An Unconditional Exact Test for the Hardy-Weinberg Equilibrium Law: Sample-Space Ordering Using the Bayes Factor

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 875-883
Author(s):  
Luis E Montoya-Delgado ◽  
Telba Z Irony ◽  
Carlos A de B. Pereira ◽  
Martin R Whittle
Keyword(s):  
Bayes Factor ◽  
Statistical Tests ◽  
Sample Space ◽  
P Value ◽  
Type I ◽  
Weighted Likelihood ◽  
Asymptotic Results ◽  
Exact Test ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Abstract Much forensic inference based upon DNA evidence is made assuming that the Hardy-Weinberg equilibrium (HWE) is valid for the genetic loci being used. Several statistical tests to detect and measure deviation from HWE have been devised, each having advantages and limitations. The limitations become more obvious when testing for deviation within multiallelic DNA loci is attempted. Here we present an exact test for HWE in the biallelic case, based on the ratio of weighted likelihoods under the null and alternative hypotheses, the Bayes factor. This test does not depend on asymptotic results and minimizes a linear combination of type I and type II errors. By ordering the sample space using the Bayes factor, we also define a significance (evidence) index, P value, using the weighted likelihood under the null hypothesis. We compare it to the conditional exact test for the case of sample size n = 10. Using the idea under the method of χ2 partition, the test is used sequentially to test equilibrium in the multiple allele case and then applied to two short tandem repeat loci, using a real Caucasian data bank, showing its usefulness.

scholarly journals Multi-allelic Exact tests for Hardy-Weinberg equilibrium that account for gender

2017 ◽  
Author(s):  
Jan Graffelman ◽  
Bruce Weir
Keyword(s):  
Permutation Test ◽  
Statistical Tests ◽  
Enumeration Algorithm ◽  
Test Procedures ◽  
Allelic Variants ◽  
Multiple Alleles ◽  
Exact Test ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
And Gender

Statistical tests for Hardy-Weinberg equilibrium are important elementary tools in genetic data analysis. X-chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X-chromosomal exact test procedures for bi-allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this paper we present the extension of the previous work for variants with multiple alleles. A full enumeration algorithm is used for the exact calculations of tri-allelic variants. For variants with many alternate alleles we use a permutation test. Some empirical examples with data from the 1000 genomes project are discussed.

scholarly journals STATISTICAL ANALYSIS WITH A BAYESIAN APPROACH TO THE HARDY-WEINBERG EQUILIBRIUM

2020 ◽  
Vol 38 (1) ◽  
pp. 69
Author(s):  
Moacyr CUNHA FILHO ◽  
David Venancio da CRUZ ◽  
Emídio Cantídio Almeida de OLIVEIRA ◽  
Victor Cassimiro PISCOYA ◽  
Guilherme Rocha MOREIRA ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Bayesian Analysis ◽  
Bayes Factor ◽  
Classical Method ◽  
Statistical Tests ◽  
Primary Concern ◽  
Chi Square ◽  
Weinberg Equilibrium ◽  
Chi Square Test ◽  
Hardy Weinberg Equilibrium

In population genetics, it is very common to use statistical analysis to test the Hardy-Weinberg genetic equilibrium in a given population. The classical method of approaching this problem is done through the chi-square test that often leads to the verification of the equilibrium hypothesis. In the present work, a Bayesian analysis was developed involving hypothesis testing, estimation and credibility intervals to test this balance. Data on M, MN and N blood groups from the MNS system were used on samples from two populations, one from Brazilians and one from North Americans, obtained by Beiguelman (1977). The HardyWeinberg equilibrium adhesion chi-square test was performed, where the acceptance of the Hardy-Weinberg equilibrium hypothesis was confirmed. By Bayesian analysis, the rejection of the Hardy-Weinberg equilibrium hypothesis was confirmed, mainly by the Bayes factor. Our primary concern was to develop a Bayesian technique as an alternative to testing HardyWeinberg equilibrium using the MNSs blood sample data. The result obtained may encourage researchers mainly in the field of biological sciences to practice Bayesian Methodology, as an alternative in statistical tests.

scholarly journals ABCB1 variants C3435T and T129C are not associated with colorectal cancer risk

2019 ◽  
Vol 19 (3) ◽  
pp. 2476-2483 ◽  
Author(s):  
Areej M Al Qahtani ◽  
Ayat B Al-Ghafari ◽  
Huda A Al Doghaither ◽  
Anas H Alzahrani ◽  
Ulfat M Omar ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Saudi Arabia ◽  
Goodness Of Fit ◽  
Allele Frequencies ◽  
Genotype Distribution ◽  
Exact Test ◽  
Weinberg Equilibrium ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
And Control

Background: Colorectal cancer (CRC) is one of the most prevalent cancers in Saudi Arabia that is highly characterized with poor survival rate and advanced metastasis. Many studies contribute this poor outcome to the expression of ABC transporters on the surface of cancer cells.Objectives: In this study, two ABCB1 variants, C3435T and T129C, were examined to evaluate their contribution to CRC risk.Methods: 125 subjects (62 CRC patients and 63 healthy controls) were involved. The DNA was isolated and analyzed with PCR-RFLP to determine the different genotypes. The hardy-Weinberg equilibrium was performed to determine genotype distribution and allele frequencies. Fisher’s exact test (two-tailed) was used to compare allele frequencies between patients and control subjects. Results: The study showed that for SNP C3435T, the population of both CRC patients and controls were out of Hardy-Weinberg equilibrium. Genotype distribution for CRC patients was (Goodness of fit χ2 = 20, df= 1, P≤0.05), whereas, for the controls the genotype distribution was (Goodness of fit χ2 = 21, df =1, P ≤0.05). For SNP T129C, all subjects showed normal (TT) genotype.Conclusion: There was no significant association between ABCB1 3435C>T and 129T>C polymorphisms with CRC risk.Keywords: Colorectal cancer, ABCB1 gene, SNP C3435T, SNP T129C, PCR-RFLP, Saudi Arabia.

scholarly journals FACTORS ASSOCIATED WITH ELDERLY’S SATISFACTION IN INTEGRATED HEALTH SERVICE POST IN VILLAGE TOBIMEITA DISTRICT OF NAMBO CITY OF KENDARI

2020 ◽  
Vol 2 (2) ◽  
pp. 13-21
Author(s):  
Sartini Risky MS ◽  
Dewi Sari Pratiwi ◽  
Muhammad Ikhsan Akbar
Keyword(s):  
Statistical Tests ◽  
Strong Relationship ◽  
The Elderly ◽  
Cross Sectional Study ◽  
P Value ◽  
Satisfaction Level ◽  
Cross Sectional ◽  
Exact Test ◽  
Factors Associated ◽  
Integrated Service

Background: Based on the results of interviews with researchers, six out of ten elderly said they were not satisfied with the service because the starting time for integrated post services was sometimes late, the lack of information obtained was related to elderly integrated service post activities. First person said he was satisfied with the service but still complained about the irregular timing of the integrated service post activities. Research is aimed to determine Factors-Factors Associated With Satisfaction Elderly In Integrated Service Post In Village Tobimeita District of Nambo city of Kendari. Methods: This type of research uses research quantitative design with cross-sectional study population of fifty six people. Sampling using purposive sampling with a sample size of fifty six respondents. The data is processed by using a test Fisher's exact test and continued with the test Coefficient Phi. Result: Based on the results of statistical tests there is a strong relationship between service quality and the level of satisfaction of the elderly with p value 0.000 < ? 0.05 , there is a moderate relationship between service and the satisfaction level of the elderly with p value 0.000 < ? 0.05, and there is a strong relationship between the attitude of officers with elderly satisfaction level p value 0.000 < ? 0.05. Conclusion: Researchers suggest that active remind and motivate the elderly to follow integrated service post elderly, other than that in running its role officers also should have to be friendly to the elderly so that the elderly feel happy to follow integrated service post elderly.

scholarly journals Genetic structure and the search for genotype-phenotype relationships: an example from disequilibrium in the Apo B gene region.

Genetics ◽  
1991 ◽  
Vol 129 (2) ◽  
pp. 525-533
Author(s):  
K E Zerba ◽  
A M Kessling ◽  
J Davignon ◽  
C F Sing
Keyword(s):  
Small Sample Size ◽  
Total Sample ◽  
Small Sample ◽  
Type I ◽  
Type Ii ◽  
Type Ii Error ◽  
Apo B ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
Error Probabilities

Abstract We analyzed allelic associations (disequilibria) for four restriction fragment length polymorphisms (RFLPs) in the region of the 43-kb Apo B gene in a sample of 233 unrelated individuals from Montreal, Canada, sampled for health. This total sample (T) included 160 individuals of known French Canadian (FC) ancestry. We present a rigorous application of current methodology to these samples, including estimation of type II error probabilities and correlations between markers for estimates of disequilibria. We then consider the utility of these estimates of allelic disequilibria for the interpretation of genotype-phenotype relations. Significant deviations from Hardy-Weinberg equilibrium were not predicted by proximity to other markers in disequilibrium. We found significant quadri-allelic disequilibrium for two marker pairs despite absence of significant deviations from Hardy-Weinberg equilibrium for either marker or tri-allelic disequilibrium, respectively. Altogether these results underscore the complexity of the genotypic structure of the data. A combination of nonevolutionary factors, including sampling for health, small sample size and data exclusion due to methodological constraints of not successfully typing all members of the sample for every RFLP, is a likely explanation for this complexity. These types of factors are common to many RFLP studies. Patterns of composite di-allelic disequilibrium indicated that some RFLP allele pairs may have a longer shared evolutionary history than others and that disequilibrium is not predicted by distance between RFLPs. Type II error probabilities were generally much higher than those for type I errors. Correlations between marker pairs for disequilibria were generally not high. We show from a review of 14 published studies of association between the XbaI RFLP and variation in a total of 15 lipid traits that deviations from Hardy-Weinberg equilibrium can cause substantial differences in the estimation of variability associated with phenotypic differences among marker genotypes relative to Hardy-Weinberg conditions.

scholarly journals Hubungan tingkat pengetahuan dan pola perilaku dengan kejadian malaria di Kabupaten Katingan Provinsi Kalimantan Tengah

2019 ◽  
Vol 3 (2) ◽  
pp. 36-41 ◽  
Author(s):  
Darmiah Darmiah ◽  
Baserani Baserani ◽  
Abdul Khair ◽  
Isnawati Isnawati ◽  
Yuniarti Suryatinah
Keyword(s):  
Statistical Tests ◽  
Public Awareness ◽  
Behavioral Pattern ◽  
High Rate ◽  
P Value ◽  
Fisher Exact Test ◽  
Knowledge Level ◽  
District Health ◽  
Exact Test ◽  
Level Of Knowledge

Malaria disease is one of the environmental health problems, Health Office of Katingan District Kasongan District Health Center. Katingan Hilir is a malaria endemic area with an API value in 2010 of 5.6 ‰ and is a red zone in malaria stratafication. Malaria discovery rates from 2008 to 2010 always increase. The high rate of malaria morbidity is due to the lack of knowledge level and community behavior pattern.The aim of this research is to know the correlation between knowledge level and behavioral pattern about malaria with malaria incident in Kasongan sub-district of Katingan Hilir district of Katingan Regency. The type of research is analytic, research design using Fisher exact test. The number of respondents in this study was 58 respondents.Chi-square statistical test results with Continuity Correction obtained p-value 0.002 indicates that there is a relationship between the level of knowledge with the incidence of malaria and the results of statistical tests with Fisher exact test obtained p-value 0.002 that there is a relationship between behavioral patterns with malariaincidence.Efforts that can be done, among others, control the factors causing malaria such as the level of knowledge and behavior patterns as well as increasing the extension of public awareness.

scholarly journals Oestrogen Receptor Alpha, Beta Genes and CYP17A Gene Polymorphism Analysis in Women with Uterine Leiomyoma

2021 ◽  
Author(s):  
Ravindra Goswami ◽  
Sukanya Gangopadhyay ◽  
Bhaskar Charana Kabi
Keyword(s):  
Uterine Leiomyoma ◽  
Tertiary Care Hospital ◽  
Tertiary Care ◽  
North India ◽  
P Value ◽  
Care Hospital ◽  
Receptor Alpha ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
Er Alpha

Introduction: Uterine Leiomyoma is a highly morbid condition with an increasing incidence in the Asian Indian ethnicity. The pathogenesis is multifactorial and not clearly delineated, making non-surgical treatment of limited success, thus making surgical intervention prevalent. Derangement of endocrinological parameters is the most evident aspect and cause of this condition. But the root genetic cause of this hormonal imbalance has seldom been explored in Indian women suffering from uterine leiomyoma. Aim: To explore the association of Single Nucleotide Polymorphism (SNPs) rs3020449, rs4986938 and rs743572 of ER alpha, ER beta and CYP17 genes respectively in women having uterine fibroid visiting a Tertiary Care Hospital in North India. Materials and Methods: Hundred patients diagnosed with uterine leiomyoma were selected from Gynaecology Out Patient Department (OPD) of a Tertiary Care Hospital in North India and equal age matched healthy women were taken as controls randomly, with a condition that they have no close blood relative with uterine leiomyoma. The blood was collected for DNA extraction and RFLP based polymorphism detection. Bands were visualised in agarose gel for Estrogen Receptor alpha (ER alpha), ER beta and CYP17 genes. Statistical analysis was performed using Graph Pad Prism 6.0. Hardy Weinberg equilibrium was tested using Chi-square goodness of fit test. Nominal variables were analysed using Fisher-exact test. Data is presented as Mean±SEM and p-value of <0.05 was considered significant. Results: Early age at menarche (cases vs control 11.51±0.19 year vs 12.04±0.12, p=0.03) and less number of previous pregnancies (cases vs control 1.06±0.09 vs 1.41±0.12, p=0.01), which are known risk factors for the uterine fibroids, was reconfirmed in this study. The genotype distribution of all subjects studied in above genes followed Hardy Weinberg equilibrium and there was no significant difference in genotype frequencies between cases and controls [ER alpha rs9322331 C allele (cases vs controls; 62% vs 64%), T allele (38% vs 36%); ER beta rs4986938 G allele (64% vs 59%), A allele (36% vs 41%); CYP17 rs743572 T allele (44.95% vs 46.53%), C allele (55.05% vs 53.47%) p-value not significant in any]. However, there was an increased propensity of TC genotype of CYP17 rs743572 towards obesity (p<0.05). Conclusion: The allelic frequencies of all the three SNPs were similar in cases and controls indicating that they do not affect susceptibility to disease. However, the association of TC allele of CYP17 SNP with higher BMI needs further analysis.

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