ArticleScientific reports2017
Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Human genetic diversity across South Asian populations: A systematic review and meta-analysis.Medicine · 2025Pooled it
- National genomic projects in Asia and Africa: a review.Human genomics · 2026Review
- Comparative GWAS using global and Indian Reference Panels reveals non-coding drivers of COVID-19 severity and mortality.PLoS neglected tropical diseases · 2026Article
- Investigating the demographic history of Sindhi population inhabited in West Coast India.Human genomics · 2025Article
- Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.Communications biology · 2024Article
- Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts.bioRxiv : the preprint server for biology · 2024Article
- The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population.Bioinformatics (Oxford, England) · 2024Article
- Novel CWF19L1 mutations in patients with spinocerebellar ataxia, autosomal recessive 17.Journal of human genetics · 2023Article
- A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer.Molecular oncology · 2021Article
- Genetic profiles of 103,106 individuals in the Taiwan Biobank provide insights into the health and history of Han Chinese.NPJ genomic medicine · 2021Article
- IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes.Nucleic acids research · 2021Article
- Imputation Performance in Latin American Populations: Improving Rare Variants Representation With the Inclusion of Native American Genomes.Frontiers in genetics · 2021Article
- Sequencing and imputation in GWAS: Cost-effective strategies to increase power and genomic coverage across diverse populations.Genetic epidemiology · 2020Article
- Review
- Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.The pharmacogenomics journal · 2019Article
- EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.Genome research · 2018Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.
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