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Hoang TH, Vu DM, Vu GM, Nguyen TK, Do NM, Duong VC, Pham TL, Tran MH, Khanh Nguyen LT, Han HTT, Can TT, Pham TH, Pham TD, Nguyen TH, Do HP, Vo NS, Nguyen XH. A study of genetic variants associated with skin traits in the Vietnamese population. BMC Genomics 2024; 25:52. [PMID: 38212682 PMCID: PMC10785522 DOI: 10.1186/s12864-023-09932-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field. OBJECTIVES We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). Also, we compared the genetic predispositions of 25 skin-related traits of Vietnamese population to others to acquire population-specific insights regarding skin health. METHODS Vietnamese cohorts of whole-genome sequencing (WGS) of 1008 healthy individuals for the reference and 96 genotyping samples (which do not have any skin cutaneous issues) by Infinium Asian Screening Array-24 v1.0 BeadChip were employed to predict skin-associated genetic variants of 25 skin-related and micronutrient requirement traits in population analysis and correlation analysis. Simultaneously, we compared the landscape of cutaneous issues of Vietnamese people with other populations by assessing their genetic profiles. RESULTS The skin-related genetic profile of Vietnamese cohorts was similar at most to East Asian cohorts (JPT: Fst = 0.036, CHB: Fst = 0.031, CHS: Fst = 0.027, CDX: Fst = 0.025) in the population study. In addition, we identified pairs of skin traits at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p = 1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3)). CONCLUSION This is the first investigation in Vietnam to explore genetic variants of facial skin. These findings could improve inadequate skin-related genetic diversity in the currently published database.
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Affiliation(s)
- Tham Hong Hoang
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | - Duc Minh Vu
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Giang Minh Vu
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | | | - Vinh Chi Duong
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | - Mai Hoang Tran
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | | | - Thu-Thuy Can
- Vinmec Times City International Hospital, Vinmec Healthcare System, Hanoi, Vietnam
| | | | - Tho Duc Pham
- View Plastic Surgery Center, Vinmec, Hanoi, Vietnam
| | - Thanh Hong Nguyen
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | | | - Nam S Vo
- GeneStory JSC, Hanoi, Vietnam.
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam.
| | - Xuan-Hung Nguyen
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam.
- College of Health Sciences, VinUniversity, Hanoi, Vietnam.
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