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Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances

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...

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Autor principal: LaFramboise, Thomas
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715261/
https://www.ncbi.nlm.nih.gov/pubmed/19570852
http://dx.doi.org/10.1093/nar/gkp552
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author LaFramboise, Thomas
author_facet LaFramboise, Thomas
author_sort LaFramboise, Thomas
collection PubMed
description 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.
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spelling pubmed-27152612009-07-24 Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances LaFramboise, Thomas Nucleic Acids Res Survey and Summary 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. Oxford University Press 2009-07 2009-07-01 /pmc/articles/PMC2715261/ /pubmed/19570852 http://dx.doi.org/10.1093/nar/gkp552 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Survey and Summary
LaFramboise, Thomas
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
title Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
title_full Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
title_fullStr Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
title_full_unstemmed Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
title_short Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
title_sort single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
topic Survey and Summary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715261/
https://www.ncbi.nlm.nih.gov/pubmed/19570852
http://dx.doi.org/10.1093/nar/gkp552
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