Nucleic Acids Research Advance Access published online on July 1, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp552
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Survey and Summary |
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
Department of Genetics, Case Western Reserve University, Cleveland, OH 44106 and Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
*To whom correspondence should be addressed. Tel: +1 216 368 0150; Fax: +1 216 368 3432; Email: thomas.laframboise{at}case.edu
Received March 2, 2009. Revised June 9, 2009. Accepted June 11, 2009.
Array manufacturers originally designed single nucleotide polymorphism (SNP) arrays to genotype human DNA at thousands of SNPs across the genome simultaneously. In the decade since their initial development, the platform's applications have expanded to include the detection and characterization of copy number variation—whether somatic, inherited, or de novo—as well as loss-of-heterozygosity in cancer cells. The technology's impressive contributions to insights in population and molecular genetics have been fueled by advances in computational methodology, and indeed these insights and methodologies have spurred developments in the arrays themselves. This review describes the most commonly used SNP array platforms, surveys the computational methodologies used to convert the raw data into inferences at the DNA level, and details the broad range of applications. Although the long-term future of SNP arrays is unclear, cost considerations ensure their relevance for at least the next several years. Even as emerging technologies seem poised to take over for at least some applications, researchers working with these new sources of data are adopting the computational approaches originally developed for SNP arrays.