In silico genotyping of blood group alleles using WGS data: a comparative study of the Orang Asli in Peninsular Malaysia with major global populations

• Published in: Journal of Genetics
• Main Author: Rophina M.; Kek T.L.; Sivasubbu S.; Scaria V.; Salleh M.Z.
• Format: Article
• Language: English
• Published: Springer 2023
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85169159161&doi=10.1007%2fs12041-023-01438-6&partnerID=40&md5=a96602cc582f75901adf1632acdf4627

Differences in the distribution of RBC antigens defining the blood group types among different populations have been well established. Fewer studies exist that have explored the blood group profiles of indigenous populations worldwide. With the availability of population-scale genomic datasets, we have explored the blood group profiles of the Orang Aslis, who are the indigenous population in Peninsular Malaysia and provide a systematic comparison of the same with major global population datasets. Variant call files from whole genome sequence data (hg19) of 114 Orang Asli were retrieved from The Orang Asli Genome Project. Systematic variant annotations were performed using ANNOVAR and only those variants mapping back to genes associated with 43 blood group systems and transcription factors KLF1 and GATA1 were filtered. Blood group-associated allele and phenotype frequencies were determined and were duly compared with other datasets including Singapore Sequencing Malay Project, aboriginal western desert Australians and global population datasets including The 1000 Genomes Project and gnomAD. This study reports four alleles (rs12075, rs7683365, rs586178 and rs2298720) of DUFFY, MNS, RH and KIDD blood group systems which were significantly distinct between indigenous Orang Asli and cosmopolitan Malaysians. Eighteen alleles that belong to 14 blood group systems were found statistically distinct in comparison to global population datasets. Although not much significant differences were observed in phenotypes of most blood group systems, major insights were observed when comparing Orang Asli with aboriginal Australians and cosmopolitan Malaysians. This study serves as the first of its kind to utilize genomic data to interpret blood group antigen profiles of the Orang Asli population. In addition, a systematic comparison of blood group profiles with related populations was also analysed and documented. © 2023, Indian Academy of Sciences.