RT Journal Article
T1 SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access
A1 Amigo Lechuga, Jorge
A1 Salas Ellacuriaga, Antonio
A1 Phillips, Christopher Paul
A1 Carracedo Álvarez, Ángel
AB Background: In the last five years large online resources of human variability have appeared,notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with populationinformation act as catalogues of human diversity, and are widely used as reference sources forpopulation genetics studies. Although many useful conclusions may be extracted by queryingdatabases individually, the lack of flexibility for combining data from within and between eachdatabase does not allow the calculation of key population variability statistics.Results: We have developed a novel tool for accessing and combining large-scale genomicdatabases of single nucleotide polymorphisms (SNPs) in widespread use in human populationgenetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data martfrom the most commonly accessed databases of genotypes containing population information: datais mined, summarized into the standard statistical reference indices, and stored into a relationaldatabase that currently handles as many as 4 × 109 genotypes and that can be easily extended tonew database initiatives. We have also built a web interface to the data mart that allows thebrowsing of underlying data indexed by population and the combining of populations, allowingintuitive and straightforward comparison of population groups. All the information served isoptimized for web display, and most of the computations are already pre-processed in the datamart to speed up the data browsing and any computational treatment requested.Conclusion: In practice, SPSmart allows populations to be combined into user-defined groups,while multiple databases can be accessed and compared in a few simple steps from a single query.It performs the queries rapidly and gives straightforward graphical summaries of SNP populationvariability through visual inspection of allele frequencies outlined in standard pie-chart format. Inaddition, full numerical description of the data is output in statistical results panels that includecommon population genetics metrics such as heterozygosity, Fst and In.
PB BMC
SN 1471-2105
YR 2008
FD 2008
LK http://hdl.handle.net/10347/22707
UL http://hdl.handle.net/10347/22707
LA eng
NO Amigo, J., Salas, A., Phillips, C. et al. SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics 9, 428 (2008). https://doi.org/10.1186/1471-2105-9-428
NO The grants from the Xunta de Galicia (PGIDIT06PXIB208079PR) and Fundación de Investigación Médica Mutua Madrileña awarded to AS partiallysupported this project
DS Minerva
RD 28 abr 2026