SNP imputation bias reduces effect size determination
نویسندگان
چکیده
منابع مشابه
SNP imputation bias reduces effect size determination
Imputation is a commonly used technique that exploits linkage disequilibrium to infer missing genotypes in genetic datasets, using a well-characterized reference population. While there is agreement that the reference population has to match the ethnicity of the query dataset, it is common practice to use the same reference to impute genotypes for a wide variety of phenotypes. We hypothesized t...
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Imputation as a method of creating low-density chips to high-density chips has been introduced to increase the accuracy of genomic selection in animals. In the current study, to investing imputation accuracy, three populations of mixed (scenario 1), pure (scenario 2) and mixed + pure (scenario 3) were simulated using QMSim. Two methods of imputation including Beagle and Flmpute were used fo...
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In the case in which all subjects are screened using a common test and only a subset of these subjects are tested using a golden standard test, it is well documented that there is a risk for bias, called verification bias. When the test has only two levels (e.g. positive and negative) and we are trying to estimate the sensitivity and specificity of the test, we are actually constructing a confi...
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The accuracy and computational complexity of five methods to impute missing genotypes in high density SNP data was investigated. The haplotype reconstruction package fastPHASE reached the highest accuracies (91% to 98%) for varying proportions (0.2% to 8%) of missing genotypes. Alternative methods based on principal component analysis were less accurate (67% to 94%), but their computational dem...
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Missing single nucleotide polymorphisms (SNPs) are quite common in genetic association studies. Subjects with missing SNPs are often discarded in analyses, which may seriously undermine the inference of SNP-disease association. In this article, we develop two haplotype-based imputation approaches and one tree-based imputation approach for association studies. The emphasis is to evaluate the imp...
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ژورنال
عنوان ژورنال: Frontiers in Genetics
سال: 2015
ISSN: 1664-8021
DOI: 10.3389/fgene.2015.00030