Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization

The Genetic Analysis Workshop 16 rheumatoid arthritis data include a set of 868 cases and 1194 controls genotyped at 545,080 single-nucleotide polymorphisms (SNPs) from the Illumina 550 k chip. We focus on investigating chromosomes 6 and 18, which have 35,574 and 16,450 SNPs, respectively. Associati...

Descripción completa

Detalles Bibliográficos
Autores principales: Guo, Wei, Liang, Chin-yuan, Lin, Shili
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Proceedings
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795930/
https://www.ncbi.nlm.nih.gov/pubmed/20018023
_version_ 1782175472830906368
author Guo, Wei
Liang, Chin-yuan
Lin, Shili
author_facet Guo, Wei
Liang, Chin-yuan
Lin, Shili
author_sort Guo, Wei
collection PubMed
description The Genetic Analysis Workshop 16 rheumatoid arthritis data include a set of 868 cases and 1194 controls genotyped at 545,080 single-nucleotide polymorphisms (SNPs) from the Illumina 550 k chip. We focus on investigating chromosomes 6 and 18, which have 35,574 and 16,450 SNPs, respectively. Association studies, including single SNP and haplotype-based analyses, were applied to the data on those two chromosomes. Specifically, we conducted a generalized linear model with regularization (rGLM) approach for detecting disease-haplotype association using unphased SNP data. A total of 444 and 43 four-SNP tests were found to be significant at the Bonferroni corrected 5% significance level on chromosome 6 and 18, respectively.
format Text
id pubmed-2795930
institution National Center for Biotechnology Information
language English
publishDate 2009
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-27959302009-12-18 Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization Guo, Wei Liang, Chin-yuan Lin, Shili BMC Proc Proceedings The Genetic Analysis Workshop 16 rheumatoid arthritis data include a set of 868 cases and 1194 controls genotyped at 545,080 single-nucleotide polymorphisms (SNPs) from the Illumina 550 k chip. We focus on investigating chromosomes 6 and 18, which have 35,574 and 16,450 SNPs, respectively. Association studies, including single SNP and haplotype-based analyses, were applied to the data on those two chromosomes. Specifically, we conducted a generalized linear model with regularization (rGLM) approach for detecting disease-haplotype association using unphased SNP data. A total of 444 and 43 four-SNP tests were found to be significant at the Bonferroni corrected 5% significance level on chromosome 6 and 18, respectively. BioMed Central 2009-12-15 /pmc/articles/PMC2795930/ /pubmed/20018023 Text en Copyright ©2009 Guo 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
Guo, Wei
Liang, Chin-yuan
Lin, Shili
Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization
title Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization
title_full Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization
title_fullStr Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization
title_full_unstemmed Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization
title_short Haplotype association analysis of North American Rheumatoid Arthritis Consortium data using a generalized linear model with regularization
title_sort haplotype association analysis of north american rheumatoid arthritis consortium data using a generalized linear model with regularization
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795930/
https://www.ncbi.nlm.nih.gov/pubmed/20018023
work_keys_str_mv AT guowei haplotypeassociationanalysisofnorthamericanrheumatoidarthritisconsortiumdatausingageneralizedlinearmodelwithregularization
AT liangchinyuan haplotypeassociationanalysisofnorthamericanrheumatoidarthritisconsortiumdatausingageneralizedlinearmodelwithregularization
AT linshili haplotypeassociationanalysisofnorthamericanrheumatoidarthritisconsortiumdatausingageneralizedlinearmodelwithregularization

Ejemplares similares