genetics study with SNP/CNV Genotypes (NGS), WGS data on dbGaP (100 participants)

phs003694 — Blood Group Genotypes and Phenotypes in Omani Blood Donors and Its Links    With Susceptibility to Malaria

The Omani population experienced endemic malaria prior to eradication in the late 1990's. Since malaria is known to be a strong selective pressure on the human genome, particularly at blood group associated loci, we aimed to understand how selective pressures from malaria may be affecting genetic variation at blood group loci. Blood samples were collected from 100 healthy, Omani blood donors. Serology testing for 10 clinically relevant blood groups and whole genome sequencing (WGS) to an average coverage of 16X were performed on all samples. Additionally, using the WGS data, genetic variants (SNPs and INDELs) were called for chromosomes 1 - 22 using GRCh38. We find signals of selection at the Plasmodium vivax associated locus, <a href="https://www.ncbi.nlm.nih.gov/gene/2532">ACKR1</a> (the Duffy blood group), but not at any Plasmodium falciparum associated loci. We also characterized several previously undescribed blood group alleles in the Omani population affecting antigenic expression, mostly at the <a href="https://www.ncbi.nlm.nih.gov/gene/6007">RHD</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/6006">RHCE</a>, and <a href="https://www.ncbi.nlm.nih.gov/gene/2994">GYPB</a> loci. The data available from this project include BAM files from 100 Omani samples aligned to GRCh38, per chromosome VCF files, and results from the serology tests for all 10 blood groups.