Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data

We explored five sex-specific quality control filters in North American Rheumatoid Arthritis Consortium's Illumina 550 k datasets. Three X chromosome and three autosomal single-nucleotide polymorphisms flagged by sex quality control filters were missed by filters of call rate at 95% and Hardy-W...

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Detalles Bibliográficos
Autores principales: Ling, Hua, Hetrick, Kurt, Bailey-Wilson, Joan E, Pugh, Elizabeth W
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Proceedings
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795957/
https://www.ncbi.nlm.nih.gov/pubmed/20018050
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author Ling, Hua
Hetrick, Kurt
Bailey-Wilson, Joan E
Pugh, Elizabeth W
author_facet Ling, Hua
Hetrick, Kurt
Bailey-Wilson, Joan E
Pugh, Elizabeth W
author_sort Ling, Hua
collection PubMed
description We explored five sex-specific quality control filters in North American Rheumatoid Arthritis Consortium's Illumina 550 k datasets. Three X chromosome and three autosomal single-nucleotide polymorphisms flagged by sex quality control filters were missed by filters of call rate at 95% and Hardy-Weinberg equilibrium at 10(-6). We applied a subset of these sex-specific quality control filters to eight chromosomes in the Framingham Heart Study samples genotyped by Affymetrix 500 k SNP arrays, and identified another two single-nucleotide polymorphisms that failed to be picked up by the above global filters.
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spelling pubmed-27959572009-12-18 Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data Ling, Hua Hetrick, Kurt Bailey-Wilson, Joan E Pugh, Elizabeth W BMC Proc Proceedings We explored five sex-specific quality control filters in North American Rheumatoid Arthritis Consortium's Illumina 550 k datasets. Three X chromosome and three autosomal single-nucleotide polymorphisms flagged by sex quality control filters were missed by filters of call rate at 95% and Hardy-Weinberg equilibrium at 10(-6). We applied a subset of these sex-specific quality control filters to eight chromosomes in the Framingham Heart Study samples genotyped by Affymetrix 500 k SNP arrays, and identified another two single-nucleotide polymorphisms that failed to be picked up by the above global filters. BioMed Central 2009-12-15 /pmc/articles/PMC2795957/ /pubmed/20018050 Text en Copyright ©2009 Ling et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Ling, Hua
Hetrick, Kurt
Bailey-Wilson, Joan E
Pugh, Elizabeth W
Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
title Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
title_full Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
title_fullStr Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
title_full_unstemmed Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
title_short Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
title_sort application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795957/
https://www.ncbi.nlm.nih.gov/pubmed/20018050
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AT hetrickkurt applicationofsexspecificsinglenucleotidepolymorphismfiltersingenomewideassociationdata
AT baileywilsonjoane applicationofsexspecificsinglenucleotidepolymorphismfiltersingenomewideassociationdata
AT pughelizabethw applicationofsexspecificsinglenucleotidepolymorphismfiltersingenomewideassociationdata

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