ArticleEuropean journal of human genetics : EJHG2015
Improving accuracy of rare variant imputation with a two-step imputation approach.
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 25 papers.
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Who cites it
25 citing papers in PubMed.
- Explaining the unexplained admixture mapping signals via rare variants: the HCHS/SOL.Human molecular genetics · 2026Article
- Explaining the unexplained admixture mapping signals via rare variants: the HCHS/SOL.bioRxiv : the preprint server for biology · 2026Article
- Old vs. new local ancestry inference in HCHS/SOL: a comparative study.Human molecular genetics · 2025Article
- Old vs. New Local Ancestry Inference in HCHS/SOL: A Comparative Study.bioRxiv : the preprint server for biology · 2025Article
- A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy.Genetics, selection, evolution : GSE · 2024Article
- Polygenic risk score in comparison with C-reactive protein for predicting incident coronary heart disease.Atherosclerosis · 2023Article
- Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response.Nature communications · 2023Article
- Imputation to whole-genome sequence and its use in genome-wide association studies for pork colour traits in crossbred and purebred pigs.Frontiers in genetics · 2022Article
- Genetic and Metabolic Determinants of Atrial Fibrillation in a General Population Sample: The CHRIS Study.Biomolecules · 2021Article
- Impact of pre- and post-variant filtration strategies on imputation.Scientific reports · 2021Article
- Comparison of Genotype Imputation for SNP Array and Low-Coverage Whole-Genome Sequencing Data.Frontiers in genetics · 2021Article
- Medium-coverage DNA sequencing in the design of the genetic association study.European journal of human genetics : EJHG · 2020Article
- New Insights From Imputed Whole-Genome Sequence-Based Genome-Wide Association Analysis and Transcriptome Analysis: The Genetic Mechanisms Underlying Residual Feed Intake in Chickens.Frontiers in genetics · 2020Article
- A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle.Genetics, selection, evolution : GSE · 2019Article
- Revisit Population-based and Family-based Genotype Imputation.Scientific reports · 2019Article
- Finding the Optimal Imputation Strategy for Small Cattle Populations.Frontiers in genetics · 2019Article
- Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies.Bioinformatics (Oxford, England) · 2018Article
- Genome-wide compound heterozygote analysis highlights alleles associated with adult height in Europeans.Human genetics · 2017Article
- Genotype imputation in the domestic dog.Mammalian genome : official journal of the International Mammalian Genome Society · 2016Article
- Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population.Genetics, selection, evolution : GSE · 2016Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genotype imputation has been the pillar of the success of genome-wide association studies (GWAS) for identifying common variants associated with common diseases. However, most GWAS have been run using only 60 HapMap samples as reference for imputation, meaning less frequent and rare variants not being comprehensively scrutinized. Next-generation arrays ensuring sufficient coverage together with new reference panels, as the 1000 Genomes panel, are emerging to facilitate imputation of low frequent single-nucleotide polymorphisms (minor allele frequency (MAF) <5%). In this study, we present a two-step imputation approach improving the quality of the 1000 Genomes imputation by genotyping only a subset of samples to create a local reference population on a dense array with many low-frequency markers. In this approach, the study sample, genotyped with a first generation array, is imputed first to the local reference sample genotyped on a dense array and hereafter to the 1000 Genomes reference panel. We show that mean imputation quality, measured by the r(2) using this approach, increases by 28% for variants with a MAF between 1 and 5% as compared with direct imputation to 1000 Genomes reference. Similarly, the concordance rate between calls of imputed and true genotypes was found to be significantly higher for heterozygotes (P<1e-15) and rare homozygote calls (P<1e-15) in this low frequency range. The two-step approach in our setting improves imputation quality compared with traditional direct imputation noteworthy in the low-frequency spectrum and is a cost-effective strategy in large epidemiological studies.
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