A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle
نویسندگان
چکیده
منابع مشابه
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele fr...
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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...
متن کاملEstimation 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 کاملEffects of reduced panel, reference origin, and genetic relationship on imputation of genotypes in Hereford cattle.
The objective of this study was to investigate alternative methods of designing and using reduced SNP panels for imputing SNP genotypes. Two purebred Hereford populations, an experimental population known as Line 1 Hereford (L1, n = 240) and registered Hereford with American Hereford Association (AHA, n = 311), were used. Using different reference samples of 62 to 311 animals with 39,497 SNP on...
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ژورنال
عنوان ژورنال: Genetics Selection Evolution
سال: 2019
ISSN: 1297-9686
DOI: 10.1186/s12711-019-0519-x