ArticleGenome research2019
Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Adjustment for Genotype Imputation Uncertainty Corrects for Inflated Type I Error in Family-Based Association Testing.Genetic epidemiology · 2025Article
- Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges.International journal of molecular sciences · 2025Review
- Genomic Exploration of Essential Hypertension in African-Brazilian Quilombo Populations: A Comprehensive Approach With Pedigree Analysis and Family-Based Association Studies.Journal of the American Heart Association · 2025Article
- A primer on sequencing and genotype imputation in cattle.Journal of animal science · 2025Review
- Graph-Based Imputation Methods and Their Applications to Single Donors and Families.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Indirect Genetic Effects: A Cross-disciplinary Perspective on Empirical Studies.The Journal of heredity · 2022Article
- Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.Tropical animal health and production · 2022Article
- The relevance of pedigrees in the conservation genomics era.Molecular ecology · 2022Article
- Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency.Genetics, selection, evolution : GSE · 2021Article
- Article
- Haplotype-resolved genome analyses of a heterozygous diploid potato.Nature genetics · 2020Article
- Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts.PLoS genetics · 2020Article
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Genotype imputation is widely used in genome-wide association studies to boost variant density, allowing increased power in association testing. Many studies currently include pedigree data due to increasing interest in rare variants coupled with the availability of appropriate analysis tools. The performance of population-based (subjects are unrelated) imputation methods is well established. However, the performance of family- and population-based imputation methods on family data has been subject to much less scrutiny. Here, we extensively compare several family- and population-based imputation methods on family data of large pedigrees with both European and African ancestry. Our comparison includes many widely used family- and population-based tools and another method, Ped_Pop, which combines family- and population-based imputation results. We also compare four subject selection strategies for full sequencing to serve as the reference panel for imputation: GIGI-Pick, ExomePicks, PRIMUS, and random selection. Moreover, we compare two imputation accuracy metrics: the Imputation Quality Score and Pearson's correlation
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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.