Abstract
The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2683 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 5 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. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.
Highlights
The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations
We studied the relationships between the Vietnamese genetic profile and common genetic disorders, and discovered pathogenic variants related to prevalent diseases in Vietnam
We showed that non-invasive prenatal testing data could be reliably used to reconstruct the genetic profile of the Vietnamese population
Summary
The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. Following the successful initiative of the 1000 genomes p roject[1], several large-scale genome and exome sequencing projects have been conducted, either as international collaboration efforts such as ExAC2, gnomAD3, or for a specific country or p opulation[4,5,6,7,8] Those projects have provided comprehensive profiles of human genetic variation in some populations, paving the way for unprecedented advance in treatment of common genetic diseases. An alternative approach has been proposed recently to re-use the low-coverage genome sequencing data from non-invasive prenatal testing (NIPT) for large-scale population genetics s tudies[12,13]. The resulted database of Vietnamese genetic variants from NIPT data is made available to facilitate future research studies in population genetics and associated traits or diseases
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