Title: Selecting SNPs for pharmacogenomic association study

Authors: Tae Jin Ahn; Kyunghee Park; Dae-Soon Son; Nam Huh; Sohee Oh; Taejung Bae; Jung-Sun Park; Ji-Hyun Lee; Kyoohyoung Rho; Sunghoon Kim; Taesung Park; Kyusang Lee

Addresses: Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-gu, Seoul 151-742, Korea; Samsung Advanced Institute of Technology, 449-712, Suwon, Korea ' Samsung Advanced Institute of Technology, 449-712, Suwon, Korea ' Samsung Advanced Institute of Technology, 449-712, Suwon, Korea ' Samsung Advanced Institute of Technology, 449-712, Suwon, Korea ' Department of Statistics, Seoul National University, Gwanak-gu, Seoul 151-742, Korea ' Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Gwanak-ro 1, Gwanak-gu, Seoul 151-742, Korea ' College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Korea ' Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Gwanak-ro 1, Gwanak-gu, Seoul 151-742, Korea ' Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Gwanak-ro 1, Gwanak-gu, Seoul 151-742, Korea ' Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Gwanak-ro 1, Gwanak-gu, Seoul 151-742, Korea ' Department of Statistics and Interdisciplinary Program, Seoul National University, Gwanak-gu, Seoul 151-742, Korea ' Samsung Advanced Institute of Technology, 449-712, Suwon, Korea

Abstract: SNP genotyping device is an essential tool in the upcoming era of personal genome and personalised medicine. Human genome has more than 10 million SNPs whereas conventional SNP genotyping device can only hold 1 million SNPs. Thus, intelligent SNP contents selection is required to maximise the value of SNP genotyping device. Here, we developed a new selection algorithm and applied this method to design genotyping contents for cancer and pharmacogenomic association study. This approach significantly increased the product value when compared with contents of competitive SNP genotyping product.

Keywords: pharmacogenomics; GWAS; genome-wide association study; SNP selection; intelligent selection; single-nucleotide polymorphisms; bioinformatics; SNP genotyping; cancer; SNPs.

DOI: 10.1504/IJDMB.2012.049317

International Journal of Data Mining and Bioinformatics, 2012 Vol.6 No.5, pp.521 - 534

Received: 21 Dec 2011
Accepted: 29 Dec 2011
Published online: 17 Dec 2014 *

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