Publication:
The Thai reference exome (T-REx) variant database

Issued Date

2021-12-01

Resource Type

Article

ISSN

13990004
00099163

DOI

10.1111/cge.14060

Other identifier(s)

2-s2.0-85115215991

Rights

Mahidol University

Rights Holder(s)

SCOPUS

Bibliographic Citation

Clinical Genetics. Vol.100, No.6 (2021), 703-712

Suggested Citation

Vorasuk Shotelersuk, Duangdao Wichadakul, Chumpol Ngamphiw, Chalurmpon Srichomthong, Chureerat Phokaew, Alisa Wilantho, Sujiraporn Pakchuen, Vorthunju Nakhonsri, Philip James Shaw, Rujipat Wasitthankasem, Jittima Piriyapongsa, Pongsakorn Wangkumhang, Adjima Assawapitaksakul, Wanna Chetruengchai, Keswadee Lapphra, Athiphat Khuninthong, Pattarapong Makarawate, Kanya Suphapeetiporn, Surakameth Mahasirimongkol, Nusara Satproedprai, Thantrira Porntaveetus, Prapaporn Pisitkun, Verayuth Praphanphoj, Piranit Kantaputra, Wichittra Tassaneeyakul, Sissades Tongsima The Thai reference exome (T-REx) variant database. Clinical Genetics. Vol.100, No.6 (2021), 703-712. doi:10.1111/cge.14060 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/75921

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Title

The Thai reference exome (T-REx) variant database

Author(s)

Vorasuk Shotelersuk
 Duangdao Wichadakul
 Chumpol Ngamphiw
 Chalurmpon Srichomthong
 Chureerat Phokaew
 Alisa Wilantho
 Sujiraporn Pakchuen
 Vorthunju Nakhonsri
 Philip James Shaw
 Rujipat Wasitthankasem
 Jittima Piriyapongsa
 Pongsakorn Wangkumhang
 Adjima Assawapitaksakul
 Wanna Chetruengchai
 Keswadee Lapphra
 Athiphat Khuninthong
 Pattarapong Makarawate
 Kanya Suphapeetiporn
 Surakameth Mahasirimongkol
 Nusara Satproedprai
 Thantrira Porntaveetus
 Prapaporn Pisitkun
 Verayuth Praphanphoj
 Piranit Kantaputra
 Wichittra Tassaneeyakul
 Sissades Tongsima

Other Contributor(s)

Siriraj Hospital
 Chulalongkorn University
 Faculty of Medicine, Khon Kaen University
 King Chulalongkorn Memorial Hospital
 Faculty of Medicine Ramathibodi Hospital, Mahidol University
 Thailand Ministry of Public Health
 Thailand National Center for Genetic Engineering and Biotechnology
 Thailand National Science and Technology Development Agency
 Chiang Mai University

Abstract

To maximize the potential of genomics in medicine, it is essential to establish databases of genomic variants for ethno-geographic groups that can be used for filtering and prioritizing candidate pathogenic variants. Populations with non-European ancestry are poorly represented among current genomic variant databases. Here, we report the first high-density survey of genomic variants for the Thai population, the Thai Reference Exome (T-REx) variant database. T-REx comprises exome sequencing data of 1092 unrelated Thai individuals. The targeted exome regions common among four capture platforms cover 30.04 Mbp on autosomes and chromosome X. 345 681 short variants (18.27% of which are novel) and 34 907 copy number variations were found. Principal component analysis on 38 469 single nucleotide variants present worldwide showed that the Thai population is most genetically similar to East and Southeast Asian populations. Moreover, unsupervised clustering revealed six Thai subpopulations consistent with the evidence of gene flow from neighboring populations. The prevalence of common pathogenic variants in T-REx was investigated in detail, which revealed subpopulation-specific patterns, in particular variants associated with erythrocyte disorders such as the HbE variant in HBB and the Viangchan variant in G6PD. T-REx serves as a pivotal addition to the current databases for genomic medicine.

Keyword(s)

Biochemistry, Genetics and Molecular Biology
 Medicine

Availability

URI

https://repository.li.mahidol.ac.th/handle/123456789/75921

Collections

Scopus 2021