Microarrays and Single Nucleotide Polymorphism (SNP) Genotyping


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

Affymetrix. Pioneering company for GeneChip arrays http://www.affymetrix.com

Asper Biotech. Genotyping based on APEX technology http://www.asperbio.com

Febit ag. This is a young German biotech company providing light‐directed microarray technology for gene variation and expression http://www.febit.com

Illumina. Large‐scale analysis of genetic variation and function http://www.illumina.com

National Center for Biotechnology Information Single Nucleotide Polymorphism. Comprehensive database of single nucleotide polymorphisms http://www.ncbi.nlm.nih.gov/SNP

NimbleGen. Maskless fabrication of light‐directed oligonucleotide microarrays using a digital micromirror array http://www.nimblegen.com

Perlegen Sciences. Technology for SNP scanning entire human genomes http://www.perlegen.com

Sequenom. Provider of mass‐array genotyping technology, SNP assay portfolio and disease gene discovery http://www.sequenom.com

The SNP Consortium Ltd. Database for SNPs (single nucleotide polymorphisms) for biomedical research http://snp.cshl.org

This article was reviewed by the authors in December 2012, when it was decided that the article was a piece of its time and did not need to be updated.

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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]