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

Distribution of drug-metabolizing enzymes coding genes CYP2D6, CYP3A4, CYP3A5 alleles in a group of healthy Turkish population

2018 ◽  
Vol 44 (2) ◽  
pp. 142-146
Author(s):  
İsmail Ün ◽  
İ. Ömer Barlas ◽  
Nisa Uyar ◽  
Bahar Taşdelen ◽  
Naci Tiftik
Keyword(s):  
Drug Therapy ◽  
Adverse Drug Reactions ◽  
Low Frequency ◽  
Turkish Population ◽  
Allele Frequencies ◽  
Drug Reactions ◽  
Metabolizing Enzymes ◽  
Frequency Distributions ◽  
Allelic Frequencies ◽  
Hardy Weinberg Equilibrium

Abstract Objective: Variant alleles in specific ethnic groups are important for personalized drug therapy regimens and adverse drug reactions. Therefore, the aim of this study was to investigate allelic frequencies of the CYP2D6*1, CYP3A4*5, CYP3A4*18, CYP3A5*2 and CYP3A5*4 in a group of Turkish population. Materials and methods: Three hundred and six unrelated healthy subjects who were accepted as blood donors to the Mersin University Blood Bank were included in the study after informed consent. Allelic frequencies of the CYP2D6*1 (rs3892097), CYP3A4*5 (rs55901263), CYP3A4*18 (rs28371759), CYP3A5*2 (rs28365083) and CYP3A5*4 (rs56411402) were determined by using polymerase chain reaction-restriction fragment length polymorphism assays. Results: CYP2D6 allele frequencies in detected group was 100% for CYP2D6*1 (WT/WT). CYP3A4 allele frequencies of subjects were 100% for CYP3A4*5 (C/C) and CYP3A4*18 (T/T). CYP3A5 allele were in Hardy-Weinberg equilibrium for CYP3A5*2 (p=0.142) and frequencies for C and A allele were 91% and 9% respectively. CYP3A5 allele frequencies of subjects was 100% for CYP3A5*4 (WT/WT). Conclusion: Screening of low frequency alleles by pharmacogenetic testing must not be omitted to optimize pharmacotherapy and avoid severe drug toxicities. Frequency distributions of the identified polymorphisms in the present study may contribute to the personalized drug therapy regimens and prediction of possible adverse drug reactions in the Turkish population.

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 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.

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

scholarly journals PCR-SSCP Analysis of Keratin - Associated Protein (KAP) 6.1 Gene in Nilagiri and Dorset x Nilagiri Cross Breeds of Sheep

2020 ◽  
pp. 97-102
Author(s):  
R. Bharathesree ◽  
R. Saravanan ◽  
M. Jeyakumar ◽  
N. Murali
Keyword(s):  
Allele Frequencies ◽  
Sscp Analysis ◽  
Effective Number ◽  
Specific Primers ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
High Degree

The present study was investigated to detect polymorphic patterns of the keratin-associated protein (KAP) 6.1 gene in 54 numbers of Nilagiri and 20 numbers of Dorset x Nilagiri breeds of sheep. DNA was isolated and amplified with ovine specific primers of KAP 6.1 gene. Allele frequencies of A, B, C, D and E was 0.79, 0.08, 0.15, 0.07 and 0.08 respectively with departure from Hardy-Weinberg equilibrium. KAP 6.1 gene was found to have a high degree of homozygosity (0.6668), and an effective number of alleles (Ne) for KAP 6.1 gene was 1.7007 in Nilagiri breeds of sheep, while the PIC value was 0.3909 with positive (0.1908) FIS value. From the study, PCR - SSCP analysis of KAP 6.1 gene revealed polymorphism in Nilagiri breeds whereas in Dorset x Nilagiri crossbred sheep two genotypes for the A/B with no polymorphism detected.

GENETIC AND PHENOTYPIC PROFILES OF ENDANGERED ANDALUSIAN SHEEP AND GOAT BREEDS

1996 ◽  
Vol 19 ◽  
pp. 69-89 ◽  
Author(s):  
E. Rodero ◽  
M.R. de la Haba ◽  
A. Rodero ◽  
M. Herrera
Keyword(s):  
Artificial Selection ◽  
Mediterranean Area ◽  
Weinberg Equilibrium ◽  
Allelic Frequencies ◽  
Hardy Weinberg Equilibrium ◽  
Selection For ◽  
The Mediterranean ◽  
Genetic Profiles ◽  
Black Goat

SUMMARYThe Grazalema Merino and Lebrija Churro Sheep and the Andalusian White and Andalusian Black goat breeds, previously chosen as priority breeds in need of conservation, were considered as having priority for this study. In order to define the genetic as well as the phenotypic profiles the following characters were used: head profile, ear size, ear orientation, ear consistency, horns, pigmentation of mucous, hoofs, udder, ñneness of fur, hair or wool, length of hair or wool, presence of wattles and goatee bear, supernumerary nipples., udder shape, orientation and pigmentation of nipple, and peculiarities of coat. The allelic frequencies for each system were calculated to obtain the genetic profiles of each breed. In the two goat breeds and in the Grazalema Merino breed, the majority of the loci were genetically in Hardy-Weinberg equilibrium, but this was not true of the Lebrijan Churro breed which seems to indicate that the latter was either subjected to natural or artificial selection for these genes or crosses with outside breeds had taken place. The profiles of the breeds were compared with foreign breeds considered traditional or unmodified by man. The profile of the Andalusian White has already been studied by Rodero and they reached the conclusion that this breed can be considered traditional, completing the studies made on other breeds from the Mediterranean area. The data on the Andalusian Black seems to indicate that this breed might be considered traditional or subtraditional with strong polymorphism in most of its characters. Although less markedly than in the latter breed, the same is true of the Lebrijan Churro. In this breed the deñning characters of Archaism fit well within those common to an archaic breed. The Grazalema Merino is more standardised than the above mentioned not as ñxed than the precocious ones.

Allele Frequencies and Statistical Parameters for Penta E and Penta D STR Loci in Córdoba (Argentina) Population

2004 ◽  
Vol 49 (2) ◽  
pp. 1-1 ◽  
Author(s):  
María C. Miozzo ◽  
Mariana K. Maxzud ◽  
Ariel E. Casanova ◽  
Silvia A. Mutal ◽  
Carla Pacharoni ◽  
...  
Keyword(s):  
Allele Frequencies ◽  
Statistical Parameters ◽  
Str Loci

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.

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 Population genetic data of the 21 autosomal STRs included in GlobalFilerTM kit of a population sample from the Kingdom of Bahrain

2019 ◽  
Author(s):  
Noora R. Al-Snan ◽  
Safia Messaoudi ◽  
Saranya R. Babu ◽  
Moiz Bakhiet
Keyword(s):  
Genetic Structure ◽  
Allele Frequency ◽  
Population Genetic ◽  
Population Parameters ◽  
Autosomal Strs ◽  
Genetic Studies ◽  
Weinberg Equilibrium ◽  
Str Loci ◽  
Hardy Weinberg Equilibrium ◽  
Bahraini Population

AbstractIntroductionBahrain’s population consists mainly of Arabs, Baharna and Persians leading Bahrain to become ethnically diverse. The exploration of the ethnic origin and genetic structure within the Bahraini population is fundamental mainly in the field of population genetics and forensic science.AimThe purpose of the study was to investigate and conduct genetic studies in the population of Bahrain to assist in the interpretation of DNA-based forensic evidence and in the construction of appropriate databases.Materials and Methods24 short-tandem repeats in the GlobalFiler™ PCR Amplification kit including 21 autosomal STR loci and three gender determination loci were amplified to characterize different genetic and forensic population parameters in a cohort of 543 Bahraini unrelated healthy men. Samples were collected during the year 2017.ResultsThe genotyping of the 21 autosomal STRs showed that most loci were in Hardy-Weinberg Equilibrium (HWE) except for three markers; D3S1358, D19S433 and D5S818 which showed deviation from HWE. We also found out no significant deviations from LD between pairwise STR loci in Bahraini population except when plotting for D3S1358-CSF1PO, CSF1PO-SE33, D19S433-D12S391, FGA-D2S1338, FGA-SE33, FGA-D7S820 and D7S820-SE33. The SE33 locus was the most polymorphic for the studied population and THO1 locus was the less polymorphic. The Allele 8 in TPOX scored the highest allele frequency of 0.496. The SE33 locus showed the highest power of discrimination (PD) in Bahraini population, whereas TPOX showed the lowest PD value. The 21 autosomal STRs showed a value of combined match probability (CMP) equal to 4.5633E-27, and a combined power of discrimination (CPD) of 99.99999999%. Off-ladders and tri-allelic variants were observed in various samples at D12S391, SE33 and D22S1045 loci.ConclusionOur study indicated that the twenty-one autosomal STRs are highly polymorphic in the Bahraini population and can be used as a powerful tool in forensics and population genetic analyses including paternity testing and familial DNA searching.Author SummaryKingdom of Bahrain is a country of 33 islands located in the Arabian Peninsula. The location of Bahrain had affected the diversity of its population, which is mainly divided into four main ethnic groups: Arabs, Baharna and Persians. Genetic studies on Bahraini population are very limited and little has been done to characterize population structure within Kingdom of Bahrain. Here, we used 21 autosomal STRs included in the GlobalFiler™ Amplification Kit to amplify DNA from 543 non-related males from Bahraini population. We conducted statistical analysis using two main different software such as STRAF and GenAlEx. Different forensic and population parameters were obtained to characterize Bahraini population. Some of the significant results obtained were the following: most of the loci were in Hardy-Weinberg Equilibrium, the most polymorphic and informative marker was SE33. Allele 8 in TPOX presented the highest allele frequency for the studied population. We also found out some of the rare variants which were recorded in STRbase website. Bahraini population was correspondingly compared to the genetic structure of the region. Our study indicated the usefulness of the 21 autosomal STRs in the GlobalFiler ™ in establishing databases, analyzing paternity and reviewing DNA-based evidences.

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