ArticleGenetics, selection, evolution : GSE2018
SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium.
Article in Genetics, selection, evolution : GSE, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 56 citations in OpenAlex.
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- Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data.Computers in biology and medicine · 2024Article
- Computing linkage disequilibrium aware genome embeddings using autoencoders.Bioinformatics (Oxford, England) · 2024Article
- Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae.Molecular plant pathology · 2024Article
- Selective Genotyping and Phenotyping for Optimization of Genomic Prediction Models for Populations with Different Diversity.Plants (Basel, Switzerland) · 2024Article
- Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics.ArXiv · 2024Article
- Statistical Inference for Maximin Effects: Identifying Stable Associations across Multiple Studies.Journal of the American Statistical Association · 2024Article
- Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets.American journal of human genetics · 2023Article
- Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora.IMA fungus · 2023Article
- Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks.PloS one · 2023Article
- Causal inference for the covariance between breeding values under identity disequilibrium.Genetics, selection, evolution : GSE · 2022Article
- Comparing heritability estimators under alternative structures of linkage disequilibrium.G3 (Bethesda, Md.) · 2022Article
- Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens.BMC genomics · 2022Article
- Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada.Molecular plant pathology · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundHigh levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, this warrants pruning of genotyping data for high LD. We developed an algorithm, named SNPrune, which enables the rapid detection of any pair of SNPs in complete or high LD throughout the genome.
methodsLD, measured as the squared correlation between phased alleles (r
resultsSNPrune removed a similar number of SNPs as PLINK from the pig data but SNPrune was almost 12 times faster than PLINK. From the simulated sequence data with 10.8 million SNPs, SNPrune removed 6.4 and 1.4 million SNPs due to complete and high LD. Results were very similar regardless of whether phased alleles or allele counts were used. Using allele counts and multi-threading with 10 threads, SNPrune completed the analysis in 21 min. Using a sliding window of up to 500,000 SNPs, PLINK removed ~ 43,000 less SNPs (0.6%) in the sequence data and SNPrune was 24 to 170 times faster, using one or ten threads, respectively.
conclusionsThe SNPrune algorithm developed here is able to remove SNPs in high LD throughout the genome very efficiently in large datasets.
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