NDLI: Copy Number Variation in Thai Population

Content Provider	PubMed Central
Author	Suktitipat, Bhoom Naktang, Chaiwat Mhuantong, Wuttichai Tularak, Thitima Artiwet, Paramita Pasomsap, Ekawat Jongjaroenprasert, Wallaya Fuchareon, Suthat Mahasirimongkol, Surakameth Chantratita, Wasan Yimwadsana, Boonsit Charoensawan, Varodom Jinawath, Natini
Editor	Seo, Jeong-sun
Copyright Year	2014
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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0104355
Starting Page	104355
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	8
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-08-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Copy Number Variation across European Populations

Copy Number Variation in Familial Parkinson Disease

Copy Number Variation of Age-Related Macular Degeneration Relevant Genes in the Korean Population

Copy Number Variation at the APOL1 Locus

Elusive Copy Number Variation in the Mouse Genome

Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?

Family-Based Benchmarking of Copy Number Variation Detection Software

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Chromosome Copy Number Variation and Control in the Ciliate Chilodonella uncinata

Copy Number Variation in Thai Population

Similar Documents

Copy Number Variation across European Populations

Copy Number Variation in Familial Parkinson Disease

Copy Number Variation of Age-Related Macular Degeneration Relevant Genes in the Korean Population

Copy Number Variation at the APOL1 Locus

Elusive Copy Number Variation in the Mouse Genome

Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?

Family-Based Benchmarking of Copy Number Variation Detection Software

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Chromosome Copy Number Variation and Control in the Ciliate Chilodonella uncinata

Copy Number Variation in Thai Population