The aim of this study was to evaluate the impact of genotype imputation on the performance of the GBLUP and Bayesian methods for genomic prediction. A total of 10,309 Holstein bulls were genotyped on the BovineSNP50 BeadChip (50 k). Five low density single nucleotide polymorphism (SNP) panels, containing 6,177, 2,480, 1,536, 768 and 384 SNPs, were simulated from the 50 k panel. A fraction of 0%...

Family-based association studies have been widely used to identify association between diseases and genetic markers. It is known that genotyping uncertainty is inherent in both directly genotyped or sequenced DNA variations and imputed data in silico. The uncertainty can lead to genotyping errors and missingness and can negatively impact the power and Type I error rates of family-based associat...

Costs of high-throughput genotyping have decreased to the point where it appears economically feasible to use molecular genetic marker information in applied breeding programs. Some practical questions remain to be addressed about how best to deal with missing data in the resulting genotype datasets, to minimize the impact of the missing data on the accuracy of breeding value prediction. Data c...

BACKGROUND Genotype imputation is an important process of predicting unknown genotypes, which uses reference population with dense genotypes to predict missing genotypes for both human and animal genetic variations at a low cost. Machine learning methods specially boosting methods have been used in genetic studies to explore the underlying genetic profile of disease and build models capable of ...

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. ...

Determination of the prevalence of accumulated antiretroviral drug resistance among persons infected with human immunodeficiency virus (HIV) is complicated by the lack of routine measurement in clinical care. By using data from 8 clinic-based cohorts from the North American AIDS Cohort Collaboration on Research and Design, drug-resistance mutations from those with genotype tests were determined...

Motivated by the overwhelming success of genome-wide association studies, droves of researchers are working vigorously to exchange and to combine genetic data to expediently discover genetic risk factors for common human traits. The primary tools that fuel these new efforts are imputation, allowing researchers who have collected data on a diversity of genotype platforms to share data in a unifo...

The increased usage of whole-genome selection (WGS) and other molecular evaluation methods in plant breeding relies on the ability to genotype a very large number of untested individuals in each breeding cycle. Many plant breeding programs evaluate large biparental populations of homozygous individuals derived from homozygous parent inbred lines. This structure lends itself to parent-progeny im...

Imputation, the process of inferring genotypes for untyped variants, is used to identify and refine genetic association findings. Inaccuracies in imputed data can distort the observed association between variants and a disease. Many statistics are used to assess accuracy; some compare imputed to genotyped data and others are calculated without reference to true genotypes. Prior work has shown t...