36 A large multi-breed reference panel and maximizes genotype imputation accuracy in cattle
نویسندگان
چکیده
منابع مشابه
Estimation of genotype imputation accuracy using reference populations with varying degrees of relationship and marker density panel
Genotype imputation from low-density to high-density (SNP) chips is an important step before applying genomic selection, because denser chips can provide more reliable genomic predictions. In the current research, the accuracy of genotype imputation from low and moderate-density panels (5K and 50K) to high-density panels in the purebred and crossbred populations was assessed. The simulated popu...
متن کاملGenotype imputation accuracy with different reference panels in admixed populations
Genome-wide association studies have successfully identified common variants that are associated with complex diseases. However, the majority of genetic variants contributing to disease susceptibility are yet to be discovered. It is now widely believed that multiple rare variants are likely to be associated with complex diseases. Using custom-made chips or next-generation sequencing to uncover ...
متن کاملGenotype Imputation Reference Panel Selection Using Maximal Phylogenetic Diversity
The recent dramatic cost reduction of next-generation sequencing technology enables investigators to assess most variants in the human genome to identify risk variants for complex diseases. However, sequencing large samples remains very expensive. For a study sample with existing genotype data, such as array data from genome-wide association studies, a cost-effective approach is to sequence a s...
متن کاملAssessing Imputation Accuracy Using a 15k Low Density Panel in a Multi-breed New Zealand Sheep Population
Imputation has enabled genomic selection in commercial livestock, taking advantage of a more cost effective Low Density (LD) panel, increasing the number of genotyped animals and hence accelerating the adoption process. A 5K LD panel has been employed commercially in New Zealand. This study investigated the accuracy of imputation to 50K and High Density (HD) panels using a new 15K panelbeing de...
متن کاملEffect of Reference Population Size and Imputation Methods on the Accuracy of Imputation in Pure and Mixed Populations
Imputation as a method of creating low-density chips to high-density chips has been introduced to increase the accuracy of genomic selection in animals. In the current study, to investing imputation accuracy, three populations of mixed (scenario 1), pure (scenario 2) and mixed + pure (scenario 3) were simulated using QMSim. Two methods of imputation including Beagle and Flmpute were used fo...
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ژورنال
عنوان ژورنال: Journal of Animal Science
سال: 2019
ISSN: 0021-8812,1525-3163
DOI: 10.1093/jas/skz122.033