ArticleScientific reports2016
Comparing performance of modern genotype imputation methods in different ethnicities.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 50 citations in OpenAlex.
- GWAS of habitual coffee consumption reveals a sex difference in the genetic effect of the 12q24 locus in the Japanese population.BMC genetics · 2019Pooled it
- Integrated Genomic Approaches to Elucidate the Genetic Basis of Brugada Syndrome in Taiwanese Patients.Bioinformatics and biology insights · 2025Article
- How local reference panels improve imputation in French populations.Scientific reports · 2024Article
- Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.Briefings in bioinformatics · 2023Article
- Record-matching of STR profiles with fragmentary genomic SNP data.European journal of human genetics : EJHG · 2023Article
- Article
- Analytical Approaches to Uncover Genetic Associations for Rare Outcomes: Lessons from West Nile Neuroinvasive Disease.Methods in molecular biology (Clifton, N.J.) · 2023Article
- 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
- Addressing the challenges of polygenic scores in human genetic research.American journal of human genetics · 2022Review
- Deciphering associations between three RNA splicing-related genetic variants and lung cancer risk.NPJ precision oncology · 2022Article
- Assessment of Imputation Quality: Comparison of Phasing and Imputation Algorithms in Real Data.Frontiers in genetics · 2021Article
- Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome.BMC genomics · 2020Article
- Sequencing and imputation in GWAS: Cost-effective strategies to increase power and genomic coverage across diverse populations.Genetic epidemiology · 2020Article
- Precise and Cost-Effective Nanopore Sequencing for Post-GWAS Fine-Mapping and Causal Variant Identification.iScience · 2020Article
- A Between Ethnicities Comparison of Chronic Obstructive Pulmonary Disease Genetic Risk.Frontiers in genetics · 2020Article
- Interferon inducible X-linked gene CXorf21 may contribute to sexual dimorphism in Systemic Lupus Erythematosus.Nature communications · 2019Article
- The Korea Biobank Array: Design and Identification of Coding Variants Associated with Blood Biochemical Traits.Scientific reports · 2019Article
- Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population.Frontiers in genetics · 2019Article
- Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence.Genetics · 2018Article
- African genetic diversity provides novel insights into evolutionary history and local adaptations.Human molecular genetics · 2018Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A variety of modern software packages are available for genotype imputation relying on advanced concepts such as pre-phasing of the target dataset or utilization of admixed reference panels. In this study, we performed a comprehensive evaluation of the accuracy of modern imputation methods on the basis of the publicly available POPRES samples. Good quality genotypes were masked and re-imputed by different imputation frameworks: namely MaCH, IMPUTE2, MaCH-Minimac, SHAPEIT-IMPUTE2 and MaCH-Admix. Results were compared to evaluate the relative merit of pre-phasing and the usage of admixed references. We showed that the pre-phasing framework SHAPEIT-IMPUTE2 can overestimate the certainty of genotype distributions resulting in the lowest percentage of correctly imputed genotypes in our case. MaCH-Minimac performed better than SHAPEIT-IMPUTE2. Pre-phasing always reduced imputation accuracy. IMPUTE2 and MaCH-Admix, both relying on admixed-reference panels, showed comparable results. MaCH showed superior results if well-matched references were available (Nei's G
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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.