Copy number variation in Thai population

Bhoom Suktitipat; Chaiwat Naktang; Wuttichai Mhuantong; Thitima Tularak; Paramita Artiwet; Ekawat Pasomsap; Wallaya Jongjaroenprasert; Suthat Fuchareon; Surakameth Mahasirimongkol; Wasan Chantratita; Boonsit Yimwadsana; Varodom Charoensawan; Natini Jinawath

doi:10.1371/journal.pone.0104355

Copy number variation in Thai population

PLoS One. 2014 Aug 13;9(8):e104355. doi: 10.1371/journal.pone.0104355. eCollection 2014.

Affiliations

¹ Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
² Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
³ Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani, Thailand.
⁴ Faculty of Information and Communication Technology, Mahidol University, Nakhon Prathom, Thailand.
⁵ Division of Virology and Molecular microbiology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
⁶ Endocrine and Metabolism Unit, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
⁷ Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Prathom, Thailand.
⁸ Medical Genetics Section, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand.
⁹ Faculty of Information and Communication Technology, Mahidol University, Nakhon Prathom, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
¹⁰ Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
¹¹ Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.

Abstract

Copy number variation (CNV) is a major genetic polymorphism contributing to genetic diversity and human evolution. Clinical application of CNVs for diagnostic purposes largely depends on sufficient population CNV data for accurate interpretation. CNVs from general population in currently available databases help classify CNVs of uncertain clinical significance, and benign CNVs. Earlier studies of CNV distribution in several populations worldwide showed that a significant fraction of CNVs are population specific. In this study, we characterized and analyzed CNVs in 3,017 unrelated Thai individuals genotyped with the Illumina Human610, Illumina HumanOmniexpress, or Illumina HapMap550v3 platform. We employed hidden Markov model and circular binary segmentation methods to identify CNVs, extracted 23,458 CNVs consistently identified by both algorithms, and cataloged these high confident CNVs into our publicly available Thai CNV database. Analysis of CNVs in the Thai population identified a median of eight autosomal CNVs per individual. Most CNVs (96.73%) did not overlap with any known chromosomal imbalance syndromes documented in the DECIPHER database. When compared with CNVs in the 11 HapMap3 populations, CNVs found in the Thai population shared several characteristics with CNVs characterized in HapMap3. Common CNVs in Thais had similar frequencies to those in the HapMap3 populations, and all high frequency CNVs (>20%) found in Thai individuals could also be identified in HapMap3. The majorities of CNVs discovered in the Thai population, however, were of low frequency, or uniquely identified in Thais. When performing hierarchical clustering using CNV frequencies, the CNV data were clustered into Africans, Europeans, and Asians, in line with the clustering performed with single nucleotide polymorphism (SNP) data. As CNV data are specific to origin of population, our population-specific reference database will serve as a valuable addition to the existing resources for the investigation of clinical significance of CNVs in Thais and related ethnicities.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
DNA Copy Number Variations*
Databases, Genetic
Genetic Variation
Genome, Human
Genotype
Humans
Markov Chains
Thailand

Grants and funding

The current project was supported by the Thailand Research Fund (http://www.trf.or.th), the Commission on Higher Education, and Mahidol University (TRF-CHE-MU grant number MRG 5480183) to NJ. BS is supported by “Chalermphrakiat” grant, Faculty of Medicine Siriraj Hospital, Mahidol University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.