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A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests

We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T(2 )tests, i.e., T(H )based on allele coding and T(G )based on genotype coding. The objective was to identify associations between single-nucleotide polymorphisms (S...

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Autores principales: Chen, Lianfu, Zhong, Ming, Chen, Wei Vivien, Amos, Christopher I, Fan, Ruzong
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795960/
https://www.ncbi.nlm.nih.gov/pubmed/20018053
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author Chen, Lianfu
Zhong, Ming
Chen, Wei Vivien
Amos, Christopher I
Fan, Ruzong
author_facet Chen, Lianfu
Zhong, Ming
Chen, Wei Vivien
Amos, Christopher I
Fan, Ruzong
author_sort Chen, Lianfu
collection PubMed
description We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T(2 )tests, i.e., T(H )based on allele coding and T(G )based on genotype coding. The objective was to identify associations between single-nucleotide polymorphisms (SNPs) or markers and rheumatoid arthritis. In specific candidate gene regions, we evaluated the performance of Hotelling's T(2 )tests. Then Hotelling's T(2 )tests were used as a tool to identify new regions that contain SNPs showing strong associations with disease. As expected, the strongest association evidence was found in the region of the HLA-DRB1 locus on chromosome 6. In the region of the TRAF1-C5 genes, we identified two SNPs, rs2900180 and rs3761847, with the largest and the second largest T(H )and T(G )scores among all SNPs on chromosome 9. We also identified one SNP, rs2476601, in the region of the PTPN22 gene that had the largest T(H )score and the second largest T(G )score among all SNPs on chromosome 1. In addition, SNPs with the largest T(H )score on each chromosome were identified. These SNPs may be located in the regions of genes that have modest effects on rheumatoid arthritis. These regions deserve further investigation.
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spelling pubmed-27959602009-12-18 A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests Chen, Lianfu Zhong, Ming Chen, Wei Vivien Amos, Christopher I Fan, Ruzong BMC Proc Proceedings We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T(2 )tests, i.e., T(H )based on allele coding and T(G )based on genotype coding. The objective was to identify associations between single-nucleotide polymorphisms (SNPs) or markers and rheumatoid arthritis. In specific candidate gene regions, we evaluated the performance of Hotelling's T(2 )tests. Then Hotelling's T(2 )tests were used as a tool to identify new regions that contain SNPs showing strong associations with disease. As expected, the strongest association evidence was found in the region of the HLA-DRB1 locus on chromosome 6. In the region of the TRAF1-C5 genes, we identified two SNPs, rs2900180 and rs3761847, with the largest and the second largest T(H )and T(G )scores among all SNPs on chromosome 9. We also identified one SNP, rs2476601, in the region of the PTPN22 gene that had the largest T(H )score and the second largest T(G )score among all SNPs on chromosome 1. In addition, SNPs with the largest T(H )score on each chromosome were identified. These SNPs may be located in the regions of genes that have modest effects on rheumatoid arthritis. These regions deserve further investigation. BioMed Central 2009-12-15 /pmc/articles/PMC2795960/ /pubmed/20018053 Text en Copyright ©2009 Chen 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
Chen, Lianfu
Zhong, Ming
Chen, Wei Vivien
Amos, Christopher I
Fan, Ruzong
A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests
title A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests
title_full A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests
title_fullStr A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests
title_full_unstemmed A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests
title_short A genome-wide association scan for rheumatoid arthritis data by Hotelling's T(2 )tests
title_sort genome-wide association scan for rheumatoid arthritis data by hotelling's t(2 )tests
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795960/
https://www.ncbi.nlm.nih.gov/pubmed/20018053
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