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• Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection - MEGA chip data

  This data was generated as part of the project titled "Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection." The study was carried out to investigate the genetic architecture of the Greenlandic population and the consequences it has for disease mapping, diagnosis and prediction.

  Study EGAS50000000658

• Targeted Illumina sequencing of 3399 plasma cfDNA samples and 1988 leukocyte DNA samples from 1995 metastatic prostate cancer patients

  Blood samples were collected from eight clinical trials and a British Columbia-based biobank. All plasma cfDNA and leukocyte DNA samples were processed with uniform methodology, and underwent targeted sequencing using a custom hybridization capture panel and Illumina instruments. Four different generations of custom hybridization capture panel were used, all providing coverage of the complete coding regions of 72 prostate cancer genes, and later panel generations also providing exhaustive coverage of the AR locus (including introns and flanking regulatory regions), as well as a genome-wide SNP grid for copy number analysis.

  Dataset EGAD50000001594

• Single-cell genotype-to-phenotype (scG2P) data of single nuclei from cell line mixing experiment and six donors

  We developed Single-cell genotype-to-phenotype (scG2P) to profile mutations in driver gene hotspots and capture mRNA targets of interest, validating this assay in a cell line mixing experiment of KYSE-270, KYSE-410, and HCT-116, and applied the assay to esophageal biopsy samples from six donors.

  Study EGAS50000001429

• Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M-mutant pediatric high-grade gliomas

  Genome-wide analysis of H3K27me3 occupancy and DNA methylation in K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs) as well as pediatric pHGG cell lines. The study aims to elucidate the connection between K27M-induced H3K27me3 reduction and changes in DNA methylation as well as gene expression.

  Study EGAS00001000578

• Collection of Genotypic and Ethnographic Information from Individuals of South African Ethnic Groups

  The hunter-gatherers and pastoralists of South Africa retain the highest genetic diversity of any population. Genetic determinants of light skin pigmentation, reduced stature etc and other basic biomedical phenotypes are unique to samples with Southern African hunter-gatherer and pastoralist ancestry or retain ancestral haplotypes not found in other populations.

  Study EGAS00001004472

• Single-cell RNA sequencing dissects gene-environment interactions on gene expression and regulation in immune cells.

  This study aims to dissect gene-environment interactions on gene expression and regulation in immune cells using scRNA-seq data from 120 donors being stimulated with 3 pathogens, for 2 different timepoints. More specifically, we identified context- and cell-type-specific eQTLs and co-expression QTLs in PBMCs.

  Study EGAS00001005376

• Mutational landscape of high-grade B-cell lymphoma with MYC-, BCL2 and/or BCL6 rearrangements characterized by whole-exome sequencing

  To inform on oncogenic drivers, mutational signatures and perturbed pathways in HGBL-DH/TH in comparison with diffuse large-B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL), we performed whole-exome sequencing and confirmatory deep panel NGS of 47 clinically annotated cases. Coupled germline DNA was analyzed when available.

  Study EGAS00001005420

• ChIP-seq data of H3K4me3, H3K27ac and H3K27me3 on multiple human embryonic tissues.

  The regulatory landscape of the human genome during organogenesis is undescribed for most tissues. We used ChIP-seq to survey histone modifications in 13 human embryonic tissues. We describe patterns of both common and tissue-specific marking of promoter activation and repression and use enhancer usage to infer regulatory pathways.

  Study EGAS00001003163

• Whole-Exome Sequences from Imazighen and non-Imazghen from Tunisia

  Study of high-coverage whole-exome sequences from Amazigh (Tamazight-speakers) and non-Amazigh individuals (Arab-speakers) from Tunisia to analyze the impact of demography in functional genomic variation in the complex demographic context of North Africa. Amazigh individuals were sampled in Chenini and Douiret, and non-Amazigh individuals were sampled in Tunis.

  Study EGAS00001005205

• The gut microbiota in prediabetes and diabetes: a population-based cross-sectional study

  The link between the gut microbiota and type 2 diabetes (T2D) warrants further investigation because of known confounding effects from antidiabetic treatment. Here we profiled the gut microbiome in a discovery (n=1011) and validation (n=484) cohort comprising Swedish subjects naive for diabetes treatment and grouped by glycemic status.

  Study EGAS00001004480