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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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Selecting single-nucleotide polymorphisms for association studies with SNPbrowser software.

Francisco M De La Vega¹

¹Applied Biosystems, Foster City, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|November 7, 2007

Summary

This summary is machine-generated.

Selecting single-nucleotide polymorphisms (SNPs) for genetic association studies is crucial for statistical power and cost-efficiency. SNPbrowser software aids this process by integrating HapMap data and annotations for optimized study design.

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Area of Science:

Genetics
Bioinformatics
Statistical Genetics

Background:

Genetic association studies rely on selecting informative single-nucleotide polymorphisms (SNPs) for statistical power and cost-effectiveness.
Maximizing linkage disequilibrium (LD) between selected markers and causative mutations is key for successful study design.
The HapMap Project provides extensive genome-wide SNP data across diverse populations, serving as a valuable resource.

Purpose of the Study:

To review workflows for selecting genetic markers for association studies.
To introduce SNPbrowser software as a tool for integrating diverse data and annotations.
To streamline the process of designing high-power, cost-effective genetic studies.

Main Methods:

Utilizing the SNPbrowser software, a standalone application.
Integrating HapMap database information with gene and SNP annotations.
Applying strategies for SNP selection based on observed LD, including haplotype tagging.

Main Results:

SNPbrowser facilitates the integration of complex algorithms and disparate data sources.
The software aids in selecting SNPs with high probability of being in LD with causative variants.
Selected SNPs are screened for genotyping platform compatibility, accelerating study setup.

Conclusions:

SNPbrowser offers a unified platform for marker selection in genetic association studies.
The software enhances the efficiency and success probability of genetic study design.
Integrating data and computational tools like SNPbrowser is essential for modern genetic research.