ArticleG3 (Bethesda, Md.)2013
Imputation-based genomic coverage assessments of current human genotyping arrays.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 2 of them syntheses that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Disparities in ABO blood type determination across diverse ancestries: a systematic review and validation in the All of Us Research Program.Journal of the American Medical Informatics Association : JAMIA · 2024Pooled it
- Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.Nature genetics · 2014Pooled it
- Pedigree-assisted genotype imputation enables cost-effective genomic prediction in Penaeus vannamei.Scientific reports · 2026Article
- A simple demonstration of a privacy-preserving de-centralised genotype imputation workflow.PloS one · 2026Article
- Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges.International journal of molecular sciences · 2025Review
- Aggregating single nucleotide polymorphisms improves filtering for false-positive associations postimputation.G3 (Bethesda, Md.) · 2025Article
- The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population.Bioinformatics (Oxford, England) · 2024Article
- Genetics of longitudinal kidney function in children and adults with systemic lupus erythematosus.Rheumatology (Oxford, England) · 2023Article
- A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations.Scientific reports · 2022Article
- Role of genetics in atrial fibrillation management.Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology · 2021Article
- APOE alleles' association with cognitive function differs across Hispanic/Latino groups and genetic ancestry in the study of Latinos-investigation of neurocognitive aging (HCHS/SOL).Alzheimer's & dementia : the journal of the Alzheimer's Association · 2021Article
- Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores.Genome medicine · 2019Article
- Pilot GWAS of caries in African-Americans shows genetic heterogeneity.BMC oral health · 2019Article
- Genome-wide Association Study of Maximum Habitual Alcohol Intake in >140,000 U.S. European and African American Veterans Yields Novel Risk Loci.Biological psychiatry · 2019Article
- Genome-wide association study of right-sided colonic diverticulosis in a Korean population.Scientific reports · 2019Article
- The Korea Biobank Array: Design and Identification of Coding Variants Associated with Blood Biochemical Traits.Scientific reports · 2019Article
- Atrial Fibrillation Genetics Update: Toward Clinical Implementation.Frontiers in cardiovascular medicine · 2019Review
- Association analysis of exome variants and refraction, axial length, and corneal curvature in a European-American population.Human mutation · 2018Article
- Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies.G3 (Bethesda, Md.) · 2018Article
- Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Microarray single-nucleotide polymorphism genotyping, combined with imputation of untyped variants, has been widely adopted as an efficient means to interrogate variation across the human genome. "Genomic coverage" is the total proportion of genomic variation captured by an array, either by direct observation or through an indirect means such as linkage disequilibrium or imputation. We have performed imputation-based genomic coverage assessments of eight current genotyping arrays that assay from ~0.3 to ~5 million variants. Coverage was determined separately in each of the four continental ancestry groups in the 1000 Genomes Project phase 1 release. We used the subset of 1000 Genomes variants present on each array to impute the remaining variants and assessed coverage based on correlation between imputed and observed allelic dosages. More than 75% of common variants (minor allele frequency > 0.05) are covered by all arrays in all groups except for African ancestry, and up to ~90% in all ancestries for the highest density arrays. In contrast, less than 40% of less common variants (0.01 < minor allele frequency < 0.05) are covered by low density arrays in all ancestries and 50-80% in high density arrays, depending on ancestry. We also calculated genome-wide power to detect variant-trait association in a case-control design, across varying sample sizes, effect sizes, and minor allele frequency ranges, and compare these array-based power estimates with a hypothetical array that would type all variants in 1000 Genomes. These imputation-based genomic coverage and power analyses are intended as a practical guide to researchers planning genetic studies.
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