ArticlePLoS computational biology2015
PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 41 citations in OpenAlex.
- Variant Prioritization by Pedigree-Based Haplotyping.Genetic epidemiology · 2026Article
- SURFBAT: a surrogate family based association test building on large imputation reference panels.G3 (Bethesda, Md.) · 2025Article
- Combining Clickstream Analyses and Graph-Modeled Data Clustering for Identifying Common Response Processes.Psychometrika · 2021Article
- Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes.Scientific reports · 2021Article
- A comparison of humans and baboons suggests germline mutation rates do not track cell divisions.PLoS biology · 2020Article
- Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma.Genome medicine · 2020Article
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
- Very low-depth whole-genome sequencing in complex trait association studies.Bioinformatics (Oxford, England) · 2019Article
- QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection.BMC genomics · 2019Article
- Characterization of a Unique Form of Arrhythmic Cardiomyopathy Caused by Recessive Mutation in LEMD2.JACC. Basic to translational science · 2019Article
- Rediscovering the value of families for psychiatric genetics research.Molecular psychiatry · 2019Review
- Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees.Genome research · 2019Article
- Parent-of-origin effects on quantitative phenotypes in a large Hutterite pedigree.Communications biology · 2019Article
- Inferring Transmission Histories of Rare Alleles in Population-Scale Genealogies.American journal of human genetics · 2018Article
- Article
- Using pseudoalignment and base quality to accurately quantify microbial community composition.PLoS computational biology · 2018Article
- Parent of origin gene expression in a founder population identifies two new candidate imprinted genes at known imprinted regions.PloS one · 2018Article
- Rare non-coding variants are associated with plasma lipid traits in a founder population.Scientific reports · 2017Article
- Composite likelihood method for inferring local pedigrees.PLoS genetics · 2017Article
- Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.Microbiome · 2017Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm), a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD) segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs), from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost.
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Registered trials
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.