Identifying disease susceptible dna regions using underlying odds ratio contour analysis
Odds ratio plays important roles in identifying and assessing disease susceptible SNPs in the case-control association study. However, the contour of odds ratio has too much variation to identify the disease susceptible DNA region. This paper proposes the Odds Ratio Contour Analysis (ORCA), a method...
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th-mahidol.191312018-07-12T09:26:15Z Identifying disease susceptible dna regions using underlying odds ratio contour analysis Santitham Prom-on Jonathan Chan Asawin Meechai Wallaya Jongjaroenprasert Boonsong Ongphiphadhanakul King Mongkuts University of Technology Thonburi Mahidol University Computer Science Engineering Odds ratio plays important roles in identifying and assessing disease susceptible SNPs in the case-control association study. However, the contour of odds ratio has too much variation to identify the disease susceptible DNA region. This paper proposes the Odds Ratio Contour Analysis (ORCA), a method for analyzing of odds ratio contour in genome-wide SNP association study. This method smoothes the odds ratio contour and discriminates disease susceptible regions out of the others. We have preliminarily tested ORCA with SNPs data from pooled DNA genome-wide SNP association study of type 2 diabetes mellitus (T2DM), including four pools as cases and five pools as controls. Each DNA pool was assayed on Affymetrix GeneChip® Mapping 10K Array. With an optimal threshold level, ORCA can effectively highlight disease-associated regions, which reduce the false positive rate that has been one of the major problems in high-throughput case-control association study. © 2008 IEEE. 2018-07-12T02:24:28Z 2018-07-12T02:24:28Z 2008-09-26 Conference Paper Proceedings - International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies, BIOTECHNO 2008. (2008), 13-16 10.1109/BIOTECHNO.2008.34 2-s2.0-52249108553 https://repository.li.mahidol.ac.th/handle/123456789/19131 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=52249108553&origin=inward |
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Computer Science Engineering Santitham Prom-on Jonathan Chan Asawin Meechai Wallaya Jongjaroenprasert Boonsong Ongphiphadhanakul Identifying disease susceptible dna regions using underlying odds ratio contour analysis |
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Odds ratio plays important roles in identifying and assessing disease susceptible SNPs in the case-control association study. However, the contour of odds ratio has too much variation to identify the disease susceptible DNA region. This paper proposes the Odds Ratio Contour Analysis (ORCA), a method for analyzing of odds ratio contour in genome-wide SNP association study. This method smoothes the odds ratio contour and discriminates disease susceptible regions out of the others. We have preliminarily tested ORCA with SNPs data from pooled DNA genome-wide SNP association study of type 2 diabetes mellitus (T2DM), including four pools as cases and five pools as controls. Each DNA pool was assayed on Affymetrix GeneChip® Mapping 10K Array. With an optimal threshold level, ORCA can effectively highlight disease-associated regions, which reduce the false positive rate that has been one of the major problems in high-throughput case-control association study. © 2008 IEEE. |
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King Mongkuts University of Technology Thonburi |
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King Mongkuts University of Technology Thonburi Santitham Prom-on Jonathan Chan Asawin Meechai Wallaya Jongjaroenprasert Boonsong Ongphiphadhanakul |
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Conference or Workshop Item |
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Santitham Prom-on Jonathan Chan Asawin Meechai Wallaya Jongjaroenprasert Boonsong Ongphiphadhanakul |
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Santitham Prom-on |
title |
Identifying disease susceptible dna regions using underlying odds ratio contour analysis |
title_short |
Identifying disease susceptible dna regions using underlying odds ratio contour analysis |
title_full |
Identifying disease susceptible dna regions using underlying odds ratio contour analysis |
title_fullStr |
Identifying disease susceptible dna regions using underlying odds ratio contour analysis |
title_full_unstemmed |
Identifying disease susceptible dna regions using underlying odds ratio contour analysis |
title_sort |
identifying disease susceptible dna regions using underlying odds ratio contour analysis |
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2018 |
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https://repository.li.mahidol.ac.th/handle/123456789/19131 |
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