title: Copy number variation in Thai population.
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.
authors.affiliation: Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
authors.forename: Bhoom
authors.initials: B
authors.lastname: Suktitipat
authors.affiliation: Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
authors.forename: Chaiwat
authors.initials: C
authors.lastname: Naktang
authors.affiliation: Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani, Thailand.
authors.forename: Wuttichai
authors.initials: W
authors.lastname: Mhuantong
authors.affiliation: Faculty of Information and Communication Technology, Mahidol University, Nakhon Prathom, Thailand.
authors.forename: Thitima
authors.initials: T
authors.lastname: Tularak
authors.affiliation: Faculty of Information and Communication Technology, Mahidol University, Nakhon Prathom, Thailand.
authors.forename: Paramita
authors.initials: P
authors.lastname: Artiwet
authors.affiliation: Division of Virology and Molecular microbiology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Ekawat
authors.initials: E
authors.lastname: Pasomsap
authors.affiliation: Endocrine and Metabolism Unit, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Wallaya
authors.initials: W
authors.lastname: Jongjaroenprasert
authors.affiliation: Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Prathom, Thailand.
authors.forename: Suthat
authors.initials: S
authors.lastname: Fuchareon
authors.affiliation: Medical Genetics Section, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand.
authors.forename: Surakameth
authors.initials: S
authors.lastname: Mahasirimongkol
authors.affiliation: Division of Virology and Molecular microbiology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Wasan
authors.initials: W
authors.lastname: Chantratita
authors.affiliation: Faculty of Information and Communication Technology, Mahidol University, Nakhon Prathom, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
authors.forename: Boonsit
authors.initials: B
authors.lastname: Yimwadsana
authors.affiliation: Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
authors.forename: Varodom
authors.initials: V
authors.lastname: Charoensawan
authors.affiliation: Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Integrative Computation BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
authors.forename: Natini
authors.initials: N
authors.lastname: Jinawath
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D014644:Genetic Variation; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008390:Markov Chains; D013785:Thailand