Microarrays and Single Nucleotide Polymorphism (SNP) Genotyping

Andres Metspalu, University of Tartu, Tartu, Estonia

Published online: January 2006

DOI: 10.1038/npg.els.0005948

Microarrays are used for genotyping projects that cover one gene, many candidate genes or whole sets of chromosomes in a genome, and are capable of analyzing thousands of Single nucleotide polymorphisms (SNPs) in parallel. SNP-based linkage disequilibrium maps and haplotypes, either measured directly or calculated from the SNP genotyping data, will be in use in the near future for studies of genome-wide genetic association in common diseases.

Keywords: microarrays; APEX; genotyping; linkage disequilibrium; haplotypes

Figure 1. The block structure of the human genome. Larger haplotype blocks (labeled 1–4) with a relatively high amount of linkage disequilibrium (LD) are separated by shorter ones with almost no detectable linkage disequilibrium. Microarrays are the most powerful method for analyzing this block structure.
Figure 2. Chromosome 22 microarray with 5600 oligonucleotides spotted onto a silanized glass slide through a 5¢-amino link. Primer extension signals are recorded with a Genorama (Asper Biotech) imager and genotypes are called by Genorama software.
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 Web Links
    ePath Affymetrix. Pioneering company for GeneChip arrays http://www.affymetrix.com
    ePath Asper Biotech. Genotyping based on APEX technology http://www.asperbio.com
    ePath Febit ag. This is a young German biotech company providing light-directed microarray technology for gene variation and expression http://www.febit.com
    ePath Illumina. Large-scale analysis of genetic variation and function http://www.illumina.com
    ePath National Center for Biotechnology Information Single Nucleotide Polymorphism. Comprehensive database of single nucleotide polymorphisms http://www.ncbi.nlm.nih.gov/SNP
    ePath NimbleGen. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array http://www.nimblegen.com
    ePath Perlegen Sciences. Technology for SNP scanning entire human genomes http://www.perlegen.com
    ePath Sequenom. Provider of mass-array genotyping technology, SNP assay portfolio and disease gene discovery http://www.sequenom.com
    ePath The SNP Consortium Ltd. Database for SNPs (single nucleotide polymorphisms) for biomedical research http://snp.cshl.org

Related Sub-Topics:

Bioinformatics | Molecular Genetics of Common and Complex Disease | Techniques and Tools in Clinical Genetics | Linkage Analysis | Inter-Individual Variation and Polymorphism | Bioinformatics and Genetic Disease | Techniques and Tools in Molecular Biology | Computational Molecular Biology
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Article Title: Microarrays and Single Nucleotide Polymorphism (SNP) Genotyping
 
How to Cite close
Metspalu, Andres(Jan 2006) Microarrays and Single Nucleotide Polymorphism (SNP) Genotyping. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005948]