ArticleHuman genetics2007
Methods to impute missing genotypes for population data.
Article in Human genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation.Cell systems · 2021Article
- Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank.Nature communications · 2016Article
- Structured Matrix Completion with Applications to Genomic Data Integration.Journal of the American Statistical Association · 2016Article
- Lung Cancer Risk Prediction Using Common SNPs Located in GWAS-Identified Susceptibility Regions.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2015Article
- Whole genome SNP genotype piecemeal imputation.BMC bioinformatics · 2015Article
- Coverage and efficiency in current SNP chips.European journal of human genetics : EJHG · 2014Article
- Recombination locations and rates in beef cattle assessed from parent-offspring pairs.Genetics, selection, evolution : GSE · 2014Article
- Comparison of different imputation methods from low- to high-density panels using Chinese Holstein cattle.Animal : an international journal of animal bioscience · 2013Article
- Genotype imputation via matrix completion.Genome research · 2013Article
- Windfalls and pitfalls: Applications of population genetics to the search for disease genes.Evolution, medicine, and public health · 2013Article
- Fast accurate missing SNP genotype local imputation.BMC research notes · 2012Article
- Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness.Frontiers in genetics · 2012Article
- Identity by descent estimation with dense genome-wide genotype data.Genetic epidemiology · 2011Article
- APOBEC3H haplotypes and HIV-1 pro-viral vif DNA sequence diversity in early untreated human immunodeficiency virus-1 infection.Human immunology · 2011Article
- An empirical evaluation of imputation accuracy for association statistics reveals increased type-I error rates in genome-wide associations.BMC genetics · 2011Article
- Effects of missing marker and segregation distortion on QTL mapping in F2 populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA.The annals of applied statistics · 2010Article
- Article
- The relationship between imputation error and statistical power in genetic association studies in diverse populations.American journal of human genetics · 2009Article
- Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies.BMC genetics · 2009Article
Corrections and comments
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2 authors.
Funding
Abstract
For large-scale genotyping studies, it is common for most subjects to have some missing genetic markers, even if the missing rate per marker is low. This compromises association analyses, with varying numbers of subjects contributing to analyses when performing single-marker or multi-marker analyses. In this paper, we consider eight methods to infer missing genotypes, including two haplotype reconstruction methods (local expectation maximization-EM, and fastPHASE), two k-nearest neighbor methods (original k-nearest neighbor, KNN, and a weighted k-nearest neighbor, wtKNN), three linear regression methods (backward variable selection, LM.back, least angle regression, LM.lars, and singular value decomposition, LM.svd), and a regression tree, Rtree. We evaluate the accuracy of them using single nucleotide polymorphism (SNP) data from the HapMap project, under a variety of conditions and parameters. We find that fastPHASE has the lowest error rates across different analysis panels and marker densities. LM.lars gives slightly less accurate estimate of missing genotypes than fastPHASE, but has better performance than the other methods.
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