Genetic profiling of 2,683 Vietnamese genomes from non-invasive prenatal testing data

Abstract Background: The under-representation of Vietnamese ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in the population. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in Vietnam and many developing countries. Non-invasive prenatal testing (NIPT) data offers an alternative untapped resource to study genetic variations in the Vietnamese population. Results: We analyzed the low-coverage genomes of 2,683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially five pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. Conclusions: We have demonstrated a successful analysis of NIPT data to reconstruct the Vietnamese genetic profiles. This application provides a powerful yet cost-effective approach for large-scale population genetic studies.