Redundancy in Genotyping Arrays

Despite their unprecedented density, current SNP genotyping arrays contain large amounts of redundancy, with up to 40 oligonucleotide features used to query each SNP. By using publicly available reference genotype data from the International HapMap, we show that 93.6% sensitivity at <5% false pos...

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Detalles Bibliográficos
Autores principales: Smemo, Scott, Borevitz, Justin O.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2007
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805688/
https://www.ncbi.nlm.nih.gov/pubmed/17356697
http://dx.doi.org/10.1371/journal.pone.0000287
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author Smemo, Scott
Borevitz, Justin O.
author_facet Smemo, Scott
Borevitz, Justin O.
author_sort Smemo, Scott
collection PubMed
description Despite their unprecedented density, current SNP genotyping arrays contain large amounts of redundancy, with up to 40 oligonucleotide features used to query each SNP. By using publicly available reference genotype data from the International HapMap, we show that 93.6% sensitivity at <5% false positive rate can be obtained with only four probes per SNP, compared with 98.3% with the full data set. Removal of this redundancy will allow for more comprehensive whole-genome association studies with increased SNP density and larger sample sizes.
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spelling pubmed-18056882007-03-14 Redundancy in Genotyping Arrays Smemo, Scott Borevitz, Justin O. PLoS One Research Article Despite their unprecedented density, current SNP genotyping arrays contain large amounts of redundancy, with up to 40 oligonucleotide features used to query each SNP. By using publicly available reference genotype data from the International HapMap, we show that 93.6% sensitivity at <5% false positive rate can be obtained with only four probes per SNP, compared with 98.3% with the full data set. Removal of this redundancy will allow for more comprehensive whole-genome association studies with increased SNP density and larger sample sizes. Public Library of Science 2007-03-14 /pmc/articles/PMC1805688/ /pubmed/17356697 http://dx.doi.org/10.1371/journal.pone.0000287 Text en Smemo, Borevitz. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Smemo, Scott
Borevitz, Justin O.
Redundancy in Genotyping Arrays
title Redundancy in Genotyping Arrays
title_full Redundancy in Genotyping Arrays
title_fullStr Redundancy in Genotyping Arrays
title_full_unstemmed Redundancy in Genotyping Arrays
title_short Redundancy in Genotyping Arrays
title_sort redundancy in genotyping arrays
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805688/
https://www.ncbi.nlm.nih.gov/pubmed/17356697
http://dx.doi.org/10.1371/journal.pone.0000287
work_keys_str_mv AT smemoscott redundancyingenotypingarrays
AT borevitzjustino redundancyingenotypingarrays

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