INTRODUCTION Donor-recipient HLA compatibility is an important determinant of transplant outcomes. Allele-group to allele-level imputations help assign HLA genotypes when allele-level genotypes are not available during donor selection. METHODS We evaluated the performance of HaploStats, an allele-level multi-locus HLA genotype imputation tool from the National Marrow Donor Program, in a cross...

A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes ac...

Multiple imputation based on chained equations (MICE) is an alternative missing genotype method that can use genetic and nongenetic auxiliary data to inform the imputation process. Previously, MICE was successfully tested on strongly linked genetic data. We have now tested it on data of the HBA2 gene which, by the experimental design used in a malaria association study in Tanzania, shows a high...

Accurate inference of local ancestry from whole-genome genetic variation data is critical for understanding the history of admixed human populations and detecting SNPs associated with disease via admixture mapping. Although several existing methods achieve high accuracy when inferring local ancestry for individuals resulting from the admixture of genetically distant ancestral populations (e.g.,...