Viability of in-house datamarting approaches for population genetics analysis of snp genotypes

Background: Databases containing very large amounts of SNP (Single Nucleotide Polymorphism) data are now freely available for researchers interested in medical and/or population genetics applications. While many of these SNP repositories have implemented data retrieval tools for general-purpose mining, these alone cannot cover the broad spectrum of needs of most medical and population genetics studies. Results: To address this limitation, we have built in-house customized data marts from the raw data provided by the largest public databases. In particular, for population genetics analysis based on genotypes we have built a set of data processing scripts that deal with raw data coming from the major SNP variation databases (e.g. HapMap, Perlegen), stripping them into single genotypes and then grouping them into populations, then merged with additional complementary descriptive information extracted from dbSNP. This allows not only in-house standardization and normalization of the genot...

• Type: Conference
• Year: 2008
• Where: CIKM
• Authors: Jorge Amigo, Christopher Phillips, Antonio Salas
• Keywords: CIKM 2008, Information Management, Population Genetics, Raw Data, SNP Repositories