Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance

• Published in: BMC research notes Vol. 14; no. 1; p. 105
• Main Authors: Khan, Salim, Akter, Shahina, Goswami, Barna, Habib, Ahashan, Banu, Tanjina Akhtar, Barton, Carl, Osman, Eshrar, Samir, Samiruzzaman, Arjuman, Farida, Hasan, Saam, Hossain, Maqsud
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 20-03-2021; BioMed Central; BMC
• Subjects: Bangladeshi; Bangladeshis; Chromosome Mapping; Chromosomes; Deoxyribonucleic acid; Disease; DNA; DNA sequencing; Ethnic Groups; Gene mapping; Gene Ontology; Genes; Genetic aspects; Genome; Genome mapping; Genomes; Health aspects; Heart; Humans; Identification and classification; Medical research; Mutation; NCBI SNP; Nucleotide sequence; Nucleotide sequencing; Polymorphism, Single Nucleotide; Population; Pre-eclampsia; Research Note; Single nucleotide polymorphisms; Single nucleotide variants; Single-nucleotide polymorphism; Values; Whole genome sequencing; Bangladesh; NCBI SNP; Bangladeshi; Whole genome sequencing; Genome mapping; Single nucleotide variants; Gene Ontology; NCBI Clinvar
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-021-05514-x

The major objective of the study was to sequence the whole genome of four Bangladeshi individuals and identify variants that are known to be associated with functional changes or disease states. We also carried out an ontology analysis to identify the functions and pathways most likely to be affected by these variants.
We identified around 900,000 common variants and close to 5 million unique ones in all four of the individuals. This included over 11,500 variants that caused nonsynonymous changes in proteins. Heart function associated pathways were heavily implicated by the ontology analysis; corroborating previous studies that claimed the Bangladeshi population as highly susceptible to heart disorders. Two variants were found that have been previously identified as pathogenic factors in familial hypercholesteremia and structural disorders of the heart. Other pathogenic variants we found were associated with pseudoxanthoma elasticum, cancer progression, polyagglutinable erythrocyte syndrome, preeclampsia, and others.