A Novel PCR-RFLP Method for Detection of POR*28 Polymorphism and its Genotype/Allele Frequencies in a Turkish Population

2019 ◽  
Vol 20 (10) ◽  
pp. 845-851
Author(s):  
Fezile Ozdemir ◽  
Merve Demirbugen Oz ◽  
Hilat S. Suzen
Keyword(s):  
Turkish Population ◽  
Allele Frequencies ◽  
Oxidation Reactions ◽  
Coding Region ◽  
Chinese Populations ◽  
Genotype Frequencies ◽  
Genotypic Analysis ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Novel Method

Background: The Cytochrome P450 (CYP) enzymes are involved in the metabolism of many endogenous and exogenous substances. They need electrons for their activity. CYP mediated oxidation reactions require cytochrome oxidoreductase (POR) as an electron donor. A common genetic variation identified in the coding region of POR gene (POR*28) leads to an alteration in POR activity by causing amino acid change. The current study aimed to determine the allele and genotype frequencies of POR*28 in a healthy Turkish population by using a novel genotyping assay. Methods: A novel PCR-RFLP assay was developed for the detection of POR*28 (rs1057868) polymorphism and the obtained frequencies were compared with the data established in various ethnic groups. Results: Genotypic analysis revealed that of 209 healthy, unrelated individuals tested for POR*28 polymorphism, 55.5% of the studied subjects were homozygous for the CC genotype, 34.9% were heterozygous for the CT genotype and 9.6% were homozygous for the TT genotype. The allele frequencies were 0.73 (C) and 0.27 (T). The present results were in accordance with the Hardy- Weinberg equilibrium. The distribution of POR*28 allele varies between populations. The frequency of the T allele among members of the Turkish population was similar to frequencies in Caucasian populations but was lower than in Japanese and Chinese populations. Conclusions: In this study, a novel method was developed, which could be applied easily in every laboratory for the genotyping of POR *28 polymorphism. The developed genotyping method and documented allele frequencies may have potential in understanding and predicting the variations in drug response/adverse reactions in pharmacotherapy and susceptibility to diseases in POR-mediated metabolism reactions.

scholarly journals The oestrogen receptor gene (ESR) PvuII polymorphism allele frequencies in Czech Large White and Landrace

2005 ◽  
Vol 53 (2) ◽  
pp. 33-38
Author(s):  
Eliška Goliášová ◽  
Josef Dvořák
Keyword(s):  
Oestrogen Receptor ◽  
Receptor Gene ◽  
Allele Frequencies ◽  
Large White ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Pvuii Polymorphism ◽  
Landrace Population ◽  
Genotype And Allele Frequencies

Genotype and allele frequencies of the oestrogen receptor gene (ESR) PvuII restriction site were investigated in populations of the main Czech maternal breeds. 1253 sows and gilts and 396 boars in Large White and 334 sows and gilts and 318 boars in Landrace were genotyped from blood samples by the modified PCR-RFLP procedure as described in Short et al. (1997). In Large White, the frequency of allele B was about 0.51. In Landrace, the frequency of allele B reached from 0.02 for boars to 0.03 for sows. No significant deviations of the observed genotype frequencies from the frequencies expected according to Hardy-Weinberg equilibrium were found in both breed. Opposite trends in allele frequencies development could be assumed for analysed sows and boars of both breeds. In Large White sows the frequency of allele B raised probably due prefering sows with BB genotype, whereas in Landrace population the frequency of allele B decreased from yet unknown reasons.

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 The −174G/C and −572G/C Interleukin 6 Promoter Gene Polymorphisms in Mexican Patients with Rheumatoid Arthritis: A Case-Control Study

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
S. A. Zavaleta-Muñiz ◽  
B. T. Martín-Márquez ◽  
L. Gonzalez-Lopez ◽  
N. G. Gonzalez-Montoya ◽  
M. L. Díaz-Toscano ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Severe Disease ◽  
Rflp Analysis ◽  
Mexican Mestizo ◽  
Lack Of Information ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Promoter Gene ◽  
Hardy Weinberg Equilibrium ◽  
Control Study

Objective. There is a lack of information about the genotype frequencies of IL-6 −174G/C and −572G/C polymorphisms in Mexicans with rheumatoid arthritis (RA). Therefore, the aim of this study was to evaluate the association of the IL-6 −174G/C and −572G/C polymorphisms in Mexican mestizo with RA.Methods. We included 137 patients with RA and 102 healthy controls. Patients were assessed for clinical characteristics. IL-6 −174G/C and −572G/C polymorphisms were genotyped using PCR-RFLP analysis. Allele and genotype frequencies and the Hardy-Weinberg equilibrium were computed. Odds ratios (ORs) were computed to identify the risk for RA associated with the presence of GG genotype in comparison with the GC or CC genotypes.Results. The genotype −174GG occurred at a higher frequency in cases and controls (77.4% versus 78.4%,P=0.845). We found similar results for the genotype −572GG (54% in patients versus 60.8% in controls,P=0.295).Conclusions. This is the first study to evaluate the association of −174G/C and −572G/C polymorphisms of the IL-6 gene with RA in Mexican mestizo patients. These two polymorphisms were not associated with RA in the studied sample. Additional studies are required to evaluate if these IL-6 polymorphisms have relevance to the development of more severe disease.

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.

scholarly journals Association of SNP T125A on KiSS1 gene with reproduction hormone levels in Kaligesing goat

2020 ◽  
Vol 45 (4) ◽  
pp. 253-260
Author(s):  
G. Hardyta ◽  
D.T. Widayati ◽  
D. Maharani
Keyword(s):  
Luteal Phase ◽  
Reproductive Traits ◽  
Genotype Distribution ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
17Β Estradiol ◽  
Hormonal Analysis ◽  
Hormonal Levels

The objective of this study was to assess the association of KiSS1 gene polymorphism with reproductive traits in Kaligesing goat. Genotypes of 48 ewes aged three years old were determined using PCR-RFLP and DNA sequencing. Sixteen out of 48 samples were monitored for the estrus cycle and determined their 17β-estradiol and progesterone levels using ELISA method. The results showed that KISS1 gene in the studied population was polymorphic with one single nucleotide polymorphism (SNP T125A). Then SNP was used to analyze genotype all individuals by PCR-RFLP method using MboII enzyme. Three genotypes (TT, TA and AA) were identified. Genotype frequencies of TA were 59.57%, AA were 40.43% while TT was not inculed in calculation for genetic diversity and assosication analysis since the number of genotype only one goat. The allele frequencies of T and A were 29.79% and 70.21%, respectively. The genotype distribution for the SNP was deviated from Hardy-Weinberg equilibrium (χ2=8.10; P<0.025). Hormonal analysis showed that the levels of 17β-estradiol in the follicular and luteal phase were 50.12±61.26 and 42.35±42.43 pg/ml, respectively, while the levels of progesterone hormone in the follicular and luteal phase were 7.87±10.59 and 12.39±15.93 ng/ml. No significant associations of the polymorphism were observed for any hormonal levels. However, it was first report about polymorfism in KiSS1 gene of local Indonesian goat especially Kaligesing goat. 

scholarly journals The association between the OPRM1 A118G polymorphism and addiction in a Turkish population

2019 ◽  
Vol 70 (2) ◽  
pp. 97-103 ◽  
Author(s):  
Hülya Türkan ◽  
Bensu Karahalil ◽  
Ela Kadıoğlu ◽  
Kenan Eren ◽  
Defne Tamar Gürol ◽  
...  
Keyword(s):  
Psychiatric Disorders ◽  
Drugs Of Abuse ◽  
Turkish Population ◽  
Control Group ◽  
Substance Addiction ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Μ Opioid Receptor ◽  
Polymerase Chain ◽  
A118g Polymorphism

AbstractSusceptibility to addiction has a complex genetic basis that includes genes associated with the action and metabolism of drugs of abuse. One important gene in that respect is OPRM1, which codes for the μ-opioid receptor and has an important role in mediating the rewarding effects of addiction substances. The aim of our study was to assess the prevalence of the OPRM1 A118G polymorphism (rs1799971) in Turkish population and to investigate its association with opioid and other substance addiction. In addition, we examined the association of rs1799971 in addicted patients who were also diagnosed with psychiatric disorders. The study included 103 patients addicted to opioids, cocaine, ecstasy, alcohol, lysergic acid diethylamide (LSD), cannabis, and sedative/hypnotic substances and 83 healthy volunteers with similar demographic features as controls. rs1799971 polymorphisms were identified with the polymerase chain reaction restriction fragment length polymorphism method (PCR-RFLP). The genotype frequencies were significantly higher in the addicted patients than controls (32.0 % vs 16.9 %, respectively; p=0.027). The prevalence of the G allele was 16.1 % in the addicted group and 8.4 % in the control group (p=0.031). Our study confirmed the association between the rs1799971(G) allele frequency and opioid and other substance addiction, but not with psychiatric disorders.

scholarly journals Analysis of Prolactin and Kappa-Casein Genes Polymorphism in Four Cattle Breeds in Turkey

2014 ◽  
Vol 14 (4) ◽  
pp. 799-806
Author(s):  
Bilal Akyüz ◽  
Mehmet Ulaş Çınar
Keyword(s):  
Restriction Enzymes ◽  
Chi Square ◽  
Brown Swiss ◽  
Weinberg Equilibrium ◽  
Cattle Breeds ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Chi Square Test ◽  
Hardy Weinberg Equilibrium ◽  
Casein Genes

Abstract The objective of this study was to identify allele and genotype frequencies of CSN3 and PRL genes in four cattle breeds in Turkey. For this purpose, a total of 390 cattle of East Anatolian Red (EAR), Zavot, Brown Swiss (BS) and Simmental (SIM) breeds were genotyped by PCR-RFLP method. A 443 bp fragment of CSN3 and a 156 bp fragment of PRL were amplified and digested with HindIII and RsaI restriction enzymes, respectively. For CSN3 and PRL genes, two types of alleles (A and B) and three types of genotypes (AA, BB, and AB) were observed. The highest frequencies for CSN3-A and CSN3-B alleles were estimated for the EAR breed (0.743) and for the BS breed (0.556), respectively. The highest frequency for PRL-A and PRL-B alleles was estimated for the SIM breed (0.801) and for the BS breed (0.315), respectively. The Chi-square test among the investigated cattle breeds showed that only the Zavot breed was in Hardy-Weinberg equilibrium (HWE) for both loci.

Prevalence of ABCB1 3435C>T polymorphism in the Cuban population

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Idania Rodeiro Guerra ◽  
Jose Herrea ◽  
Elizabeth Cuétara ◽  
Gabino Garrido ◽  
Elizabeth Reyes ◽  
...  
Keyword(s):  
Ethnic Origin ◽  
Allelic Frequency ◽  
Ethnic Background ◽  
Similar Distribution ◽  
Genotype Distribution ◽  
Chinese Populations ◽  
Genotype Frequencies ◽  
Clinical Consequences ◽  
Santiago De Cuba ◽  
Hardy Weinberg Equilibrium

Abstract Objectives ABCB1 gene polymorphisms can modify P-glycoprotein function with clinical consequences. Methods The 3435C>T polymorphism prevalence was analyzed using oligonucleotide probes and next-generation sequencing in 421 unrelated healthy individuals living in Cuba. Data were stratified by gender, ethnic background and residence. The genotype and allelic frequencies were determined. Results The genotype distribution met the Hardy–Weinberg equilibrium assumption. The allelic frequency was 63.5% for the 3435C variant. The genotype frequencies were 41.1% for CC, 44.9% for CT and 14.0% for TT. The allele and genotype distributions differed between individuals living in La Habana and Santiago de Cuba (p<0.05) when ethnic background was analyzed. The allelic distribution was similar among Admixed and Black subjects, and they differed from Caucasians. The CC genotype was equally distributed among Admixed and Black subjects, and they differed from Caucasians. The TT genotype frequency differed between Caucasians and Admixed. The CT genotype was distributed differently among the three groups. Similar distribution was obtained in Brazilians, whereas some similarities were observed in African, Spanish and Chinese populations, consistent with the mixed Cuban ethnic origin. Conclusions This is the first report on allele and genotype frequencies of the 3435C>T polymorphism in Cuba, which may support personalized medicine programs.

Genetic Variants of β-casein Gene in Indigenous and Exotic Dairy Cattle Breeds in Sri Lanka

2020 ◽  
Author(s):  
S. Wickramasinghe ◽  
R. K. Rupasinghe ◽  
N. Shanjayan ◽  
L. G.S. Lokugalappatti
Keyword(s):  
Sri Lanka ◽  
Bos Indicus ◽  
Bovine Milk ◽  
Cattle Population ◽  
Health Issues ◽  
Genotype Frequencies ◽  
Holstein Friesian ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
White Cattle

Background: Bovine milk contains two types of β-casein (CSN2); A1 and A2, in which A1 type has shown associations with certain health issues. This study was conducted to identify the abundance of CSN2 A1/A2 variants in European and indigenous dairy breeds in Sri Lanka. Methods: The study included 123 Ayrshire, 101 Holstein Friesian and 92 indigenous White cattle (Bos indicus) populations. Genotyping was performed by PCR-RFLP method using Dde1. Allele and genotype frequencies and population genetic indices were calculated. Result: Results showed A1A2 to be predominant in both Holstein Friesian (0.63) and Ayrshire (0.68) populations while A2A2 (0.82) was predominant in the White cattle population. A1 and A2 allele frequencies were 0.52 and 0.48 in Ayrshire; 0.39 and 0.61 in Holstein Friesian and 0.09 and 0.91 in White cattle populations. Ayrshire and Holstein Friesian populations showed significant deviation from the Hardy-Weinberg equilibrium (p£0.05). When compared to the imported breeds, the White cattle population showed inbreeding and less genetic diversity.

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