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.

The polymorphism at the microRNA-155 binding site in AGTR1 gene is not significantly associated with rheumatic heart disease in Saudi Arabia population

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
S. Justin Carlus ◽  
Fiona Hannah Carlus ◽  
Mazen Khalid Al-Harbi ◽  
Abdulhadi H Al-Mazroea ◽  
Khalid M Al- Harbi ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Heart Disease ◽  
Rheumatic Heart Disease ◽  
Clinical Features ◽  
Left Ventricular ◽  
Genotype Distribution ◽  
Allelic Discrimination ◽  
Children And Young Adults ◽  
And Control ◽  
Rheumatic Heart

Background: Rheumatic heart disease (RHD) remains a major cause of cardiovascular diseases and the most devastating effects are on children and young adults. RHD is caused due to the interaction between microbial, environmental, immunologic, and genetic factors. The renin-angiotensin aldosterone system (RAAS) has been strongly implicated as the susceptibility pathway in the pathogenesis of cardiovascular disease. Objective: The present study investigated the modulating effect of Angiotensin II type 1 receptor (AGTR1) 1166A>C polymorphism on the RHD and its clinical features in Saudi Arabia. Methods: AGTR1 1166A>C polymorphism was genotyped in 96 echocardiographically confirmed RHD patients and 142 ethnically matched controls by TaqMan allelic discrimination method. Results: Genotype distribution of the AGTR1 1166A>C polymorphism was not significantly different between RHD and control groups. Further, AGTR1 1166A>C genotypes are not associated with the clinical features of RHD. These data support that there was no evidence for an association between AGTR1 1166A>C polymorphism and RHD in Saudi Arabia. Conclusion: To our knowledge, this is the first study that has investigated the possible association between AGTR1 1166A>C polymorphism and susceptibility to RHD and its clinical features. Even though AGTR1 gene is 1166A>C (rs5186) was reported to be associated with hypertension, left ventricular hypertrophy and coronary heart disease. Present study did not find any association between AGTR1 1166A>C polymorphism and RHD in Saudi Arabia. Further studies are needed to confirm our findings.

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

scholarly journals MDR1 polymorphisms are not related to Xeliri and Xelox chemoresistance in colorectal cancer

2019 ◽  
Author(s):  
Ayat B. Al-Ghafari ◽  
Areej M. Alqahtani ◽  
Suzan N. Alturki ◽  
Huda Abdulaziz Al Doghaither ◽  
Hanaa M. Tashkandi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Drug Response ◽  
Fragment Length Polymorphism ◽  
Protective Role ◽  
Genotype Distribution ◽  
Chain Reaction ◽  
P Glycoprotein ◽  
Significant Difference ◽  
Pcr Rflp ◽  
Polymerase Chain

Abstract Background Multidrug resistance member 1 (MDR1) is located on chromosome 7 and encodes P-glycoprotein (Pgp), which is universally accepted as a drug resistance biomarker. MDR1 polymorphisms may change either the protein expression or function, suggesting its possible association with cancers, including colorectal cancer (CRC). Thus, this study aimed to determine the effects of MDR1 polymorphisms on the drug response of Saudi CRC patients.Methods DNA samples were obtained from 62 CRC patients and 100 healthy controls. The genotypes and allele frequencies of the MDR1 polymorphisms G2677T and T1236C were determined by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP).Results No significant difference was observed in the genotype distribution and allele frequency of T1236C between the CRC the patients and the controls. However, G2677T was found to play a highly significant protective role against the progression of CRC. Moreover, the results showed that none of the genotypes in SNPs T1236C and G2677T affected chemoresistance to Xeliri and Xelox.Conclusions T1236C in the MDR1 gene is not related to CRC risk, and G2677T protects against the development of CRC. Both MDR1 polymorphisms are not associated with the risk of chemoresistance.

scholarly journals Effect of β-lactoglobulin gene polymorphism, lactation stage and breed on milk traits in Chios and Karagouniko sheep breeds

2017 ◽  
Vol 17 (2) ◽  
pp. 371-384 ◽  
Author(s):  
Kostas A. Triantaphyllopoulos ◽  
Panagiota Koutsouli ◽  
Athanassios Kandris ◽  
Dimitris Papachristou ◽  
Kalliopi E. Markopoulou ◽  
...  
Keyword(s):  
Milk Yield ◽  
Milk Traits ◽  
Weinberg Equilibrium ◽  
Sheep Breeds ◽  
Lactation Stage ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Daily Milk Yield ◽  
Β Lactoglobulin ◽  
Daily Milk

Abstract The animal selection with favourable phenotypes of the past has been, currently, replaced by the genotype selection on quantitative traits, assisted by the expanding molecular techniques in the context of livestock improvement. In this study, the c.112T>C polymorphism in exon II of β-lactoglobulin (β-LG) gene was investigated in Karagouniko and Chios sheep breeds by using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP), and possible associations with milk traits were examined. In total, 125 blood DNA samples were isolated for PCR-RFLP analysis and the respective 217 milk samples′ composition profile was obtained. The goodness of fit test to Hardy-Weinberg equilibrium (HWE) for β-LG genotypes was estimated and associations found between β-LG genotypes and raw milk composition. Two alleles and three genotypes were observed (AA, AB and BB) in both breeds, and Chios breed significantly deviated (P≤0.05) from Hardy-Weinberg equilibrium (HWE). Conclusively, linear mixed model analysis on samples, from both breeds collectively, showed significant effects of β-LG genotype on lactose percentage and somatic cell count (SCC), lactation stage on daily milk yield and protein, while the breed effect was significant only on daily milk yield.

scholarly journals Response to ‘Hardy–Weinberg equilibrium and control subjects’

2006 ◽  
Vol 70 (7) ◽  
pp. 1375
Author(s):  
C.-C. Lin ◽  
C.S.-J. Fann ◽  
M.-Y. Chung
Keyword(s):  
Weinberg Equilibrium ◽  
Control Subjects ◽  
Hardy Weinberg Equilibrium ◽  
And Control

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 Genetic polymorphisms of Vascular Endothelial Growth Factor (VEGF) associated with endometriosis in Nigerian women

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Ochuwa Adiketu Babah ◽  
Oyesola Oyewole Ojewunmi ◽  
Akinniyi Adediran Osuntoki ◽  
Melissa A. Simon ◽  
Bosede Bukola Afolabi
Keyword(s):  
Enzyme Linked Immunosorbent Assay ◽  
Vascular Endothelial ◽  
Nucleotide Polymorphisms ◽  
Nigerian Women ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Elisa Technique ◽  
Genomic Dnas ◽  
And Control ◽  
Endothelial Growth Factor

Abstract Objective To determine if genetic polymorphism of VEGF is associated with the development of endometriosis in Nigerian women. Study design Case control study of 100 women (50 healthy controls and 50 with endometriosis). Serum VEGF concentration of participants were determined using enzyme-linked immunosorbent assay (ELISA) technique. Genomic DNAs were isolated from peripheral blood samples and quantified by nanodrop spectrophotometer one. Single nucleotide polymorphisms genotyping was carried out by polymerase chain reaction and restriction fragment length polymorphism (PCR–RFLP). Results Mean age of participants was 32.96 ± 6.91 years for control and 32.04 ± 7.56 years for cases. VEGF levels in case and control groups were not statistically different (82.68 pg/ml [69.11–121.11 pg/ml] vs. 82.81 pg/ml [72.90–113.82 pg/ml] respectively; p = 0.967). All four genotypes examined were in Hardy–Weinberg equilibrium. Minor allele frequency of − 460T > C, − 1154G > A, + 936C > T and + 2578C > A were 24%, 8%, 6% and 10% in the control and 19%, 9%, 5% and 14% in endometriosis patients. However, allele and genotype distributions of − 460T > C, − 1154G > A, + 936C > T and + 2578C > A VEGF polymorphisms in endometriosis patients and control were not significantly different (p > 0.05). Conclusion Our preliminary findings revealed no association between endometriosis and − 460T > C, − 1154G > A, + 936C > T and + 2578C > A of VEGF genes among Nigerian women.

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 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.

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.

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