ArticlePloS one2012
Assessment of genotype imputation performance using 1000 Genomes in African American studies.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 3 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
32 citing papers in PubMed, 3 syntheses or guidelines pooled it, 52 citations in OpenAlex.
- A large-scale genome-wide association study meta-analysis of cannabis use disorder.The lancet. Psychiatry · 2020Pooled it
- Cis-Expression Quantitative Trait Loci Mapping Reveals Replicable Associations with Heroin Addiction in OPRM1.Biological psychiatry · 2015Pooled it
- Pooled it
- A reanalysis of a genome-wide association study on breast cancer in Asian populations using the SG10K_Health reference panel for imputation: a multi-Centre case-control analysis.Human molecular genetics · 2026Article
- Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.Advanced genetics (Hoboken, N.J.) · 2022Article
- A data harmonization pipeline to leverage external controls and boost power in GWAS.Human molecular genetics · 2022Article
- Genetic Risk Stratification: A Paradigm Shift in Prevention of Coronary Artery Disease.JACC. Basic to translational science · 2021Review
- Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats.BMC genetics · 2020Article
- The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles.Frontiers in plant science · 2020Article
- A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle.Genetics, selection, evolution : GSE · 2019Article
- Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population.Frontiers in genetics · 2019Article
- Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools.Frontiers in genetics · 2019Article
- Protocols, Methods, and Tools for Genome-Wide Association Studies (GWAS) of Dental Traits.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders.Nature neuroscience · 2018Article
- Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants.Scientific reports · 2018Article
- Genotype imputation performance of three reference panels using African ancestry individuals.Human genetics · 2018Article
- Genome-Wide Association Studies of Cancer in Diverse Populations.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2018Review
- Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy.Scientific reports · 2017Article
- Leveraging electronic health records to study pleiotropic effects on bipolar disorder and medical comorbidities.Translational psychiatry · 2016Article
- Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture.Arthritis & rheumatology (Hoboken, N.J.) · 2016Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Genotype imputation, used in genome-wide association studies to expand coverage of single nucleotide polymorphisms (SNPs), has performed poorly in African Americans compared to less admixed populations. Overall, imputation has typically relied on HapMap reference haplotype panels from Africans (YRI), European Americans (CEU), and Asians (CHB/JPT). The 1000 Genomes project offers a wider range of reference populations, such as African Americans (ASW), but their imputation performance has had limited evaluation. Using 595 African Americans genotyped on Illumina's HumanHap550v3 BeadChip, we compared imputation results from four software programs (IMPUTE2, BEAGLE, MaCH, and MaCH-Admix) and three reference panels consisting of different combinations of 1000 Genomes populations (February 2012 release): (1) 3 specifically selected populations (YRI, CEU, and ASW); (2) 8 populations of diverse African (AFR) or European (AFR) descent; and (3) all 14 available populations (ALL). Based on chromosome 22, we calculated three performance metrics: (1) concordance (percentage of masked genotyped SNPs with imputed and true genotype agreement); (2) imputation quality score (IQS; concordance adjusted for chance agreement, which is particularly informative for low minor allele frequency [MAF] SNPs); and (3) average r2hat (estimated correlation between the imputed and true genotypes, for all imputed SNPs). Across the reference panels, IMPUTE2 and MaCH had the highest concordance (91%-93%), but IMPUTE2 had the highest IQS (81%-83%) and average r2hat (0.68 using YRI+ASW+CEU, 0.62 using AFR+EUR, and 0.55 using ALL). Imputation quality for most programs was reduced by the addition of more distantly related reference populations, due entirely to the introduction of low frequency SNPs (MAF≤2%) that are monomorphic in the more closely related panels. While imputation was optimized by using IMPUTE2 with reference to the ALL panel (average r2hat = 0.86 for SNPs with MAF>2%), use of the ALL panel for African American studies requires careful interpretation of the population specificity and imputation quality of low frequency SNPs.
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