SNPforID browser

The existence of different online genotyping data repositories for population studies forces the researcher not only to query them all, but to have to adapt to the different results obtained. We have developed a simple yet powerful web framework for any given population based SNP genotype database that is able to deal even with virtually any number of genotypes, and that is also capable of summarizing all that information into the most common population genetics indices such as allele frequencies, heterozygosity, FST or In.

We have also built a web interface to present the statistical summaries in a succinct but informative manner. These aids, that go from: allowing the combination of different populations into a single user-defined query to presenting allele frequencies in pie charts, will allow the researcher to obtain the critical information underlying each SNP, and to be able to compare the results of different and customizable population sets of interest.

References

Amigo J, Phillips C, Lareu M, Carracedo A. The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med 2008, 122(5):435-440.

M. Fondevila, C. Phillips, C. Santos, A. Freire Aradas, P.M. Vallone, J.M. Butler, M.V. Lareu, A´. Carracedo Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies Forensic Sci. Int. Genet. 2012, http://dx.doi.org/10.1016/ j.fsigen.2012.06.007

C. Phillips, A. Salas, J.J. Sanchez, M. Fondevila, A. Gómez-Tato, J. Álvarez-Dios, M. Calaza, M. Casares de Cal, D. Ballard, M.V. Lareu, Á. Carracedo, The SNPforID Consortium. Inferring ancestral origin using a single multiplex assay of autosomal ancestry-informative marker SNPs. Forensic Sci. Int. Genetics 2007, 1:273-280.

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Latest News

XSS attack patched
Thursday, 13th August 2015 10:00:00
Due to a XSS attack exposure fix, the SPSmart site has been returning search errors for a few hours. It has now been patched. Thank you to all the users that have reported the issue to us.

popSTR update
Wednesday, 15th April 2015 15:00:00
Two new STR groups were added: Illumina ForenSeq and NIST Mini-STRs

Population updates
  • jul 2012: Egypt (46), Libya (101), Yemen (86)
SPSmart's Changelog
  • nov 2012: SPSmart v5.1.2
    • reviewed gene search search
  • apr 2012: SPSmart v5.1.1
    • reviewed chr:pos search
  • sep 2011: SPSmart v5.1
    • 1000 Genomes Phase I interim analysis updated (1093 individuals)
    • improved datasets' snp list comparison
    • reviewed live support on "contact" section
  • feb 2011: SPSmart v5.0
    • support for whole genome sequencing variant calls
    • 1000 Genomes Phase I interim analysis included (629 individuals)
    • dbSNP mapping data updated to build #132
    • added gene information and link to Ensembl's genome browser for non-rs SNPs
  • sep 2010: SPSmart v5.0 beta
    • HapMap data updated to release #28
    • gene names normalization using HGNC aproved codes
    • discordant gene names listed in results' "messages" tab
    • customizable pagination of results for large queries
    • reviewed population filters
    • added filtering option for multi-allelic SNPs
    • population size displayed on search page when mousing over
    • reviewed FST and In calculation and display
    • reviewed pie chart generator for multi-allelic SNPs
    • added hosting server resources monitoring to debug possible errors
    • lighter and faster web interface, now using CSS3 standards
  • jan 2010: SPSmart v4.1
    • dbSNP mapping data updated to build #130
    • updated scripts for the datamart generation
  • sep 2009: SPSmart v4.0
    • major recode to reduce database queries performance
    • SPSmart framework adapted to STR data
  • feb 2009: SPSmart v3.4
    • HapMap data updated to release #27
    • SNPs not genotyped on every compared dataset filtered by default
  • jan 2009: SPSmart v3.3
    • allele frequencies added to the downloadable full statistics file
    • optimized results page generation
  • dec 2008: SPSmart v3.2
    • HapMap data updated to release #26
    • merged snp codes revised
  • oct 2008: SPSmart v3.1
    • HapMap Phase II data updated to release #24
    • HapMap Phase III first draft release data included
    • genotypes and sample lists available for download
    • In values revised to take missing data into account
    • deprecated SNP codes listed on results' "messages" tab
  • aug 2008: SPSmart v3.0
    • data mart structure migrated to mysql
    • available databases can be compared
    • populations and their combinations may be filtered by MAF, FST and In
    • lists of filtered snps displayed at results' "messages" tab
    • optional filter of snps not genotyped on every compared database
    • optional results for download only (saving displaying time)
    • snp search engine optimized and adapted to mysql
    • SNPforID datasets' snp lists resorted
    • live support available from "contact" section
  • jul 2008: SPSmart v2.3.1
    • snp search engine revised
    • improved web navigation among datasets
  • jul 2008: SPSmart v2.3
    • HapMap Phase III data (preliminary release) included
    • dbSNP data updated to build 129
    • added new colombian samples to the SNPforID's 52-plex dataset
    • chromosome tagging discrepancies solved using dbSNP's reference
    • added a results' "messages" tab for displaying query issues (if any)
    • not found snps listed on results' "messages" tab
  • jun 2008: SPSmart v2.2
    • Michigan's HGDP-CEPH data included
    • In values added to "statistics" results' tab
    • FST negative values filtered (shown as null)
  • may 2008: SPSmart v2.1
    • dbSNP's merged snps information considered
      • latest dbSNP's merged snp codes point to corresponding data
      • merged dataset's snp codes allowed (greyed on results page)
    • reduced web code to decrease loading time
    • reduced web interface's javascript dependency
  • apr 2008: SPSmart v2.0
    • dbSNP descriptive data included
    • Stanford's HGDP-CEPH data included
    • HapMap Phase II data updated to release #23a
    • new data displayed for each snp on the "statistics" results tab
      • chromosome
      • chromosome position
      • validation status
      • genes where the snp is found
      • reference allele on snp strand
      • ancestral allele from chimp
    • all chromosome positions are mapped to latest dbSNP build
    • search function added based on genes
    • image maps revised
  • feb 2008: SPSmart v1.5
    • Perlegen's complete set included mapped to dbSNP build 123
    • Hapmap alleles reviewed, considering monomorphic and non biallelic snps
    • significant code optimization for preprocessing at genotype level
    • added a "downloads" results' tab for downloading flat data files
    • snp list function reviewed
      • case-insensitive
      • duplicates removed
      • internal snps considered
    • web interface optimized for flash and javascript compatibility
  • jan 2008: SPSmart v1.0
    • HapMap Phase II release #22 included mapped to dbSNP build 126
    • the SNPforID browser becomes part of SPSmart
    • perl scripts created to precalculate all the statistics
    • results divided in tabs to allow more information to be displayed
    • Heterozygosity and FST values added to "statistics" results' tab
    • major code review to deal with digested data
    • HapMap piecharts generated on-the-fly
    • HapMap data links for comparisons updated
    • web interface reviewed for web standards compliancy
  • oct 2007: SNPforID browser v1.3
    • SNPforID's 34-plex dataset added
    • major code review to deal with non-biallelic snps
    • data from each selected population set is downloadable
    • results layout recoded for a faster display
    • map engine updated, legend added
    • images preloading function reviewed
  • sep 2007: SNPforID browser v1.2
    • results layout compressed to allow more information to be displayed
    • up to 5 population/group comparisons permitted
    • symmetrical SNPs reviewed
    • improved images preloading, including HapMap Phase II data
  • dec 2006: SNPforID browser v1.1
    • population grouping in the search page
    • dynamic checkboxes filling in the search page
    • HapMap Phase II data retrieval is now optional
    • piecharts library preloading for a faster results display
  • dec 2005: SNPforID browser v1.0
    • the SNPforID browser is now online
    • SNPforID's 52-plex dataset added
    • up to 2 population/group comparisons permitted
    • allele frequencies are displayed as piecharts for visual inspection
    • data retrieved from HapMap Phase II and displayed for additional comparisons