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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Related Experiment Video

Updated: Jun 29, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

Jorge Amigo¹, Antonio Salas, Christopher Phillips

¹Spanish National Genotyping Center (CeGen), Genomic Medicine Group, CIBERER, University of Santiago de Compostela, Galicia, Spain. jorge.amigo@usc.es

BMC Bioinformatics

|October 14, 2008

Summary

SPSmart enables researchers to combine and analyze human genetic diversity data from multiple large databases. This tool facilitates population genetics studies by rapidly calculating key variability statistics and providing graphical summaries.

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Infinium Assay for Large-scale SNP Genotyping Applications

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

Genomics
Population Genetics
Bioinformatics

Background:

Large online resources of human genetic variability, such as HapMap, Perlegen, and CEPH, catalog human diversity.
These databases are crucial for population genetics studies but lack flexibility for combined data analysis.
Existing tools do not allow for the calculation of key population variability statistics across different datasets.

Purpose of the Study:

To develop a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs).
To enable flexible calculation of population variability statistics by integrating data from multiple sources.
To provide an intuitive interface for comparing human population groups.

Main Methods:

Developed SPSmart (SNPs for Population Studies), a tool with a fast pipeline to create and maintain a data mart from genotype databases.
Mined, summarized, and stored data into a relational database capable of handling billions of genotypes.
Built a web interface for browsing data, combining populations, and performing rapid computations.

Main Results:

SPSmart allows combining populations into user-defined groups and accessing multiple databases via a single query.
The tool rapidly performs queries and provides graphical summaries of SNP population variability, including allele frequencies.
Full numerical descriptions of data, including heterozygosity and Fst, are available in statistical results panels.

Conclusions:

SPSmart offers a flexible and efficient solution for analyzing human genetic diversity across multiple large-scale databases.
The tool simplifies complex population genetics analyses, enabling straightforward comparisons of population groups.
It accelerates research by pre-processing computations and optimizing data for web display and analysis.