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.

Genetics of Cronartium ribicola. III. Mating System

1996 ◽  
Vol 74 (11) ◽  
pp. 1852-1859 ◽  
Author(s):  
Matthew A. Gitzendanner ◽  
Gayle E. Dupper ◽  
Eleanor E. White ◽  
Brett M. Foord ◽  
Paul D. Hodgskiss ◽  
...  
Keyword(s):  
Mating System ◽  
Genetic Recombination ◽  
Random Mating ◽  
Cronartium Ribicola ◽  
White Pine Blister Rust ◽  
Mendelian Segregation ◽  
Weinberg Equilibrium ◽  
Forest Pathogen ◽  
Genotype Frequencies ◽  
Hardy Weinberg Equilibrium

Lack of genetic markers has hindered the study of the mating system of Cronartium ribicola, an exotic forest pathogen Meeting natural and cultivated white pines throughout North America. Isozymes, randomly amplified polymorphic DNA (RAPDs), and restriction length polymorphisms (RFLPs) were used to study the mating system of this rust. Heterozygosity (outcrossing) in diploid telia was demonstrated by analysis of cultures derived from the meiotic products (basidiospores) of individual telia. Families of basidiospores cultured from single telia were used to test for Mendelian segregation and for conformance of loci to Hardy–Weinberg equilibrium. A total of 18 polymorphic loci were identified with the three marker systems. All except for three RAPD loci showed Mendelian segregation in the single-telium families. To quantify the level of outcrossing, gene and genotype frequencies were calculated for families from a single population. Up to 24 families were surveyed with isozymes, 14 with RAPDs, and 18 with RFLPs. Except for one isozyme locus (MPI) in one sample, all 14 loci tested with these families were in Hardy–Weinberg equilibrium, indicating random mating. Further studies, with a different sample from the same population, showed all three isozyme loci to be in Hardy–Weinberg equilibrium. The three marker systems were consistent as to the amount of variation detected. Resistance selection and breeding programs must consider the implications of genetic recombination that outcrossing affords the rust. Keywords: isozymes, RAPDs, RFLPs, Hardy–Weinberg equilibrium, white pine blister rust.

Temporal and spatial patterns of allele and genotype frequencies at the Ng locus in blue grouse (Dendragapus obscurus)

1972 ◽  
Vol 50 (12) ◽  
pp. 1657-1662 ◽  
Author(s):  
J. A. Redfield ◽  
F. C. Zwickel ◽  
J. F. Bendell ◽  
A. T. Bergerud
Keyword(s):  
Spatial Patterns ◽  
Population Studies ◽  
Allele Frequencies ◽  
Equilibrium Conditions ◽  
Weinberg Equilibrium ◽  
Temporal And Spatial Patterns ◽  
Genotype Frequencies ◽  
Dendragapus Obscurus ◽  
Hardy Weinberg Equilibrium ◽  
Temporal And Spatial

The frequency of alleles and genotypes at the Ng locus in blue grouse from nine populations on Vancouver Island and the adjacent mainland was examined in an effort to detect systematic variations. There were no significant variations in allele frequencies between populations. Three of the nine populations sampled had significant departures from Hardy-Weinberg equilibrium conditions. Samples of four different cohorts indicated no significant shifts in allele or genotype frequencies between cohorts. These data, combined with other observations, suggest that the alleles at this locus are being maintained by selection. Thus, the utility of this locus as a marker in population studies is strengthened.

scholarly journals The general relationship between average effect and average excess

1987 ◽  
Vol 49 (1) ◽  
pp. 69-70 ◽  
Author(s):  
Alan R. Templeton
Keyword(s):  
Analytical Solution ◽  
Random Mating ◽  
General Relationship ◽  
Single Locus ◽  
Average Effect ◽  
Matrix Notation ◽  
Weinberg Equilibrium ◽  
General Analytical Solution ◽  
Genotype Frequencies ◽  
Hardy Weinberg Equilibrium

SummaryThe average effect and average excess both measure the phenotypic effects of gametes in a population. A matrix notation is introduced that provides a general analytical solution for the average effects at a single locus with k alleles that can be solved for any population regardless of its genotype frequencies. This same notation also provides an easy way of deriving and generalizing to k alleles the well-known relationships between average effects and average excesses that exist under random-mating and regular deviations from Hardy–Weinberg equilibrium due to inbreeding.

Isozyme variation in quaking aspen in Minnesota

1992 ◽  
Vol 22 (4) ◽  
pp. 521-524 ◽  
Author(s):  
Steven T. Lund ◽  
Glenn R. Furnier ◽  
Carl A. Mohn
Keyword(s):  
Gene Flow ◽  
Mating System ◽  
Allele Frequencies ◽  
Quaking Aspen ◽  
Isozyme Variation ◽  
Weinberg Equilibrium ◽  
Genotype Frequencies ◽  
Hardy Weinberg Equilibrium ◽  
Isozyme Loci

Variation at 10 polymorphic isozyme loci was examined for nine populations of quaking aspen (Populustremuloides Michx.) in Minnesota. Mean observed and expected estimates of isozyme heterozygosity were 0.217 and 0.220, respectively, with no significant differences in allele frequencies among populations and no significant deviations from genotype frequencies expected under Hardy–Weinberg equilibrium. These results suggest relatively high levels of gene flow among populations and a mating system involving little inbreeding.

scholarly journals Allele Frequencies of 15 AmpFISTR Identifiler loci in the Nepalese population

2012 ◽  
Vol 10 (10) ◽  
pp. 20-23 ◽  
Author(s):  
Dinesh Kumar Jha ◽  
Luis Javier Martinez Gonzalez ◽  
Jiwan Prasad Rijal ◽  
Bhinu Shova Tuladhar ◽  
Nirajan Thapa Chhetri
Keyword(s):  
Allele Frequencies ◽  
Statistical Parameters ◽  
Weinberg Equilibrium ◽  
Allelic Frequencies ◽  
Str Loci ◽  
Scientific World ◽  
Hardy Weinberg Equilibrium

Allele frequencies for the 15 STR loci in the AmpFlSTR® Identifiler® and statistical parameters were estimated from a sample of 233 unrelated individuals from different area of Nepal. A total of 161 alleles were found, with corresponding allelic frequencies ranging from 0.0021 to 0.4077. The MP, PD, PIC, PE, TPI, Ho and He ranged from 0.0282 to 0.1511, 0.8489 to 0.9717, 0.6478 to 0.8700, 0.4546 to 0.7631, 1.7651 to 4.3148, 0.7167 to 0.8841 and 0.7009 to 0.8833 respectively. Deviations from the Hardy–Weinberg Equilibrium were observed for D16S539, D18S51, D21S11 and TPOX Markers. One new allele has been detected in the process. Scientific World, Vol. 10, No. 10, July 2012 p20-23 DOI: http://dx.doi.org/10.3126/sw.v10i10.6856

Solving Hardy-Weinberg with Geometry: An Integration of Biology and Math

2017 ◽  
Vol 79 (4) ◽  
pp. 309-312
Author(s):  
Laura A. Schoenle ◽  
Matthew Thomas
Keyword(s):  
Scientific Theory ◽  
Geometric Interpretation ◽  
Student Understanding ◽  
Weinberg Equilibrium ◽  
The Core ◽  
Distributive Property ◽  
Genotype Frequencies ◽  
Hardy Weinberg Equilibrium ◽  
Using Data ◽  
And Mathematics

Introducing Hardy-Weinberg equilibrium into the high school or college classroom can be difficult because many students struggle with the mathematical formalism of the Hardy-Weinberg equations. Despite the potential difficulties, incorporating Hardy-Weinberg into the curriculum can provide students with the opportunity to investigate a scientific theory using data and integrate across the disciplines of biology and mathematics. We present a geometric way to interpret and visualize Hardy-Weinberg equilibrium, allowing students to focus on the core ideas without algebraic baggage. We also introduce interactive applets that draw on the distributive property of mathematics to allow students to experiment in real time. With the applets, students can observe the effects of changing allele frequencies on genotype frequencies in a population at Hardy-Weinberg equilibrium. Anecdotally, we found use of the geometric interpretation led to deeper student understanding of the concepts and improved the students' ability to solve Hardy-Weinberg-related problems. Students can use the ideas and tools provided here to draw connections between the biology and mathematics, as well as between algebra and geometry.

Disequilibrium of Human Platelet Antigen 1 (HPA-1) in U.S. Population

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 5466-5466
Author(s):  
Tyler Davi d Hutchinson ◽  
Yuhua Song ◽  
Kevin Trainor ◽  
Ghazala Hashmi
Keyword(s):  
Human Platelet ◽  
Embryo Implantation ◽  
The United States ◽  
Implantation Failure ◽  
Random Group ◽  
Weinberg Equilibrium ◽  
Genotype Frequencies ◽  
Chi Squared ◽  
Human Platelet Antigen ◽  
Hardy Weinberg Equilibrium

Abstract Background: Alloimmunization against Human Platelet Antigens (HPA) is associated with Neonatal Alloimmune Thrombocytopenia (NAIT), post-transfusion purpura and refractoriness for platelet transfusion. A flexible BeadChip™ design was developed to simultaneously detect 22 platelet antigens, including HPA-1, and used to assay over 1,000 random blood donors from across the United States. Methods: Samples from 19 labs/centers from across the country were assayed for 11 HPA loci (HPA-1 through 9, 11 and 15) using the BioArray Solutions HPA Assay. Each locus was independently assessed for Hardy-Weinberg Equilibrium. Results: Allele and genotype frequencies for each locus were reported. Platelet antigens HPA-2 through HPA-9, HPA-11 and HPA-15 were all found to be in Hardy-Weinberg Equilibrium with a Chi-Squared value of <3.84 (1 degree of freedom, 5% confidence interval). HPA-1, however, did not exhibit Hardy-Weinberg Equilibrium yielding a Chi-Squared value of 43.4. Conclusions: After reaffirming there was no sampling preference by inclusion of a second blinded random group, it was acknowledged that HPA-1 did not conform to a Mendelian distribution of alleles. The lower incidence of heterozygote HPA-1 individuals may lend credence to the recent finding by Ivanov et al (Akush Ginekol, 2007) linking the polymorphism in GPIIIa that is responsible for the HPA-1 antigen with embryo implantation failure. Further research may help elucidate the causes behind the HPA-1 disequilibrium and how much implantation failure impacts HPA-1 frequencies.

A Reality Check on Hardy–Weinberg

2013 ◽  
Vol 16 (4) ◽  
pp. 782-789 ◽  
Author(s):  
Alan E. Stark ◽  
Eugene Seneta
Keyword(s):  
Random Mating ◽  
Weinberg Equilibrium ◽  
Reality Check ◽  
Hardy Weinberg Equilibrium ◽  
The Law

G. H. Hardy (1877–1947) and Wilhelm Weinberg (1862–1937) had very different lives, but in the minds of geneticists, the two are inextricably linked through the ownership of an apparently simple law called the Hardy–Weinberg law. We demonstrate that the simplicity is more apparent than real. Hardy derived the well-known trio of frequencies {q2, 2pq, p2} with a concise demonstration, whereas for Weinberg it was the prelude to an ingenious examination of the inheritance of twinning in man. Hardy's recourse to an identity relating to the distribution of types among offspring following random mating, rather than an identity relating to the mating matrix, may be the reason why he did not realize that Hardy–Weinberg equilibrium can be reached and sustained with non-random mating. The phrase ‘random mating’ always comes up in reference to the law. The elusive nature of this phrase is part of the reason for the misunderstandings that occur but also because, as we explain, mathematicians are able to use it in a different way from the man-in-the-street. We question the unthinking appeal to random mating as a model and explanation of the distribution of genotypes even when they are close to Hardy–Weinberg proportions. Such sustained proportions are possible under non-random mating.

How to link call rate and p -values for Hardy-Weinberg equilibrium as measures of genome-wide SNP data quality

2010 ◽  
Vol 29 (22) ◽  
pp. 2347-2358 ◽  
Author(s):  
Helmut Finner ◽  
Klaus Strassburger ◽  
Iris M. Heid ◽  
Christian Herder ◽  
Wolfgang Rathmann ◽  
...  
Keyword(s):  
Data Quality ◽  
Call Rate ◽  
P Values ◽  
Weinberg Equilibrium ◽  
Snp Data ◽  
Genome Wide ◽  
Hardy Weinberg Equilibrium
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