Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
نویسندگان
چکیده
منابع مشابه
A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples
Imputation using the 1000 Genomes haplotype reference panel has been widely adapted to estimate genotypes in genome wide association studies. To evaluate imputation quality with a relatively larger reference panel and a reference panel composed of different ethnic populations, we conducted imputations in the Framingham Heart Study and the North Chinese Study using a combined reference panel fro...
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Background: While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. In the present study, we sequenced at full-depth (≥30x) a moderately large (n=738) cohort of samples drawn from the Ashkenazi Jewish population across two plat...
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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...
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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...
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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: Scientific Reports
سال: 2017
ISSN: 2045-2322
DOI: 10.1038/s41598-017-06905-6