Tailored Selection of Study Individuals to be Sequenced in Order to Improve the Accuracy of Genotype Imputation [Source Code] (ICPSR doi:10.11588/data/TT4VM3)

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Document Description

Citation

Title:

Tailored Selection of Study Individuals to be Sequenced in Order to Improve the Accuracy of Genotype Imputation [Source Code]

Identification Number:

doi:10.11588/data/TT4VM3

Distributor:

heiDATA

Date of Distribution:

2018-10-15

Version:

1

Bibliographic Citation:

Peil, Barbara; Kabisch, Maria; Fischer, Christine; Hamann, Ute; Lorenzo Bermejo, Justo, 2018, "Tailored Selection of Study Individuals to be Sequenced in Order to Improve the Accuracy of Genotype Imputation [Source Code]", https://doi.org/10.11588/data/TT4VM3, heiDATA, V1

Study Description

Citation

Title:

Tailored Selection of Study Individuals to be Sequenced in Order to Improve the Accuracy of Genotype Imputation [Source Code]

Identification Number:

doi:10.11588/data/TT4VM3

Authoring Entity:

Peil, Barbara (Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany)

Kabisch, Maria (Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Fischer, Christine (Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany)

Hamann, Ute (Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Lorenzo Bermejo, Justo (Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany)

Distributor:

heiDATA

Date of Distribution:

2018-10-15

Study Scope

Keywords:

Medicine, Health and Life Sciences, genotype imputation, sequencing, reference panel, HapMap, statistical depth

Abstract:

The addition of sequence data from own‐study individuals to genotypes from external data repositories, for example, the HapMap, has been shown to improve the accuracy of imputed genotypes. Early approaches for reference panel selection favored individuals who best reflect recombination patterns in the study population. By contrast, a maximization of genetic diversity in the reference panel has been recently proposed. We investigate here a novel strategy to select individuals for sequencing that relies on the characterization of the ancestral kernel of the study population. The simulated study scenarios consisted of several combinations of subpopulations from HapMap. HapMap individuals who did not belong to the study population constituted an external reference panel which was complemented with the sequences of study individuals selected according to different strategies. In addition to a random choice, individuals with the largest statistical depth according to the first genetic principal components were selected. In all simulated scenarios the integration of sequences from own‐study individuals increased imputation accuracy. The selection of individuals based on the statistical depth resulted in the highest imputation accuracy for European and Asian study scenarios, whereas random selection performed best for an African‐study scenario. Present findings indicate that there is no universal ‘best strategy’ to select individuals for sequencing. We propose to use the methodology described in the manuscript to assess the advantage of focusing on the ancestral kernel under own study characteristics (study size, genetic diversity, availability and properties of external reference panels, frequency of imputed variants…).

Methodology and Processing

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Source_Code_Tailored_Selection_of_Study_Individuals_to_be_Sequenced_in_Order_to_Improve_the_Accuracy_of_Genotype_Imputation.pdf

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application/pdf

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step1.r

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step5.r

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