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Permanent link (DOI): https://doi.org/10.7939/R3416TC6G

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Fast accurate missing SNP genotype local imputation Open Access

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Author or creator
Wang, Yining
Cai, Zhipeng
Stothard, Paul
Moore, Steve S.
Goebel, Randy
Wang, Lusheng
Lin, Guohui
Additional contributors
Subject/Keyword
Cattle
Haplotypes
Alleles
Reproducibility of Results
Humans
Genotype
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Mice
Animals
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
Background Single nucleotide polymorphism (SNP) genotyping assays normally give rise to certain percents of no-calls; the problem becomes severe when the target organisms, such as cattle, do not have a high resolution genomic sequence. Missing SNP genotypes, when related to target traits, would confound downstream data analyses such as genome-wide association studies (GWAS). Existing methods for recovering the missing values are successful to some extent – either accurate but not fast enough or fast but not accurate enough. Results To a target missing genotype, we take only the SNP loci within a genetic distance vicinity and only the samples within a similarity vicinity into our local imputation process. For missing genotype imputation, the comparative performance evaluations through extensive simulation studies using real human and cattle genotype datasets demonstrated that our nearest neighbor based local imputation method was one of the most efficient methods, and outperformed existing methods except the time-consuming fastPHASE; for missing haplotype allele imputation, the comparative performance evaluations using real mouse haplotype datasets demonstrated that our method was not only one of the most efficient methods, but also one of the most accurate methods. Conclusions Given that fastPHASE requires a long imputation time on medium to high density datasets, and that our nearest neighbor based local imputation method only performed slightly worse, yet better than all other methods, one might want to adopt our method as an alternative missing SNP genotype or missing haplotype allele imputation method.
Date created
2012
DOI
doi:10.7939/R3416TC6G
License information

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Attribution 4.0 International
Citation for previous publication
Wang, Y., Cai, Z., Stothard, P., Moore, S. S., Goebel, R., Wang, L., & Lin, G. (2012). Fast accurate missing SNP genotype local imputation. BMC Research Notes, 5(404), [12 pages].  http://dx.doi.org/10.1186/1756-0500-5-404

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