from 15 dispersed regions in Argentina, from the Andean populations in the Northwest to the river lands of the Northeast. Our preliminary data includes genome-scale Illumina Exome Array 250K genotypes, plus next-generation sequencing data from uniformly spaced genomic regions targeted with a genotype-by- sequencing strategy (which covers 1.5% of the genome), for 375 participants from 9 of the 15 populations. We will identify proportions and patterns of European, African and Indigenous American ancestry in the Argentinean cohort via local ancestry inference. The first series of analyses will focus on genomic tracts of Indigenous American ancestry for fine-scale examination of sub-continental structure by comparing to a panel of 493 samples from 52 Indigenous American populations from throughout the Americas. Furthermore, this work will serve as a test of different low-cost strategies (exome genotype array vs. genotype-by-sequencing) for accurate inference of population structure in extant populations.

  Study EGAS00001001663

• Molecular features of adenomas predicting metachronous colorectal cancer: a nested-case control study

  "Background & Aims: Current morphological features defining advanced adenomas (size ≥10 mm, high grade dysplasia or >25% villous component) cannot optimally distinguish individuals at high-risk or low-risk of metachronous colorectal cancer (me-CRC), which may result in suboptimal surveillance. Certain DNA copy number alterations are associated with adenoma-to-carcinoma progression (cancer-associated events; CAEs). We aimed to evaluate whether CAEs can better predict an individual’s risk of me-CRC than the morphological advanced adenoma features. Methods: In this nested case-control study, 529 individuals with a single adenoma at their first colonoscopy were selected from a Norwegian adenoma cohort. DNA copy number profiles were determined, by means of low-coverage whole genome sequencing. We assessed the prevalence of CAEs in advanced and non-advanced adenomas and its association with me-CRC. For the latter, cases (with CRC) were matched to controls (without CRC), with the same follow-up period as cases, as well as age and sex. Subsequently, odds ratios (OR) for the association of the presence of an advanced adenoma or a molecularly-defined high-risk adenoma with me-CRC were calculated. Results: Molecular high-risk features were observed in 85/267 (32%) of advanced adenomas and in 27/262 (10%) of non-advanced adenomas. Me-CRC was more strongly associated with advanced adenomas (OR 3.58; 95% CI 2.27-5.72) than with molecular high-risk adenomas (OR 1.90; 95% CI 1.14–3.16). After adjusting for other variables, only advanced adenoma remained significantly associated with me-CRC (OR 3.39; 95% CI 2.10–5.55). Conclusion: Molecularly-defined high-risk adenomas were associated with me-CRC, but the association of advanced adenoma with me-CRC was stronger. " Project goal: Evaluate the value of DNA copy numbers alterations detected in a baseline adenoma, in the prediction of risk of metachronous CRC

  Study EGAS00001007039

• Molecular characterization of Barrett’s esophagus at single cell resolution

  Backgrounds & Aims: Patient with Barrett’s esophagus (BE) have an increased risk to develop esophageal adenocarcinoma and are under periodical endoscopic surveillance for malignant transformation. Pathologists distinguish between different BE stages to identify high-risk patients, but this process remains difficult as stage-specific markers are still missing. We established BE organoid cultures, applied single cell sequencing approaches to identify differences in gene expression and genomic alterations, and validated candidate genes for their predictive value on histological sections. Methods: We collected 43 epithelial biopsies from 21 patients, established organoids for the clonal expansion of matching healthy and diseased tissue from two patients to identify genomic alterations by whole genome sequencing (WGS). We performed single cell DNA-sequencing (scDNAseq) to analyse DNA alterations within biopsies from 8 patients and single cell RNA-sequencing (scRNAseq) to identify gene expression differences between BE stages from 19 patients. Candidate marker genes were then validated by RNA in situ hybridization experiments on histological resection specimen. Results: Most BE biopsies were chromosomal stable (CS) and their single base substitution (SBS) signatures were indistinguishable from the healthy control tissues. Dysplastic BE cells contained areas of chromosomal instabilities (CIN), which differed by the presence of the SBS17 signatures from biopsy-matching CS cells or patient-matching healthy control cells. Such CIN areas affected efficient clustering of the scRNAseq data. We identified two sets of marker genes (SLC5A5, PSCA, LIPF and ANPEP, CEACAM6, REG4), which distinguish columnar BE epithelium from non-dysplastic/dysplastic stages. CLDN2 allowed the distinction between dysplastic and more advanced stages as its expression level increased and spread in dysplastic BE glands. Conclusions: Molecular characterization of BE samples identified a correlation between the presence of CIN and COSMIC signature 17, and we report seven marker genes that help in distinguishing different BE stages.

  Study EGAS00001005221

• EpiMatch_DNA_Methylation_Resource

  Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals. Additional raw data (IDAT files) and associated phenotype information are available for all individuals included in this study (n=570) 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

  Dataset EGAD00010002283