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PanSNPdb: the Pan-Asian SNP genotyping database.

Chumpol Ngamphiw1, Anunchai Assawamakin, Shuhua Xu

  • 1National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, Thailand.

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Summary

The HUGO Pan-Asian SNP consortium surveyed human genetic diversity across 71 Asian populations, creating a comprehensive database (PanSNPdb) for population structure and variation analysis.

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Area of Science:

  • Human Genetics
  • Population Genetics
  • Bioinformatics

Background:

  • Understanding human genetic diversity is crucial for biomedical research.
  • Previous surveys have not comprehensively captured the genetic landscape of Asian populations.

Purpose of the Study:

  • To conduct the largest survey of human genetic diversity among Asian populations.
  • To create a comprehensive database (PanSNPdb) for analyzing population structure, linkage disequilibrium, haplotype distributions, and copy number variations.

Main Methods:

  • Sampled 1,719 unrelated individuals from 71 diverse Asian populations.
  • Constructed PanSNPdb, integrating SNP and CNV data.
  • Developed an interactive comparison with existing genetic variation databases (HapMap3, JSNP, dbSNP, DGV).

Main Results:

  • Established PanSNPdb as a significant resource for human genetic diversity in Asia.
  • Provided detailed analyses of linkage disequilibrium, haplotype distributions, and copy number variations.
  • Enabled interactive comparisons with other major genetic databases.

Conclusions:

  • PanSNPdb offers a comprehensive resource for studying Asian population structure and genetic variation.
  • The database facilitates research into human genetic diversity and comparative genomics.
  • PanSNPdb is accessible via a user-friendly graphical interface for broad research community use.