TAILIEUCHUNG - Báo cáo sinh học: "The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học quốc tế đề tài: The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits | Uleberg and Meuwissen Genetics Selection Evolution 2011 43 20 http content 43 1 20 GSE Ge n et i cs Selection Evolution RESEARCH Open Access The complete linkage disequilibrium test a test that points to causative mutations underlying quantitative traits Eivind Uleberg1 2 and Theo HE Meuwissen1 Abstract Background Genetically SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium CLD test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets. Methods The CLD test consists of two steps . analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution the best SNP is in greater LD with the QTL than the second best while under the alternative-CLD-hypothesis the best SNP is alike-in-state with the QTL. To find a significance threshold the test was also performed on data excluding the causative SNP. The 5th 10th and 50th highest TCLD value from 1000 replicated analyses were used to control the type-I-error rate of the test at p p and p respectively. Results In a situation where the QTL explained 48 of the phenotypic variance analysis I detected a QTL in 994 replicates p where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis 714 replicates detected evidence of a QTL p . In analysis II the CLD test confirmed 280 causative SNP from 1000 simulations p . power was 28 . When the effect of the QTL was reduced by doubling the error variance the power of the test reduced relatively little to 23

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