ArticleGenetics2014
Using Mendelian inheritance to improve high-throughput SNP discovery.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 44 citations in OpenAlex.
- Adaptive value of marginal populations: integrating selective signals, neutral processes and temporal scales.Heredity · 2026Article
- Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.Molecular ecology resources · 2025Article
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- Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data.Genome biology · 2024Article
- Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication.Genome biology and evolution · 2023Article
- Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays,Evolutionary applications · 2022Article
- Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species.Molecular ecology resources · 2022Article
- The relevance of pedigrees in the conservation genomics era.Molecular ecology · 2022Article
- Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Plants (Basel, Switzerland) · 2021Article
- Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs.BMC genomics · 2020Article
- Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.Frontiers in genetics · 2020Review
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- Genotyping Polyploids from Messy Sequencing Data.Genetics · 2018Article
- Characteristic and influencing factors of Taqman genotyping calling error.Journal of clinical laboratory analysis · 2018Article
- Insights into the Structure of the Spruce Budworm (G3 (Bethesda, Md.) · 2018Article
- Article
- Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants.3 Biotech · 2018Article
- Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates.Royal Society open science · 2017Article
- Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay.Current biology : CB · 2016Article
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Restriction site-associated DNA sequencing or genotyping-by-sequencing (GBS) approaches allow for rapid and cost-effective discovery and genotyping of thousands of single-nucleotide polymorphisms (SNPs) in multiple individuals. However, rigorous quality control practices are needed to avoid high levels of error and bias with these reduced representation methods. We developed a formal statistical framework for filtering spurious loci, using Mendelian inheritance patterns in nuclear families, that accommodates variable-quality genotype calls and missing data--both rampant issues with GBS data--and for identifying sex-linked SNPs. Simulations predict excellent performance of both the Mendelian filter and the sex-linkage assignment under a variety of conditions. We further evaluate our method by applying it to real GBS data and validating a subset of high-quality SNPs. These results demonstrate that our metric of Mendelian inheritance is a powerful quality filter for GBS loci that is complementary to standard coverage and Hardy-Weinberg filters. The described method, implemented in the software MendelChecker, will improve quality control during SNP discovery in nonmodel as well as model organisms.
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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.