Statistical Tests and Algorithms

2021 ◽  
pp. 65-92
Author(s):  
Áki J. Láruson ◽  
Floyd A. Reed
Keyword(s):  
Expectation Maximization ◽  
Statistical Tests ◽  
Allele Frequencies ◽  
Genotype Frequency ◽  
Frequency Data ◽  
Working Through

In this chapter statistical tests are performed in R, including the χ‎2 tests; testing can be started if allele and genotype frequency data match the reader’s expectations. Writing and running algorithms are introduced as functions, specifically working through building an Expectation Maximization function. The function is then used to estimate and update the reader’s inferences of allele frequencies from observed and expected genotypes.

scholarly journals Improved identification of abdominal aortic aneurysm using the Kernelized Expectation Maximization algorithm

2021 ◽  
Vol 379 (2200) ◽  
Author(s):  
Daniel Deidda ◽  
Mercy I. Akerele ◽  
Robert G. Aykroyd ◽  
Marc R. Dweck ◽  
Kelley Ferreira ◽  
...  
Keyword(s):  
Abdominal Aortic Aneurysm ◽  
Aortic Aneurysm ◽  
Expectation Maximization ◽  
Kernel Method ◽  
Statistical Tests ◽  
Statistical Significance ◽  
Reconstruction Algorithms ◽  
Edge Preserving ◽  
Abdominal Aortic ◽  
Risk Of Rupture

Abdominal aortic aneurysm (AAA) monitoring and risk of rupture is currently assumed to be correlated with the aneurysm diameter. Aneurysm growth, however, has been demonstrated to be unpredictable. Using PET to measure uptake of [ 18 F]-NaF in calcified lesions of the abdominal aorta has been shown to be useful for identifying AAA and to predict its growth. The PET low spatial resolution, however, can affect the accuracy of the diagnosis. Advanced edge-preserving reconstruction algorithms can overcome this issue. The kernel method has been demonstrated to provide noise suppression while retaining emission and edge information. Nevertheless, these findings were obtained using simulations, phantoms and a limited amount of patient data. In this study, the authors aim to investigate the usefulness of the anatomically guided kernelized expectation maximization (KEM) and the hybrid KEM (HKEM) methods and to judge the statistical significance of the related improvements. Sixty-one datasets of patients with AAA and 11 from control patients were reconstructed with ordered subsets expectation maximization (OSEM), HKEM and KEM and the analysis was carried out using the target-to-blood-pool ratio, and a series of statistical tests. The results show that all algorithms have similar diagnostic power, but HKEM and KEM can significantly recover uptake of lesions and improve the accuracy of the diagnosis by up to 22% compared to OSEM. The same improvements are likely to be obtained in clinical applications based on the quantification of small lesions, like for example cancer. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 1’.

Breeding for scrapie resistance in the Hungarian sheep population

2008 ◽  
Vol 56 (2) ◽  
pp. 173-180 ◽  
Author(s):  
László Fésüs ◽  
Attila Zsolnai ◽  
István Anton ◽  
László Sáfár
Keyword(s):  
Capillary Electrophoresis ◽  
Prion Protein ◽  
Genotype Frequency ◽  
Breeding Programme ◽  
Atypical Scrapie ◽  
Frequency Data ◽  
Sheep Population ◽  
New Developments ◽  
First Results ◽  
Efficiency Of Selection

The first results of the Hungarian sheep prion protein (PrP) genotyping programme are discussed in this paper. To obtain initial genotype frequency data 10 commercial (Hungarian Merino, German Mutton Merino, Merino Landschaf, German Blackheaded, Suffolk, Texel, Ile de France, Charollais, Lacaune, British Milksheep) and 4 indigenous (Gyimes Racka, Hortobágy Racka, Tsigaja, Cikta) breeds were sampled in 2003 and 2004, and the PrP genotypes were determined by microsequencing analysis with capillary electrophoresis. In all commercial breeds, a higher number of sheep were genotyped in 2005 (3648) and in 2006 (3834) within the breeding programme to increase scrapie resistance, and the estimated frequency data were compared to the initial figures to evaluate the efficiency of selection. The new developments arising from the identification of the so-called ‘atypical’ scrapie cases are also discussed.

scholarly journals FREQUENCY DISTRIBUTION OF ESTERASE-5 ALLELES IN TWO POPULATIONS OF DROSOPHILA PSEUDOOBSCURA

Genetics ◽  
1983 ◽  
Vol 105 (1) ◽  
pp. 135-155
Author(s):  
Tim Perri Keith
Keyword(s):  
Sex Ratio ◽  
Statistical Tests ◽  
Large Population ◽  
Natural Populations ◽  
Purifying Selection ◽  
Allele Frequencies ◽  
Drosophila Pseudoobscura ◽  
Frequency Distributions ◽  
Neutral Models ◽  
The Individual

ABSTRACT Statistical tests comparing allele frequencies in natural populations with those predicted by various theories of genic variation depend critically on the accurate enumeration of alleles. This study used a series of five sequential electrophoretic conditions to characterize the allele frequency distributions of esterase-5 in two large population samples of Drosophila pseudoobscura from California. In Standard chromosome lines 12 electromorphs were discriminated using a single electrophoretic condition. When four additional criteria were used, the number of electromorphs increased to 41, 33 in one population and 22 in the other. Both populations had the same two alleles in high frequency, with other alleles present in frequencies of 6% or less. Although each population had a number of unique alleles, a χ2 contingency test demonstrated no significant genetic divergence between them. A statistical comparison of allele frequencies in both populations with that predicted by neutral models suggests that the individual and combined distributions deviate from neutrality in the direction of purifying selection.—Sex-Ratio chromosomes differed markedly from Standard chromosomes in both allelic content and diversity. In 32 Sex-Ratio chromosomes from one population only three alleles were found, all of which were detected under the initial "standard" electrophoretic conditions. Moreover, none of these alleles was found in the Standard chromosome lines.

scholarly journals TaqMan Real-Time Polymerase Chain Reaction and Pyrosequencing using Single Nucleotide Polymorphism Protocol for Rapid Determination of ALDH2 *2 in a Chinese Population

2015 ◽  
Vol 14 (9) ◽  
pp. 1679-1684
Author(s):  
J Li ◽  
J Wu ◽  
Y Zhang ◽  
X Wang ◽  
J Jin ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Aldehyde Dehydrogenase ◽  
Real Time Pcr ◽  
Chinese Population ◽  
Allele Frequencies ◽  
Genotype Frequency ◽  
Aldehyde Dehydrogenase 2 ◽  
Chain Reaction ◽  
Polymerase Chain

Purpose: To establish a rapid molecular method for the detection of aldehyde dehydrogenase 2 (ALDH2), and determine whether the polymorphic ALDH2 gene is associated with drinking behavior in a Chinese population.Methods: The gene polymorphism of ALDH2 *2 was detected using pyrosequencing and TaqMan realtime polymerase chain reaction (PCR) techniques. Genotyping of 176 volunteers were performed at The Third Hospital of Wuhan, Hubei, China. Genetic associations with alcohol use behavior was assessed.Results: Pyrosequencing and TaqMan real time PCR methods were successfully developed to identify ALDH2 *2 polymorphisms. The allele frequencies of ALDH2 *2 were 21.31 % in the Chinese population. While the genotype frequency of heterozygous ALDH2 *1/ *2 plus homozygous ALDH2 *2/ *2 was 46.67 % in non-drinkers, it was 30.17 % in the alcoholics group (p = 0.030). The allele frequency of ALDH2 *2 was 15.09 % in the alcoholics group and 28.33 % among non-drinkers (p = 0.011). There were  substantial differences in allele frequencies of ALDH2 genotypes between this study’s Chinese sample and other ethnic groups in Asia; the frequency of ALDH2 *2 allele was significantly higher than that in European and Americans.Conclusion: The developed pyrosequencing and TaqMan real time PCR methods are rapid, accurate, high-throughput, convenient, and reliable for detecting ALDH2 polymorphisms. ALDH2 *2 gene protects against the development of alcoholism. The frequencies of ALDH2 in this Chinese population differ from those of other  ethnic populations.Keywords: Aldehyde dehydrogenase 2, Polymorphism, TaqMan real time Polymerase Chain Reaction, Pyrosequencing, Allele, Alcoholics, Genotype frequency

Geographic distribution of the 3435C>T polymorphism of the MDR1 gene in Peruvian populations

2019 ◽  
Vol 34 (3) ◽  
Author(s):  
Edward Valencia Ayala ◽  
Pool Marcos Carbajal ◽  
Eduardo Barbosa Coelho ◽  
Jose Sandoval Sandoval ◽  
Alberto Salazar Granara
Keyword(s):  
Genetic Polymorphisms ◽  
Geographic Distribution ◽  
Allele Frequencies ◽  
Genotype Frequency ◽  
Mdr1 Gene ◽  
Frequency Distributions ◽  
Weinberg Equilibrium ◽  
Pearson Test ◽  
Hardy Weinberg Equilibrium ◽  
Genotype And Allele Frequencies

Abstract Background The MDR1 gene presents several genetic polymorphisms with pharmacological implications. Therefore, the aim of the present study is to establish the genotype and allele frequencies of 3435C>T polymorphism of MDR1 gene into Peruvian populations (Coastal, Andean and Amazonian ecoregions), even considering the altitude (lowland <2500 m and highland >2500 m). Methods The polymorphism was analyzed by TaqMan genotyping assays in a group of 181 healthy unrelated Peruvian individuals. The comparison of genotype and allele frequencies of 3435C>T polymorphism was made with the Pearson test (X2), and, to calculate the genotype distributions, the Hardy-Weinberg equilibrium (HWE) was used. Results In all populations evaluated in this study, the genotype frequency distributions met HWE assumptions. The comparison between genotype and allele frequencies showed significant differences (p < 0.05), when the Andean, Coastal and Amazonian populations were compared. Also, significant differences (p < 0.05) were obtained when these populations were compared considering their altitudes. Likewise, in comparison with countries like USA, Finland, Nigeria and Kenya, the results showed significant differences (p < 0.05). Conclusions This investigation allowed us to establish the genotype and allele frequencies of 3435C>T polymorphism in different Peruvian populations, considering the geographic localization and even the altitude.

Detection of natural selection by methods based on models of the behaviour of neutral alleles

1980 ◽  
Vol 12 (4) ◽  
pp. 469-479
Author(s):  
B. K. Averill
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Allele Frequency ◽  
Allele Frequencies ◽  
Frequency Data ◽  
Allele Frequency Data

SummaryThe allele frequency data of artificial populations were examined by several methods which test whether various configurations of allele frequencies are the result of drift or selection. Although no genotypic selective differences were included in these populations the methods indicated that selection was operating in some instances; hence the models are not reliable. Distinguishing between the actions of drift and selection would be facilitated if data for many loci were included, so that a notion of the variance of the genetic variation measure could be obtained.

scholarly journals Genetic Study of Phenylthiocarbamide (PTC) Taste Sensitivity In Population of The Osing in Kemiren Village-Banyuwangi

2021 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Fenny Indriani ◽  
Rike Oktarianti ◽  
Syubbanul Wathon
Keyword(s):  
Genetic Study ◽  
Gene Frequency ◽  
Serial Dilution ◽  
Allele Frequencies ◽  
Genotype Frequency ◽  
Taste Sensitivity ◽  
Dilution Method ◽  
Serial Dilution Method ◽  
Different Populations ◽  
Age Range

The ability to taste phenylthiocarbamide (PTC), is autosomal trait inherited in a simple Mendelian recessive pattern. The frequency of Taster and non-Taster allele is varies in different populations. The purpose of the research is to investigate the prevalence, gene frequency and genotype frequency of taster (T) and non taster (ts of Osing population in Kemiren-Banyuwangi. PTC serial dilution method was used to assess the PTC Taster and non-Taster phenotypes. The Hardy–Weinberg method was used to determine allele frequencies. The total of samples were 227 people, male were 117 and female were 110 with age range of 15–30 years were randomly selected. The result showed that the Osing population as Taster were 210 (92,52%) and non Taster were 17samples (7,48%) . The allele frecuency of Taster (T) was 0,73 and non Taster (t) was 0,27 respectively. The genotype frequency of dominant Taster (TT) was 0,54, heterozygosity Taster (Tt) was 0,39, and genotype of non Taster (tt) was 0,07.

scholarly journals Using Maximum Likelihood to Estimate Population Size From Temporal Changes in Allele Frequencies

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 755-761 ◽  
Author(s):  
Ellen G Williamson ◽  
Montgomery Slatkin
Keyword(s):  
Maximum Likelihood ◽  
Population Size ◽  
Exponential Growth ◽  
Temporal Changes ◽  
Allele Frequencies ◽  
Frequency Data ◽  
Effective Population ◽  
Likelihood Estimator ◽  
Allele Frequency Data ◽  
Estimate Population Size

Abstract We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the performance of this estimator to an F-statistic estimator of variance effective population size. The maximum-likelihood estimator had a lower variance and smaller bias. Taking advantage of the likelihood framework, we extend the model to include exponential growth and show that temporal allele frequency data from three or more sampling events can be used to test for population growth.

scholarly journals Association of NCF2, NCF4, and CYBA Gene Polymorphisms with Rheumatoid Arthritis in a Chinese Population

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Tian-Ping Zhang ◽  
Rui Li ◽  
Qian Huang ◽  
Han-Feng Pan ◽  
Dong-Qing Ye ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Nadph Oxidase ◽  
Gene Polymorphisms ◽  
Chinese Population ◽  
Allele Frequencies ◽  
Genotype Frequency ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Normal Controls ◽  
Cyba Gene

Objective. Recent studies have focused on the special roles of NADPH-oxidase in multiple autoimmune diseases. Nevertheless, the association of genetic variation in NADPH-oxidase genes with rheumatoid arthritis (RA) was not extensively studied in a Chinese population. We performed this study to examine the association of NCF2, NCF4, and CYBA gene polymorphisms with RA susceptibility in a Chinese population. Methods. Six single nucleotide polymorphisms (SNPs) (NCF2 rs10911363, NCF4 rs1883112, rs4821544, rs729749, CYBA rs3794624, and rs4673) were genotyped in a cohort composed of 593 RA patients and 596 normal controls. Improved multiple ligase detection reaction (iMLDR) was used for genotyping. Results. We observed that NCF4 rs4821544 CT genotype and C allele frequencies in RA patients were significantly decreased when compared to controls (CT vs. TT: P = 0.043 ; C vs. T: P = 0.031 ), and rs4821544 polymorphism was significantly associated with an increased RA risk under the dominant model (TT vs. CT+CC: P = 0.031 ). Our results also indicated that rs729749 CT genotype frequency was significantly lower in RA patients than that in controls (CT vs. CC: P = 0.033 ). Moreover, the rs729749 CT genotype frequency was also significantly decreased in RA patients in males (CT vs. CC: P = 0.024 ). No significant association between NCF2 and CYBA gene polymorphisms and RA susceptibility was observed. There were significant associations between rs4821544 TT genotype and T allele frequencies and anti-CCP in male RA patients. Conclusions. In summary, NCF4 rs4821544 and rs729749 polymorphisms might contribute to RA susceptibility, while NCF2 and CYBA gene polymorphisms were not associated with RA susceptibility.

Sign in / Sign up

Export Citation Format

Share Document