Journal article

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis

Clare C Constantine, Lyle C Gurrin, Christine E McLaren, Melanie Bahlo, Gregory J Anderson, Chris D Vulpe, Susan M Forrest, Katrina J Allen, Dorota M Gertig

BMC MEDICAL GENETICS | BMC | Published : 2008

Abstract

BACKGROUND: We report our experience of selecting tag SNPs in 35 genes involved in iron metabolism in a cohort study seeking to discover genetic modifiers of hereditary hemochromatosis. METHODS: We combined our own and publicly available resequencing data with HapMap to maximise our coverage to select 384 SNPs in candidate genes suitable for typing on the Illumina platform. RESULTS: Validation/design scores above 0.6 were not strongly correlated with SNP performance as estimated by Gentrain score. We contrasted results from two tag SNP selection algorithms, LDselect and Tagger. Varying r2 from 0.5 to 1.0 produced a near linear correlation with the number of tag SNPs required. We examined the..

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Awarded by NCI NIH HHS


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Awarded by NATIONAL HEART, LUNG, AND BLOOD INSTITUTE


Awarded by NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES