Abstract
BackgroundIn the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, although both family- and population-based imputation methods have been proposed. With the recent surge of family-based designs, family-based imputation has become more important. Imputation methods for both designs are based on identity-by-descent (IBD) information. Apart from imputation, the use of IBD information is also common for several types of genetic analysis, including pedigree-based linkage analysis.MethodsWe compared the performance of several family- and population-based imputation methods in large pedigrees provided by Genetic Analysis Workshop 19 (GAW19). We also evaluated the performance of a new IBD mapping approach that we propose, which combines IBD information from known pedigrees with information from unrelated individuals.ResultsDifferent combinations of the imputation methods have varied imputation accuracies. Moreover, we showed gains from the use of both known pedigrees and unrelated individuals with our IBD mapping approach over the use of known pedigrees only.ConclusionsOur results represent accuracies of different combinations of imputation methods that may be useful for data sets similar to the GAW19 pedigree data. Our IBD mapping approach, which uses both known pedigree and unrelated individuals, performed better than classical linkage analysis.
Highlights
In the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, both family- and population-based imputation methods have been proposed
We evaluated and compared the performance of several family- and population-based imputation approaches in the Mexican American pedigree data provided by Genetic Analysis Workshop 19 (GAW19)
We evaluated the effect on imputation accuracy of the number of selected individuals for sequencing and the way they were selected, randomly or by tailored selection with Genotype Imputation Given Inheritance (GIGI)-Pick [5]
Summary
In the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, both family- and population-based imputation methods have been proposed. In the last few years, imputation approaches have been widely used in genetic studies, especially in the context of genome-wide association studies and populationbased designs. This is a result of an attractive feature of imputation: it increases genetic information at low-cost. The availability of the International Haplotype Map Project (HapMap) [1] and the 1000 Genomes Project [2] have allowed population-based imputation to become widespread.
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