Project description:The Sahel/Savannah belt harbours diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals—comprising 14 ethnolinguistic groups, including ten previously unsampled populations. DNA samples were genotyped on the Illumina H3Africa Consortium Array (BeadChip type: H3Africa_2017_20021485_A2; designed for SNP-genotyping of 2,267,346 SNPs) at the SNP&SEQ Technology Platform, NGI/SciLifeLab Genomics (Sweden). Reference: Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt. Fortes-Lima C, Tříska P, Čížková M, Podgorná E, Diallo MY, Schlebusch CM, Černý V. Molecular Biology and Evolution 2022 39(10):msac209. doi: 10.1093/molbev/msac209. PMID: 36173804 .
Project description:This collection of samples were genotyped to use altogether with other data to gain insight into the mechanism behind celiac disease.
Project description:The samples were genotyped on the H3Africa array (~2.3M SNPs) using the Illumina FastTrack Sequencing Service2. The default Illumina pipeline was used for the genotype calling (build GRCh37/hg19). The data was converted to PLINK using the h3abionet/h3agwas/call2plink pipeline and QC done using the h3abionet/h3agwas/qc pipeline
Project description:A genome-wide eQTL analysis was performed in whole blood samples collected from 76 Japanese subjects. RNA microarray analysis was performed for 3 independent samples that were genotyped in a genome-wide scan. The correlations between the genotypes of 534,404 autosomal single nucleotide polymorphisms (SNPs) and the expression levels of 30,465 probes were examined for each sample. The SNP-probe pairs with combined correlation coefficients of all 3 samples corresponding to P < 3.10 × 10-12 (i.e., Bonferroni-corrected P < 0.05) were considered significant. SNP-probe pairs with a high likelihood of cross-hybridization and SNP-in-probe effects were excluded to exclude false positive results. We identified 102 cis-acting and 5 trans-acting eQTL regions. The cis-eQTL regions were widely distributed both upstream and downstream of the gene, as well as within the gene.
Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).
Project description:H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011060 (dataset).
Project description:Pilot study on the interplay between genetic, epigenetic, and environmental risk factors for obesity and related cardiometabolic diseases with 973 samples from South Africa genotyped on Illumina Human MetaboChip array.
Project description:Comparison of Genotyping using pooled DNA samples (Allelotyping) and Individual Genotyping using the Affymetrix Genome-Wide Human SNP Array 6.0 In this study, data from 100 DNA samples individually genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0 were used to estimate the error of the pooling approach by comparing the results with those obtained using the same array type but DNA pools each composed of 50 of the same samples. Newly developed and established methods for signal intensity correction were applied. Furthermore, the relative allele intensity signals (RAS) obtained by allelotyping were compared to the corresponding values derived from individual genotyping. Similarly, differences in RAS values between pools were determined and compared.
Project description:To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 55 samples from 54 patients that were genotyped with Omni1-Quad.