scholarly journals Testing for Hardy–Weinberg equilibrium at biallelic genetic markers on the X chromosome

Heredity ◽  
2016 ◽  
Vol 116 (6) ◽  
pp. 558-568 ◽  
Author(s):  
J Graffelman ◽  
B S Weir
Keyword(s):  
Genetic Markers ◽  
X Chromosome ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

scholarly journals A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations

2019 ◽  
Author(s):  
Daniel Backenroth ◽  
Shai Carmi
Keyword(s):  
X Chromosome ◽  
Random Mating ◽  
Allele Frequencies ◽  
Ratio Test ◽  
Weinberg Equilibrium ◽  
Genotype Frequencies ◽  
Genome Wide ◽  
Control Step ◽  
Hardy Weinberg Equilibrium ◽  
Males And Females

AbstractGenome-wide scans for deviations from Hardy-Weinberg equilibrium (HWE) are commonly applied to detect genotyping errors. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations towards equilibrium. Several populations world-wide have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry and thus in allele frequencies. Sex-biased admixture makes testing for HWE difficult on X, because deviations are naturally expected, even under random mating post-admixture and error-free genotyping. In this paper, we develop a likelihood ratio test and a χ2 test that detect deviations from HWE on X while allowing for natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations (e.g., as a quality control step), our tests reject fewer SNPs (among those showing frequency differences between the sexes) than other tests.

scholarly journals Extending Tests of Hardy-Weinberg Equilibrium to Structured Populations

2017 ◽  
Author(s):  
Wei Hao ◽  
John D. Storey
Keyword(s):  
Population Structure ◽  
Genetic Markers ◽  
Population Genetic ◽  
Genetic Data ◽  
Structured Populations ◽  
Weinberg Equilibrium ◽  
Population Genetic Data ◽  
Special Cases ◽  
Hardy Weinberg Equilibrium ◽  
Almost All

AbstractTesting for Hardy-Weinberg equilibrium (HWE) is an important component in almost all analyses of population genetic data. Genetic markers that violate HWE are often treated as special cases; for example, they may be flagged as possible genotyping errors or they may be investigated more closely for evolutionary signatures of interest. The presence of population structure is one reason why genetic markers may fail a test of HWE. This is problematic because almost all natural populations studied in the modern setting show some degree of structure. Therefore, it is important to be able to detect deviations from HWE for reasons other than structure. To this end, we extend statistical tests of HWE to allow for population structure, which we call a test of “structural HWE” (sHWE). Additionally, our new test allows one to automatically choose tuning parameters and identify accurate models of structure. We demonstrate our approach on several important studies, provide theoretical justification for the test, and present empirical evidence for its utility. We anticipate the proposed test will be useful in a broad range of analyses of genome-wide population genetic data.

A robust and powerful test for case–control genetic association study on X chromosome

2018 ◽  
Vol 28 (10-11) ◽  
pp. 3260-3272 ◽  
Author(s):  
Peng Wang ◽  
Si-Qi Xu ◽  
Bei-Qi Wang ◽  
Wing Kam Fung ◽  
Ji-Yuan Zhou
Keyword(s):  
X Chromosome ◽  
Dosage Compensation ◽  
Genetic Model ◽  
Association Studies ◽  
Disease Genes ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Human Beings ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Hundreds of genome-wide association studies were conducted to map the disease genes on autosomes in human beings. It is known that many complex diseases are sex-determined and X chromosome is expected to play an important role. However, only a few single-nucleotide polymorphisms on X chromosome were found to be significantly associated with the diseases under study. On the other hand, to balance the genetic effect between two sexes, X chromosome inactivation occurs in most of X-linked genes by silencing one copy of two X chromosomes in females and dosage compensation is achieved. A few association studies on X chromosome incorporated the information on dosage compensation. However, some of them require the assumption of Hardy–Weinberg equilibrium and some need to specify the underlying genetic model. Therefore, in this article, we propose a novel method for association by taking account of different dosage compensation patterns. The proposed test is a robust approach because it requires neither specifying the underlying genetic models nor the assumption of Hardy–Weinberg equilibrium. Further, the proposed method allows for different deviations from Hardy–Weinberg equilibrium between cases and controls. Simulation results demonstrate that our proposed method generally outperforms the existing methods in terms of controlling the size and the test power. Finally, we apply the proposed test to the meta-analysis of the Graves' disease data for its practical use.

Significance of Hardy-Weinberg Equilibrium in Case Control

2004 ◽  
Vol 73 (1) ◽  
pp. 95-95
Author(s):  
Hemant Kumar Bid ◽  
Rama D. Mittal
Keyword(s):  
Case Control ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Spondyloepiphyseal dysplasia tarda: linkage with genetic markers from the distal short arm of the X chromosome

1988 ◽  
Vol 81 (1) ◽  
pp. 61-63 ◽  
Author(s):  
S. Szpiro-Tapia ◽  
A. Sefiani ◽  
M. Guilloud-Bataille ◽  
S. Heuertz ◽  
B. Le Marec ◽  
...  
Keyword(s):  
Genetic Markers ◽  
X Chromosome ◽  
Spondyloepiphyseal Dysplasia ◽  
Spondyloepiphyseal Dysplasia Tarda

scholarly journals Underuse of Hardy-Weinberg equilibrium

2004 ◽  
Vol 66 (4) ◽  
pp. 1711 ◽  
Author(s):  
Gere Sunder-Plassmann ◽  
Manuela Födinger
Keyword(s):  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium
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