ArticleAmerican journal of human genetics2013
GIGI: an approach to effective imputation of dense genotypes on large pedigrees.
Article in American journal of human genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Variant Prioritization by Pedigree-Based Haplotyping.Genetic epidemiology · 2026Article
- Adjustment for Genotype Imputation Uncertainty Corrects for Inflated Type I Error in Family-Based Association Testing.Genetic epidemiology · 2025Article
- Genetic and Molecular Determinants of Familial Transmission of Skeletal Malocclusions.Orthodontics & craniofacial research · 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
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Reconstructing parent genomes using siblings and other relatives.bioRxiv : the preprint server for biology · 2024Article
- Leveraging family history in genetic association analyses of binary traits.BMC genomics · 2022Article
- Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.Tropical animal health and production · 2022Article
- Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Accuracy of genotype imputation based on reference population size and marker density in Hanwoo cattle.Journal of animal science and technology · 2021Article
- Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family.Human genetics · 2021Article
- Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates.Translational psychiatry · 2020Article
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
- Article
- Rediscovering the value of families for psychiatric genetics research.Molecular psychiatry · 2019Review
- Revisit Population-based and Family-based Genotype Imputation.Scientific reports · 2019Article
- Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees.Genome research · 2019Article
- Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees.Genetics, selection, evolution : GSE · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Recent emergence of the common-disease-rare-variant hypothesis has renewed interest in the use of large pedigrees for identifying rare causal variants. Genotyping with modern sequencing platforms is increasingly common in the search for such variants but remains expensive and often is limited to only a few subjects per pedigree. In population-based samples, genotype imputation is widely used so that additional genotyping is not needed. We now introduce an analogous approach that enables computationally efficient imputation in large pedigrees. Our approach samples inheritance vectors (IVs) from a Markov Chain Monte Carlo sampler by conditioning on genotypes from a sparse set of framework markers. Missing genotypes are probabilistically inferred from these IVs along with observed dense genotypes that are available on a subset of subjects. We implemented our approach in the Genotype Imputation Given Inheritance (GIGI) program and evaluated the approach on both simulated and real large pedigrees. With a real pedigree, we also compared imputed results obtained from this approach with those from the population-based imputation program BEAGLE. We demonstrated that our pedigree-based approach imputes many alleles with high accuracy. It is much more accurate for calling rare alleles than is population-based imputation and does not require an outside reference sample. We also evaluated the effect of varying other parameters, including the marker type and density of the framework panel, threshold for calling genotypes, and population allele frequencies. By leveraging information from existing genotypes already assayed on large pedigrees, our approach can facilitate cost-effective use of sequence data in the pursuit of rare causal variants.
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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.