High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation
نویسندگان
چکیده
منابع مشابه
High-depth whole genome sequencing of a large population-specific reference panel: Enhancing sensitivity, accuracy, and imputation
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...
متن کاملSequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
The Ashkenazi Jewish (AJ) population is a genetic isolate close to European and Middle Eastern groups, with genetic diversity patterns conducive to disease mapping. Here we report high-depth sequencing of 128 complete genomes of AJ controls. Compared with European samples, our AJ panel has 47% more novel variants per genome and is eightfold more effective at filtering benign variants out of AJ ...
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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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Genetic variation at the Human Leucocyte Antigen (HLA) genes is associated with many autoimmune and infectious disease phenotypes, is an important element of the immunological distinction between self and non-self, and shapes immune epitope repertoires. Determining the allelic state of the HLA genes (HLA typing) as a by-product of standard whole-genome sequencing data would therefore be highly ...
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: Human Genetics
سال: 2018
ISSN: 0340-6717,1432-1203
DOI: 10.1007/s00439-018-1886-z