Departure from Hardy Weinberg equilibrium and gnotyping error
Objective: Departure from Hardy Weinberg Equilibrium (HWE) may occur due to a variety of causes, including purifying selection, inbreeding, population substructure, copy number variation or genotyping error. We searched for specific characteristics of HWE-departure due to genotyping error. Methods:...
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| Main Authors: | , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
2017
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| In: |
Frontiers in genetics
Year: 2017, Volume: 8, Pages: 1-6 |
| ISSN: | 1664-8021 |
| DOI: | 10.3389/fgene.2017.00167 |
| Online Access: | Verlag, kostenfrei, Volltext: http://dx.doi.org/10.3389/fgene.2017.00167 Verlag, kostenfrei, Volltext: https://www.frontiersin.org/articles/10.3389/fgene.2017.00167/full 
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| Author Notes: | Bowang Chen, John W. Cole and Caspar Grond-Ginsbach |
| Summary: | Objective: Departure from Hardy Weinberg Equilibrium (HWE) may occur due to a variety of causes, including purifying selection, inbreeding, population substructure, copy number variation or genotyping error. We searched for specific characteristics of HWE-departure due to genotyping error. Methods: Genotypes of a random set of genetic variants were obtained from the Exome Aggregation Consortium (ExAC) database. Variants with 98%, LoH d-HWE was found in 29 (1.3%) variants, but no GoH d-HWE was detected. The findings of the non-random distribution of HWE-violating SNPs along the chromosome, the association with common deletion polymorphisms and indel-variant type, and the finding of excess heterozygotes in genomic regions that are prone to cross-hybridization were confirmed in a large sample of short variants from the 1000 Genomes Project. Conclusions: We differentiated between two types of HWE-departure. GoH d-HWE was suggestive for genotyping error. LoH d-HWE, on the contrary, pointed to natural variabilities such as population substructure or common deletion polymorphisms. |
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| Item Description: | Published: 31 October 2017 Gesehen am 25.06.2018 |
| Physical Description: | Online Resource |
| ISSN: | 1664-8021 |
| DOI: | 10.3389/fgene.2017.00167 |