ArticleEuropean journal of human genetics : EJHG2014
Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'.
Article in European journal of human genetics : EJHG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 5 of them syntheses that pooled it.
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Who cites it
67 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Integrated genome-wide association studies, meta-analysis, and Bayesian fine mapping reveal novel quantitative trait loci's and functional candidate genes for vulva traits in large white pigs.Journal of animal science · 2025Pooled it
- Multiomic integration analysis identifies atherogenic metabolites mediating between novel immune genes and cardiovascular risk.Genome medicine · 2024Pooled it
- Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.American journal of human genetics · 2022Pooled it
- Multitrait genome association analysis identifies new susceptibility genes for human anthropometric variation in the GCAT cohort.Journal of medical genetics · 2018Pooled it
- Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.Nature communications · 2015Pooled it
- Genetically determined ancestry associates with morphological and molecular carotid plaque features.Atherosclerosis · 2026Article
- Genomic variance partitioning of carcass and meat quality traits in Angus beef cattle.Frontiers in veterinary science · 2025Article
- Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.Communications biology · 2024Article
- How local reference panels improve imputation in French populations.Scientific reports · 2024Article
- Article
- Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.Briefings in bioinformatics · 2023Article
- A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population.Scientific reports · 2023Article
- Article
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
- Extent to which array genotyping and imputation with large reference panels approximate deep whole-genome sequencing.American journal of human genetics · 2022Article
- Genotype imputation and polygenic score estimation in northwestern Russian population.PloS one · 2022Article
- RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks.Briefings in bioinformatics · 2021Article
- Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes.Nature communications · 2021Article
- Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population.Communications biology · 2021Article
- Impact of pre- and post-variant filtration strategies on imputation.Scientific reports · 2021Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with 'true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05-0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r(2), increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r(2) improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r(2) increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results.
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