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Imputation-Based Genomic Coverage Assessments of Current Genotyping Arrays: Illumina HumanCore, OmniExpress, Multi-Ethnic global array and sub-arrays, Global Screening Array, Omni2.5M, Omni5M, and Affymetrix UK Biobank

View ORCID ProfileSarah C. Nelson, Jane M. Romm, Kimberly F. Doheny, Elizabeth W. Pugh, Cathy C. Laurie
doi: https://doi.org/10.1101/150219
Sarah C. Nelson
1Genetic Analysis Center, Dept. of Biostatistics, University of Washington
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Jane M. Romm
2Center for Inherited Disease Research, Johns Hopkins University School of Medicine
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Kimberly F. Doheny
2Center for Inherited Disease Research, Johns Hopkins University School of Medicine
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Elizabeth W. Pugh
2Center for Inherited Disease Research, Johns Hopkins University School of Medicine
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Cathy C. Laurie
1Genetic Analysis Center, Dept. of Biostatistics, University of Washington
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Abstract

Genotyping arrays have been widely adopted as an efficient means to interrogate variation across the human genome. Genetic variants may be observed either directly, via genotyping, or indirectly, through linkage disequilibrium with a genotyped variant. The total proportion of genomic variation captured by an array, either directly or indirectly, is referred to as “genomic coverage.” Here we use genotype imputation and Phase 3 of the 1000 Genomes Project to assess genomic coverage of several modern genotyping arrays. We find that in general, coverage increases with increasing array density. However, arrays designed to cover specific populations may yield better coverage in those populations compared to denser arrays not tailored to the given population. Ultimately, array choice involves trade-offs between cost, density, and coverage, and our work helps inform investigators weighing these choices and trade-offs.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 14, 2017.
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Imputation-Based Genomic Coverage Assessments of Current Genotyping Arrays: Illumina HumanCore, OmniExpress, Multi-Ethnic global array and sub-arrays, Global Screening Array, Omni2.5M, Omni5M, and Affymetrix UK Biobank
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Imputation-Based Genomic Coverage Assessments of Current Genotyping Arrays: Illumina HumanCore, OmniExpress, Multi-Ethnic global array and sub-arrays, Global Screening Array, Omni2.5M, Omni5M, and Affymetrix UK Biobank
Sarah C. Nelson, Jane M. Romm, Kimberly F. Doheny, Elizabeth W. Pugh, Cathy C. Laurie
bioRxiv 150219; doi: https://doi.org/10.1101/150219
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Imputation-Based Genomic Coverage Assessments of Current Genotyping Arrays: Illumina HumanCore, OmniExpress, Multi-Ethnic global array and sub-arrays, Global Screening Array, Omni2.5M, Omni5M, and Affymetrix UK Biobank
Sarah C. Nelson, Jane M. Romm, Kimberly F. Doheny, Elizabeth W. Pugh, Cathy C. Laurie
bioRxiv 150219; doi: https://doi.org/10.1101/150219

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