ArticleBMC genomics2020
How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 papers, 1 of them a synthesis that pooled it.
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187 citing papers in PubMed, 1 synthesis or guideline pooled it, 376 citations in OpenAlex.
- Pooled it
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- Genomic partitioning and functional dissection of inbreeding depression for stature in Brown Swiss cattle.Genetics, selection, evolution : GSE · 2026Article
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- Allelic association analyses: estimation recommendations.Genetics · 2026Article
- Silent Erosion: Impact of Forest Logging on Genetic Diversity in Tropical Understorey Birds.Genome biology and evolution · 2026Article
- Genetic Diversity and Population Structure of the Black-Footed Cat: Insights intobioRxiv : the preprint server for biology · 2026Article
- Genome-wide analysis of inbreeding patterns and candidate genes for adaptation in indigenous chickens of Botswana.Poultry science · 2026Article
- Genomic Variation and Population Structure of Portuguese Native Dog Breeds.Animal genetics · 2026Article
- Genetic Diversity and Population Structure of Two Mexican Creole Cattle Populations.Animals : an open access journal from MDPI · 2026Article
- Genome-Wide Homozygosity Predicts Inbreeding Depression in the Hihi/Stitchbird (Evolutionary applications · 2026Article
- Genomic insights into the admixture and diversity of Kerala crossbred cattle.Scientific reports · 2026Article
127 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundPLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and pet species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown.
resultsWe introduce the genome coverage parameter to appropriately estimate F
conclusionsIn this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis' validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.
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