ArticleEuropean journal of human genetics : EJHG2015
Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs.
Article in European journal of human genetics : EJHG, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 4 of them syntheses that pooled it.
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Who cites it
79 citing papers in PubMed, 4 syntheses or guidelines pooled it, 113 citations in OpenAlex.
- Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.American journal of human genetics · 2022Pooled it
- Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes.PLoS genetics · 2018Pooled it
- New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR*D studies: rare variant analysis and high-density imputation.The pharmacogenomics journal · 2018Pooled it
- Methods for association analysis and meta-analysis of rare variants in families.Genetic epidemiology · 2015Pooled it
- The Soifua Manuia reference panel with 2,570 Samoan haplotypes improves genotype imputation quality among Samoans.Communications biology · 2026Article
- Article
- Genetic co-regulation of neopterin and Parkinson's disease.NPJ Parkinson's disease · 2026Article
- A multi-ancestry genetic reference for the Quebec population.Nature communications · 2026Article
- A simple demonstration of a privacy-preserving de-centralised genotype imputation workflow.PloS one · 2026Article
- Boosting the Power of Rare Variant Association Studies by Imputation Using Large-scale Sequencing Population.Genomics, proteomics & bioinformatics · 2025Article
- Age-Associated Increase in Growth Differentiation Factor 15 Levels Correlates With Central Arterial Stiffness and Predicts All-Cause Mortality in a Sardinian Population Cohort.Journal of the American Heart Association · 2025Article
- STICI: Split-Transformer with integrated convolutions for genotype imputation.Nature communications · 2025Article
- Association of antibiotic use with rheumatoid arthritis: A Mendelian randomization study.Medicine · 2025Article
- Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.Communications biology · 2024Article
- Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility.Communications biology · 2024Article
- MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric.American journal of human genetics · 2024Article
- A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome.NPJ genomic medicine · 2024Article
- How local reference panels improve imputation in French populations.Scientific reports · 2024Article
- Causal relationship between rheumatoid arthritis and epilepsy in a European population: a univariate and multivariate Mendelian randomization study.Frontiers in immunology · 2024Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
26 authors at 5 institutions in 2 countries.
Funding
Abstract
The utility of genotype imputation in genome-wide association studies is increasing as progressively larger reference panels are improved and expanded through whole-genome sequencing. Developing general guidelines for optimally cost-effective imputation, however, requires evaluation of performance issues that include the relative utility of study-specific compared with general/multipopulation reference panels; genotyping with various array scaffolds; effects of different ethnic backgrounds; and assessment of ranges of allele frequencies. Here we compared the effectiveness of study-specific reference panels to the commonly used 1000 Genomes Project (1000G) reference panels in the isolated Sardinian population and in cohorts of European ancestry including samples from Minnesota (USA). We also examined different combinations of genome-wide and custom arrays for baseline genotypes. In Sardinians, the study-specific reference panel provided better coverage and genotype imputation accuracy than the 1000G panels and other large European panels. In fact, even gene-centered custom arrays (interrogating ~200 000 variants) provided highly informative content across the entire genome. Gain in accuracy was also observed for Minnesotans using the study-specific reference panel, although the increase was smaller than in Sardinians, especially for rare variants. Notably, a combined panel including both study-specific and 1000G reference panels improved imputation accuracy only in the Minnesota sample, and only at rare sites. Finally, we found that when imputation is performed with a study-specific reference panel, cutoffs different from the standard thresholds of MACH-Rsq and IMPUTE-INFO metrics should be used to efficiently filter badly imputed rare variants. This study thus provides general guidelines for researchers planning large-scale genetic studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.