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International Conference on Computational Systems-Biology and Bioinformatics

CSBio 2010: Computational Systems-Biology and Bioinformatics pp 130–140Cite as

Catalog of Genetic Variations (SNPs and CNVs) and Analysis Tools for Thai Genetic Studies

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 115))

Abstract

The Thailand SNP database (ThaiSNPdb) initiative is the first attempt to catalog both Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) from 32 healthy individuals in the central region of Thailand using the 5th generation Affymetrix SNP genotyping arrays. The aim of this initiative is to facilitate genetic studies of Thais by systematically cataloging large-scale population genetic polymorphism data from Thais combining with data from other different populations. Comparative views of both SNPs and CNVs were made possible with standard comprehensive and interactive graphic technology, called GBrowse. The database allows easy browsing and comparisons of genetic polymorphism data from Thai populations as well as others, which were retrieved from several public variation databases including NCBI dbSNP, HapMap3, JSNP and Database of Genomic Variant (DGV). As a result, this database can be considered as one of the largest collections of SNPs and CNVs. Furthermore, to enable genetic analysis, ThaiSNPdb offers three common genetic tools including linkage disequilibrium (LD), haplotype blocks and tagging SNPs. In conclusion, ThaiSNPdb is an invaluable platform to support the studies in personalized medicine, forensic sciences and even cytogenetic studies in the case of CNV analyses. ThaiSNPdb is available on the Internet and can be publicly accessed at http://www.biotec.or.th/thaisnp .

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Author information

Authors and Affiliations

  1. Bioinformatics and Systems Biology Program, King Mongkut’s University of Technology, Thonburi, Bangkok, Thailand, 10140

    Sattara Hattirat

  2. Biostatistics and Informatics Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Patumthani, 12120, Thailand

    Chumpol Ngamphiw, Anunchai Assawamakin & Sissades Tongsima

  3. School of Information and Technology, King Mongkut University of Technology, Thonburi, Bangkok, Thailand, 10140

    Jonathan Chan

Authors
  1. Sattara Hattirat
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  2. Chumpol Ngamphiw
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  3. Anunchai Assawamakin
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  4. Jonathan Chan
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  5. Sissades Tongsima
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Editor information

Editors and Affiliations

  1. School of Information Technology, King Mongkut’s University of Technology Thonburi, 126 Pracha U-Thit Rd, Bangmod, Thungkru, 10140, Bangkok, Thailand

    Jonathan H. Chan

  2. School of Computer Engineering, Nanyang Technological University, Block N4, 2b-39,Nanyang Avenue, 639798, Singapore

    Yew-Soon Ong

  3. Dept. of Computer Science, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, 120-749, Seoul, South Korea

    Sung-Bae Cho

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© 2010 Springer-Verlag Berlin Heidelberg

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Hattirat, S., Ngamphiw, C., Assawamakin, A., Chan, J., Tongsima, S. (2010). Catalog of Genetic Variations (SNPs and CNVs) and Analysis Tools for Thai Genetic Studies. In: Chan, J.H., Ong, YS., Cho, SB. (eds) Computational Systems-Biology and Bioinformatics. CSBio 2010. Communications in Computer and Information Science, vol 115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16750-8_12

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  • DOI: https://doi.org/10.1007/978-3-642-16750-8_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16749-2

  • Online ISBN: 978-3-642-16750-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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