ArticleHuman genetics2018
Genotype imputation for Han Chinese population using Haplotype Reference Consortium as reference.
Article in Human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-trait genome-wide association study identifies new loci associated with optic disc parameters.Communications biology · 2019Pooled it
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.bioRxiv : the preprint server for biology · 2024Article
- A genome-wide association study of Chinese and English language phenotypes in Hong Kong Chinese children.NPJ science of learning · 2024Article
- Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.Frontiers in genetics · 2024Article
- 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
- Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans.Genome biology · 2023Article
- Partitioning heritability analyses unveil the genetic architecture of human brain multidimensional functional connectivity patterns.Human brain mapping · 2020Article
- Overcoming the challenges of imputation of rare variants in a Taiwanese cohort.Translational cancer research · 2020Article
- NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants.Genome medicine · 2019Article
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Authors and funding
7 authors.
Funding
Abstract
Genotype imputation is now routinely performed in genomic analysis. Reference panel size, that is, the number of haplotypes in the reference panel, has been well established to be one major driving factor of imputation accuracy. For that reason, huge efforts have been made worldwide to provide large reference panels, with the Haplotype Reference Consortium (HRC) being currently the largest available in the public domain. The imputation performance of HRC, whose major samples are Europeans, has been mainly evaluated in Europeans. We conducted whole-genome genotype imputation on two independent genome-wide genotyping datasets, one with 1000 European samples and the other with 1000 Han Chinese samples. We compared the results obtained using HRC with those using Phase III of the 1000 Genomes Project (1000G) reference panel. For the European dataset, using HRC improved imputation quality, especially for rare variants with minor allele-frequency (MAF) < 0.1%. However, 1000G demonstrates better performance in the Han Chinese dataset, in both imputation quality and number of well-imputed variants. We validated the performance of 1000G reference panel in a second, independent cohort of Han Chinese (N = 2402). Our study showcases the limitations of HRC for Han Chinese populations, strongly suggesting the necessity of building population-specific reference panels.
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