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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

SNPSTR: a database of compound microsatellite-SNP markers.

I Agrafioti¹, M P H Stumpf

¹Centre for Bioinformatics, Division of Molecular Biosciences, London, UK.

Nucleic Acids Research

|January 5, 2007

Summary

Researchers have developed SNPSTRs, a novel genetic marker combining microsatellites and SNPs. This tool aids in understanding population genetics and evolutionary history across various species.

Area of Science:

Population Genetics
Molecular Evolution
Genomics

Background:

Genetic markers like single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) are crucial for population genetic studies.
Analyzing past demographic events and selection requires robust genetic markers.

Purpose of the Study:

To introduce and catalogue a new type of compound genetic marker, SNPSTRs.
To highlight the utility of SNPSTRs for population genetic inferences.

Main Methods:

Developed a database (SNPSTR database) cataloguing SNPSTRs.
Defined SNPSTRs as microsatellite markers tightly linked (less than 250 bp apart) with one or more SNPs.
Ensured no recombination occurs between linked SNP and STR components.

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Main Results:

SNPSTRs function as small haplotypes due to close linkage.
The SNPSTR database includes human, mouse, rat, dog, and chicken SNPSTRs.
SNPSTRs offer potential as a valuable tool in population genetics.

Conclusions:

SNPSTRs represent a novel and powerful genetic marker for population genetics.
The SNPSTR database provides a comprehensive resource for multiple species.
SNPSTRs can enhance the study of population history and selection effects.