Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing

Choochuen, Pongsakorn; Sangkhathat, Surasak; Sukpan, Nattanan; Singkhamanan, Kamonnat; Wonglapsuwan, Monwadee; Sukpan, Panupong; Surachat, Komwit

doi:10.3390/life16101651

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Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing

by

Pongsakorn Choochuen

¹,

Surasak Sangkhathat

²

,

Nattanan Sukpan

³,

Kamonnat Singkhamanan

¹

,

Monwadee Wonglapsuwan

⁴,

Panupong Sukpan

^5,*

and

Komwit Surachat

^1,*

¹

Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand

²

Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand

³

Tak Bai Hospital, Tak Bai, Narathiwat 96110, Thailand

⁴

Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand

⁵

Medical Education Center, Naradhiwas Rajanagarindra Hospital, Narathiwat 96000, Thailand

^*

Authors to whom correspondence should be addressed.

Life 2026, 16(10), 1651; https://doi.org/10.3390/life16101651

Submission received: 14 July 2026 / Revised: 14 September 2026 / Accepted: 28 September 2026 / Published: 30 September 2026

(This article belongs to the Section Genomics and Proteomics)

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Abstract

Population-specific genomic references remain limited for many Southeast Asian communities, particularly in Southern Thailand. We characterized the broad genetic affinity of 24 unrelated adults from Che He Subdistrict, Tak Bai District, Narathiwat Province, using whole-exome sequencing. Reads were processed against GRCh38, and population structure was assessed using reference-defined principal component analysis (PCA), ADMIXTURE, pairwise FST, EthSEQ, and KING-based relatedness analysis. A mean of 114.5 million reads per participant was retained (99.03%), with 99.98–99.99% mapping and a mean depth of 117.07× across the manufacturer-defined Agilent V8 targets. Joint genotyping identified 421,801 PASS variants. For expanded analysis, 24 Che He samples were compared with 3380 high-quality unrelated HGDP–1000 Genomes references. Group-specific missingness control retained 183,930 callable autosomal SNPs; reference-only minor-allele-frequency filtering and LD pruning retained 43,353 SNPs for projection. Che He clustered within the East Asian reference space, with its centroid closest to Cambodian across higher-dimensional summaries. Unpruned Weir–Cockerham FST was also lowest versus Cambodian (0.00256), followed by Dai (0.00892), KHV (0.00956), CDX (0.01149), and Lahu (0.01202). These results indicate relative genetic proximity within the available reference panel and should not be interpreted as definitive ancestry or ethnicity assignment.

Keywords: Che He; Tai Tak Bai; Southern Thailand; whole-exome sequencing; population structure; genetic ancestry; EthSEQ

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MDPI and ACS Style

Choochuen, P.; Sangkhathat, S.; Sukpan, N.; Singkhamanan, K.; Wonglapsuwan, M.; Sukpan, P.; Surachat, K. Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing. Life 2026, 16, 1651. https://doi.org/10.3390/life16101651

AMA Style

Choochuen P, Sangkhathat S, Sukpan N, Singkhamanan K, Wonglapsuwan M, Sukpan P, Surachat K. Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing. Life. 2026; 16(10):1651. https://doi.org/10.3390/life16101651

Chicago/Turabian Style

Choochuen, Pongsakorn, Surasak Sangkhathat, Nattanan Sukpan, Kamonnat Singkhamanan, Monwadee Wonglapsuwan, Panupong Sukpan, and Komwit Surachat. 2026. "Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing" Life 16, no. 10: 1651. https://doi.org/10.3390/life16101651

APA Style

Choochuen, P., Sangkhathat, S., Sukpan, N., Singkhamanan, K., Wonglapsuwan, M., Sukpan, P., & Surachat, K. (2026). Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing. Life, 16(10), 1651. https://doi.org/10.3390/life16101651

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing

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