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

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.

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

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.45.4.253-260 ◽

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.

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

Current Drug Metabolism ◽

10.2174/1389200220666190913121052 ◽

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.

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Evaluation of PECAM-1 Gene Polymorphism in Patients with Periodontal Disease and Healthy Individuals

ISRN Dentistry ◽

10.5402/2012/751920 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5

Author(s):

Mahdi Kdkhodazadeh ◽

Mehrdad Hajilooi ◽

Behzad Houshmand ◽

Sara Khazaei ◽

Leila Gholami ◽

...

Keyword(s):

Chronic Periodontitis ◽

Aggressive Periodontitis ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Healthy Individuals ◽

Single Nucleotide ◽

Genotypic Distribution ◽

Genotype Frequencies ◽

Significant Difference ◽

Polymerase Chain

Objective. Our aim in this paper was to investigate the possible genetic association between three Ser563Asn, Leu125Val and Arg670Gly polymorphisms of the PECAM-1 gene and periodontitis. Methods. Genomic DNA was isolated from whole blood of 105 periodontal patient (52 with chronic periodontitis and 53 with aggressive periodontitis) and 101 healthy individuals. Samples were genotyped and analyzed for the three single-nucleotide polymorphisms (SNPs) of PECAM-1 using polymerase chain reaction with sequence-specific primers (PCR-SSPs). Results. A statistically significant difference was found between the genotypic distribution of the Ser563Asn polymorphism in patients with periodontitis compared to controls (P=0.02). But there were no statistically significant difference between the allele frequencies in the different groups (P=0.05). The other two polymorphisms did not show a statistically significant difference in their allele and genotype frequencies between the groups. There was no statistically significant difference found for any of the polymorphisms allele and genotype distribution in aggressive and chronic periodontitis either. Conclusions. No significant association was found between the polymorphism tested and the subgroups of periodontitis, further research is still necessary to determine whether this polymorphism can be used as a genetic marker of periodontitis.

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Estimation of genotype distributions and posterior genotype probabilities for beta-mannosidosis in Salers cattle.

Genetics ◽

10.1093/genetics/135.3.855 ◽

1993 ◽

Vol 135 (3) ◽

pp. 855-868

Author(s):

J F Taylor ◽

B Abbitt ◽

J P Walter ◽

S K Davis ◽

J T Jaques ◽

...

Keyword(s):

Enzyme Activity ◽

Medical Diagnostics ◽

Relative Fitness ◽

Model Parameters ◽

Genotype Distribution ◽

Lysosomal Storage ◽

Genotypic Distribution ◽

Genotype Assignment ◽

Genotype Frequencies ◽

Systematic Effects

Abstract beta-Mannosidosis is a lethal lysosomal storage disease inherited as an autosomal recessive in man, cattle and goats. Laboratory assay data of plasma beta-mannosidase activity represent a mixture of homozygous normal and carrier genotype distributions in a proportion determined by genotype frequency. A maximum likelihood approach employing data transformations for each genotype distribution and assuming a diallelic model of inheritance is described. Estimates of the transformation and genotype distribution parameters, gene frequency, genotype fitness and carrier probability were obtained simultaneously from a sample of 2,812 observations on U.S. purebred Salers cattle with enzyme activity, age, gender, month of pregnancy, month of testing, and parents identified. Transformations to normality were not required, estimated gene and carrier genotype frequencies of 0.074 and 0.148 were high, and the estimated relative fitness of heterozygotes was 1.36. The apparent overdominance in fitness may be due to a nonrandom sampling of progeny genotypes within families. The mean of plasma enzyme activity was higher for males than females, higher in winter months, lower in summer months and decreased with increased age. Estimates of carrier probabilities indicate that the test is most effective when animals are sampled as calves, although effectiveness of the plasma assay was less for males than females. Test effectiveness was enhanced through averaging repeated assays of enzyme activity on each animal. Our approach contributes to medical diagnostics in several ways. Rather than assume underlying normality for the distributions comprising the mixture, we estimate transformations to normality for each genotype distribution simultaneously with all other model parameters. This process also excludes potential biases due to data preadjustment for systematic effects. We also provide a method for partitioning phenotypic variation within each genotypic distribution which allows an assessment of the value of repeat measurements of the predictive variable for genotype assignment.

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Distribution Of Phenotypic And Genotypic Abo And Rhesus Blood Groups Among Bangladeshi Population

Ibrahim Medical College Journal ◽

10.3329/imcj.v5i2.10101 ◽

1970 ◽

Vol 5 (2) ◽

pp. 59-62

Author(s):

Tashmim Farhana Dipta ◽

Md Roushan Iqbal ◽

Ahmed Zahid Hossain ◽

Md Tahminur Rahman ◽

Subhagata Chowdhury

Keyword(s):

Blood Group ◽

Blood Donors ◽

Allelic Frequency ◽

Blood Groups ◽

Weinberg Equilibrium ◽

Changing Trend ◽

Hardy Weinberg Equilibrium ◽

Bangladeshi Population ◽

Group B ◽

Positive Groups

The present study is a retrospective analysis of allelic frequency of ABO and Rhesus (D) blood groups of donors attending the Deaprtment of Transfusion Medicine of Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders (BIRDEM), Dhaka. BIRDEM IS a 625 bed hospital, where patients and blood donors come from all parts of Bangladesh. A total of 1, 28,506 blood donors of both genders were included in the study over fourteen years from June 1995 to June 2009 for analysis. Blood group was determined by performing the both tube and slide method blood grouping method. The distribution of blood groups in our population was B>O>A>AB in Rh positive groups donors and O>B>A>AB among Rh negative donors. Blood group B was more common among the males (37.42%) while O was predominant among female donors (33.83 %). On the other hand, blood group O negative was predominant in both genders (36.88%). In this study, Hardy- Weinberg equilibrium law was used to calculate the allelic frequency for ABO/ Rh system. Homozygous allelic frequency for Rh negative population was only 0.0007. Although phenotypically B group was dominant and AB was rare in our population, but according to Hardy- Weinberg equilibrium law the estimated allelic frequency of A (0.3694) and O (0.3040) showed higher frequency than B type (0.2300) in Bangladeshi population in both homozygous and heterozygous state. So, with increasing population of Bangladesh, this changing trend in estimated blood group in ABO system may play an important role in our genetic pattern. DOI: http://dx.doi.org/10.3329/imcj.v5i2.10101 IMCJ 2011; 5(2): 59-62

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TLR4 T399I Polymorphism and Endometriosis in a Cohort of Italian Women

Diagnostics ◽

10.3390/diagnostics10050255 ◽

2020 ◽

Vol 10 (5) ◽

pp. 255 ◽

Cited By ~ 2

Author(s):

Enrica Marchionni ◽

Maria Grazia Porpora ◽

Francesca Megiorni ◽

Ilaria Piacenti ◽

Agnese Giovannetti ◽

...

Keyword(s):

Molecular Mechanisms ◽

Categorical Variables ◽

P Value ◽

Genotype Distribution ◽

Exact Test ◽

Fisher's Exact Test ◽

Genotype Frequencies ◽

Significant Difference ◽

Fisher’S Exact Test ◽

Italian Women

Background: Endometriosis is a widespread multifactorial disease in which environmental, genetic, and epigenetic factors contribute to the phenotype. Single Nucleotide Polymorphisms (SNPs) in genes implicated in pivotal molecular mechanisms have been investigated as susceptible risk factors in distinct populations. Among these, Toll-like receptor 4 (TLR4) represents a good candidate due to its role in the immune/inflammatory response and endometriosis pathogenesis. Methods: The TRL4 gene T399I SNP (C/T transition, rs4986791) was investigated in 236 Italian endometriosis patients and 150 controls by using the PCR-RFLP method. One-tailed Fisher’s exact test was used to compare differences between categorical variables. T399I genotype distribution was evaluated for Hardy–Weinberg equilibrium in both groups using the Chi-squared test for given probabilities. Results: Fisher’s exact test comparing C and T allele frequencies showed a difference in the frequency of T alleles between patients and controls (OR = 1.96, 95% confidence interval 0.91–4.23; p-value = 0.0552). Genotype frequencies did not show any significant difference between patients and controls. The homozygous TT genotype was observed in 2% of endometriosis women and not in controls. Conclusions: Our results show that the TLR4 rs4986791 T variant may be considered a genetic risk factor for endometriosis in Italian women. More extensive studies in other populations are needed to confirm this result.

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

The American Biology Teacher ◽

10.1525/abt.2017.79.4.309 ◽

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.

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Allele frequency in loci which control coat colours in Hucul horse population

Czech Journal of Animal Science ◽

10.17221/5893-cjas ◽

2012 ◽

Vol 57 (No. 4) ◽

pp. 178-186 ◽

Cited By ~ 4

Author(s):

A. Stachurska ◽

A. Brodacki ◽

J. Grabowska

Keyword(s):

Genetic Structure ◽

Allele Frequency ◽

Global Strategy ◽

Recessive Allele ◽

Genotype Distribution ◽

Horse Population ◽

Wahlund Effect ◽

Animal Genetic Resources ◽

Genotype Frequencies ◽

Its Gene

The objective of the study was to determine the frequency of alleles which produce coat colours in Hucul horse population in Poland. The breed is included in the Global Strategy for Management of Farm Animal Genetic Resources, hence its gene pool should remain in unaltered state. Huculs are bay, black, blue dun, yellow dun, tobiano, and chestnut. Grey and chestnut Huculs have always been undesirable. The material consisted of all 1022 matings which resulted in subpopulations recorded in Studbook volumes. The recessive allele frequency was estimated as the square root of recessive genotype frequencies in ASIP (A), MC1R (E), DUN (D), KIT (To region), and STX17 (G) loci. The frequency in A and E loci in total parental generation was also estimated in test matings. Genotype distribution in the population was anticipated according to gamete frequency in sires and dams. Small Wahlund effect, F<sub>ST</sub>and χ<sup>2</sup> values for allele distributions show that division into subpopulations did not influence the population genetic structure significantly. Mean recessive allele frequency in A, E, D, To, and G loci amounted to 0.521, 0.115, 0.878, 0.929, and 0.997, respectively, and in A and E loci it was similar to that assessed in test matings. More bay horses and fewer D diluted horses appeared in offspring than expected. A, e, d, and To allele frequency showed a rising tendency. The genetic structure in Hucul population is not constant and does not comply strictly with the preservation aim. Bay, non-diluted, and tobiano horses are preferred. The linkage between MC1R and KIT loci can make the selection against e allele difficult. Breeders’ preferences may lead to undesired changes in the allele frequency. To avoid such risk, it is recommended to select horses strictly complying with the rules included in the breeding programme and mate the horses randomly from this aspect.  

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ADIPOQ single nucleotide polymorphisms and breast cancer in northeastern Mexican women

BMC Medical Genetics ◽

10.1186/s12881-020-01125-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Ricardo M. Cerda-Flores ◽

Karen Paola Camarillo-Cárdenas ◽

Gabriela Gutiérrez-Orozco ◽

Mónica Patricia Villarreal-Vela ◽

Raquel Garza-Guajardo ◽

...

Keyword(s):

Breast Cancer ◽

Single Nucleotide Polymorphisms ◽

Mexican Women ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Allelic Discrimination Assay ◽

Allelic Discrimination ◽

Single Nucleotide ◽

Significant Difference ◽

Hardy Weinberg Equilibrium

Abstract Background Adiponectin gene (ADIPOQ) polymorphisms have been shown to affect adiponectin serum concentration and some have been associated with breast cancer (BC) risk. The aims of this study were to describe the frequency of single nucleotide polymorphisms (SNPs) of ADIPOQ in Mexican women with BC and to determine if they show an association with it. Methods DNA samples from 397 patients and 355 controls were tested for the ADIPOQ gene SNPs: rs2241766 (GT) and rs1501299 (GT) by TaqMan allelic discrimination assay. Hardy–Weinberg equilibrium (HWE) was tested. Multiple SNP inheritance models adjusted by age and body mass index (BMI) were examined for the SNP rs1501299. Results We found that in the frequency analysis of rs1501299 without adjusting the BMI and age, the genotype distribution had a statistically significant difference (P = 0.003). The T allele was associated with a BC risk (OR, 1.99; 95% CI 1.13–3.51, TT vs. GG; OR, 1.53; 95% CI 1.12–2.09, GT vs. GG). The SNP rs2241766 was in HW disequilibrium in controls. In conclusion, the rs1501299 polymorphism is associated with a BC risk. Conclusions Identification of the genotype of these polymorphisms in patients with BC can contribute to integrate the risk profile in both patients and their relatives as part of a comprehensive approach and increasingly more personalized medicine.

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Prevalence of Some Genetic Risk Factors for Nicotine Dependence in Ukraine

Genetics Research International ◽

10.1155/2019/2483270 ◽

2019 ◽

Vol 2019 ◽

pp. 1-8

Author(s):

Vitalina Bashynska ◽

Alexander Koliada ◽

Kateryna Murlanova ◽

Oksana Zahorodnia ◽

Yuliia Borysovych ◽

...

Keyword(s):

Risk Factors ◽

Risk Factor ◽

Nicotine Dependence ◽

Genetic Risk ◽

Strong Risk Factor ◽

Genotype Frequencies ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Variants ◽

Larger Sample ◽

European Populations

Tobacco smoking is known to be a strong risk factor for developing many diseases. The development and severity of smoking dependence results from interaction of environmental and lifestyle factors, psycho-emotional predispositions, and also from genetic susceptibility. In present study, we investigated polymorphic variants in genes contributed to nicotine dependence, as well as to increased impulsivity, known to be an important risk factor for substance use disorders, in Ukraine population. The genotype frequencies at CYP2A6, DNMT3B, DRD2, HTR2A, COMT, BDNF, GABRA2, CHRNA5, and DAT1 polymorphisms were determined in 171 Ukraine residents, and these data were compared with data for several other European populations and main ethnic groups. It has been found that genotype frequencies for all studied loci are in Hardy-Weinberg equilibrium in the Ukrainian population and correspond to the respective frequencies in European populations. These findings suggest a similar impact of these loci on nicotine dependence in Ukraine. Further studies with larger sample sizes are, however, needed to draw firm conclusions about the effect size of these polymorphisms.

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