ArticleAmerican journal of human genetics2002
Detection and integration of genotyping errors in statistical genetics.
Article in American journal of human genetics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers.
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Who cites it
149 citing papers in PubMed.
- Article
- Pairwise Paternity Assignment With Forward-Backward Simulations: Refining CERVUS Using Trio-Based Likelihood and Locus-Specific Error Rates.Ecology and evolution · 2025Article
- Repeated chip analysis for reducing the effect of genotyping errors on gene mapping for two recombinant inbred line populations in wheat (Triticum aestivum L.).BMC plant biology · 2025Article
- Simultaneous estimation of genotype error and uncalled deletion rates in whole genome sequence data.PLoS genetics · 2024Article
- Effect of genotyping errors on linkage map construction based on repeated chip analysis of two recombinant inbred line populations in wheat (Triticum aestivum L.).BMC plant biology · 2024Article
- Genotype error biases trio-based estimates of haplotype phase accuracy.American journal of human genetics · 2022Article
- Genetic variation and urine cadmium levels: ABCC1 effects in the Strong Heart Family Study.Environmental pollution (Barking, Essex : 1987) · 2021Article
- Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.BMC genomics · 2021Article
- Distinct error rates for reference and nonreference genotypes estimated by pedigree analysis.Genetics · 2021Article
- Estimation of DNA contamination and its sources in genotyped samples.Genetic epidemiology · 2019Article
- ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest.PLoS computational biology · 2019Article
- Fine mapping and identification of serum urate loci in American Indians: The Strong Heart Family Study.Scientific reports · 2019Article
- Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Genome-wide scans of myopia in Pennsylvania Amish families reveal significant linkage to 12q15, 8q21.3 and 5p15.33.Human genetics · 2019Article
- Rediscovering the value of families for psychiatric genetics research.Molecular psychiatry · 2019Review
- Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families.BMC medical genetics · 2019Article
- Article
- geck: trio-based comparative benchmarking of variant calls.Bioinformatics (Oxford, England) · 2018Article
- Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides.Journal of plant research · 2018Article
- Genetic and genomic monitoring with minimally invasive sampling methods.Evolutionary applications · 2018Article
89 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Detection of genotyping errors and integration of such errors in statistical analysis are relatively neglected topics, given their importance in gene mapping. A few inopportunely placed errors, if ignored, can tremendously affect evidence for linkage. The present study takes a fresh look at the calculation of pedigree likelihoods in the presence of genotyping error. To accommodate genotyping error, we present extensions to the Lander-Green-Kruglyak deterministic algorithm for small pedigrees and to the Markov-chain Monte Carlo stochastic algorithm for large pedigrees. These extensions can accommodate a variety of error models and refrain from simplifying assumptions, such as allowing, at most, one error per pedigree. In principle, almost any statistical genetic analysis can be performed taking errors into account, without actually correcting or deleting suspect genotypes. Three examples illustrate the possibilities. These examples make use of the full pedigree data, multiple linked markers, and a prior error model. The first example is the estimation of genotyping error rates from pedigree data. The second-and currently most useful-example is the computation of posterior mistyping probabilities. These probabilities cover both Mendelian-consistent and Mendelian-inconsistent errors. The third example is the selection of the true pedigree structure connecting a group of people from among several competing pedigree structures. Paternity testing and twin zygosity testing are typical applications.
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