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Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

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,...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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

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SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system.

Alexander R Pico¹, Ivan V Smirnov, Jeffrey S Chang

¹Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA. apico@gladstone.ucsf.edu

Nucleic Acids Research

|November 6, 2008

Summary

This summary is machine-generated.

SNPLogic is a comprehensive system for selecting and annotating single nucleotide polymorphisms (SNPs) for genotyping projects. It integrates diverse data to aid in SNP prioritization and the interpretation of SNP-disease associations.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Single nucleotide polymorphisms (SNPs) are crucial genetic markers.
Effective selection and annotation of SNPs are vital for genotyping projects.
Existing SNP resources often lack comprehensive integration of diverse data types.

Purpose of the Study:

To introduce SNPLogic, a unified system for SNP selection, annotation, and prioritization.
To facilitate the design and analysis of genotyping projects.
To enhance the interpretation of SNP-disease association data.

Main Methods:

Integrated genetic context, genotypic data, commercial array coverage, and functional predictions.
Developed a web interface for user-defined SNP list construction, annotation, saving, sharing, and exporting.
Combined SNP annotation with pathway information and functional prediction scores.

Main Results:

SNPLogic provides a comprehensive resource for SNP information from multiple sources.
The system enables efficient identification and prioritization of candidate SNPs.
User-defined SNP lists can be easily managed and annotated.
Facilitated assessment of custom and commercial genotyping arrays.
Enabled annotation of new SNP data with publicly available information.

Conclusions:

SNPLogic offers a powerful, integrated approach to SNP analysis and prioritization.
The system aids in the design and analysis of complex genotyping projects.
Integrating SNP annotation with pathway and functional data enhances SNP-disease association interpretation.