Fast accurate missing SNP genotype local imputation

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

21 Scopus Citations
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Author(s)

  • Yining Wang
  • Zhipeng Cai
  • Paul Stothard
  • Steve Moore
  • Randy Goebel
  • Guohui Lin

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Detail(s)

Original languageEnglish
Article number404
Journal / PublicationBMC Research Notes
Volume5
Publication statusPublished - 2012

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Abstract

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. © 2012 Wang et al.; licensee BioMed Central Ltd.

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Citation Format(s)

Fast accurate missing SNP genotype local imputation. / Wang, Yining; Cai, Zhipeng; Stothard, Paul et al.
In: BMC Research Notes, Vol. 5, 404, 2012.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

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