ArticleGenetic epidemiology2012
Genotype imputation of Metabochip SNPs using a study-specific reference panel of ~4,000 haplotypes in African Americans from the Women's Health Initiative.
Article in Genetic epidemiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 6 of them syntheses that pooled it.
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Who cites it
49 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.Nature communications · 2019Pooled it
- Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI.International journal of obesity (2005) · 2018Pooled it
- Pooled it
- Fine-mapping, novel loci identification, and SNP association transferability in a genome-wide association study of QRS duration in African Americans.Human molecular genetics · 2016Pooled it
- Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study.Circulation. Cardiovascular genetics · 2014Pooled it
- Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study.PloS one · 2014Pooled it
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric.American journal of human genetics · 2024Article
- Characterizing local pig breeds as reservoirs for the domestic pig genetic variability worldwide via contributions to gene diversity and allelic richness.Journal of animal science · 2024Article
- Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.Briefings in bioinformatics · 2023Article
- Australian genome-wide association study confirms higher female risk for adult glioma associated with variants in the region of CCDC26.Neuro-oncology · 2023Article
- MagicalRsq: Machine-learning-based genotype imputation quality calibration.American journal of human genetics · 2022Article
- Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients.HGG advances · 2022Article
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- SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression.Nature communications · 2021Article
- Article
- Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study.Human molecular genetics · 2018Article
- Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium.Diabetologia · 2017Article
- HFPRM: Hierarchical Functional Principal Regression Model for Diffusion Tensor Image Bundle Statistics.Information processing in medical imaging : proceedings of the ... conference · 2017Article
- Article
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17 authors.
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Abstract
Genetic imputation has become standard practice in modern genetic studies. However, several important issues have not been adequately addressed including the utility of study-specific reference, performance in admixed populations, and quality for less common (minor allele frequency [MAF] 0.005-0.05) and rare (MAF < 0.005) variants. These issues only recently became addressable with genome-wide association studies (GWAS) follow-up studies using dense genotyping or sequencing in large samples of non-European individuals. In this work, we constructed a study-specific reference panel of 3,924 haplotypes using African Americans in the Women's Health Initiative (WHI) genotyped on both the Metabochip and the Affymetrix 6.0 GWAS platform. We used this reference panel to impute into 6,459 WHI SNP Health Association Resource (SHARe) study subjects with only GWAS genotypes. Our analysis confirmed the imputation quality metric Rsq (estimated r(2) , specific to each SNP) as an effective post-imputation filter. We recommend different Rsq thresholds for different MAF categories such that the average (across SNPs) Rsq is above the desired dosage r(2) (squared Pearson correlation between imputed and experimental genotypes). With a desired dosage r(2) of 80%, 99.9% (97.5%, 83.6%, 52.0%, 20.5%) of SNPs with MAF > 0.05 (0.03-0.05, 0.01-0.03, 0.005-0.01, and 0.001-0.005) passed the post-imputation filter. The average dosage r(2) for these SNPs is 94.7%, 92.1%, 89.0%, 83.1%, and 79.7%, respectively. These results suggest that for African Americans imputation of Metabochip SNPs from GWAS data, including low frequency SNPs with MAF 0.005-0.05, is feasible and worthwhile for power increase in downstream association analysis provided a sizable reference panel is available.
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