scholarly journals Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2689
Author(s):  
Augusto Anguita-Ruiz ◽  
Concepción M. Aguilera ◽  
Ángel Gil
Keyword(s):  
Genetic Basis ◽  
Human Populations ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Genetic Mechanisms ◽  
Visualization Tools ◽  
Available Information ◽  
Static World ◽  
Interactive Resources

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

scholarly journals Genetic Variants in Smoking-Related Genes in Two Smoking Cessation Programs: A Cross-Sectional Study

2021 ◽  
Vol 18 (12) ◽  
pp. 6597
Author(s):  
Gloria Pérez-Rubio ◽  
Luis Alberto López-Flores ◽  
Ana Paula Cupertino ◽  
Francisco Cartujano-Barrera ◽  
Luz Myriam Reynales-Shigematsu ◽  
...  
Keyword(s):  
Smoking Cessation ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphisms ◽  
Sectional Study ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Quitting Smoking ◽  
Genes Encoding ◽  
Genomic Regions

Previous studies have identified variants in genes encoding proteins associated with the degree of addiction, smoking onset, and cessation. We aimed to describe thirty-one single nucleotide polymorphisms (SNPs) in seven candidate genomic regions spanning six genes associated with tobacco-smoking in a cross-sectional study from two different interventions for quitting smoking: (1) thirty-eight smokers were recruited via multimedia to participate in e-Decídete! program (e-Dec) and (2) ninety-four attended an institutional smoking cessation program on-site. SNPs genotyping was done by real-time PCR using TaqMan probes. The analysis of alleles and genotypes was carried out using the EpiInfo v7. on-site subjects had more years smoking and tobacco index than e-Dec smokers (p < 0.05, both); in CYP2A6 we found differences in the rs28399433 (p < 0.01), the e-Dec group had a higher frequency of TT genotype (0.78 vs. 0.35), and TG genotype frequency was higher in the on-site group (0.63 vs. 0.18), same as GG genotype (0.03 vs. 0.02). Moreover, three SNPs in NRXN1, two in CHRNA3, and two in CHRNA5 had differences in genotype frequencies (p < 0.01). Cigarettes per day were different (p < 0.05) in the metabolizer classification by CYP2A6 alleles. In conclusion, subjects attending a mobile smoking cessation intervention smoked fewer cigarettes per day, by fewer years, and by fewer cumulative pack-years. There were differences in the genotype frequencies of SNPs in genes related to nicotine metabolism and nicotine dependence. Slow metabolizers smoked more cigarettes per day than intermediate and normal metabolizers.

Single Nucleotide Polymorphisms of TRAF2 and TRAF5 Gene in Ankylosing Spondylitis: A Case-Control Study

2021 ◽  
Author(s):  
Shanshan Xu ◽  
Jiangping Kong ◽  
Li Huang ◽  
Huimin Xie ◽  
Feier Wang ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
Single Nucleotide Polymorphisms ◽  
Tumor Necrosis Factor Receptor ◽  
Nucleotide Polymorphisms ◽  
Permutation Testing ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Open Questions ◽  
Genotype Frequencies ◽  
Marginal Association

Abstract ObjectiveTo investigate the role of eight locus polymorphisms of tumor necrosis factor receptor associated factor 2 (TRAF2) and TRAF5 gene and their interaction in the susceptibility to ankylosing spondylitis (AS) in Chinese Han population.MethodsEight single nucleotide polymorphisms (SNPs) (rs3750511, rs10781522, rs17250673, rs59471504, rs6540679, rs12569232, rs4951523, rs7514863) of TRAF2 and TRAF5 gene were genotyped in 673 AS patients and 687 controls.ResultsThe SNPs of TRAF2 and TRAF5 does not indicate a correlation with the susceptibility of AS in Chinese Han population. Genotype frequencies of rs3750511were statistically significant in females between patients and controls. The genotype frequencies of rs12569232 and allele frequencies of rs3750511were statistically significant between groups of different diseases activity. One three-locus model, TRAF2 (rs10781522, rs17250673) and TRAF5 (rs12569232), had a maximum testing accuracy of 52.67% and a maximum cross-validation consistency (10/10) that was significant at the level of P=0.0001, after determined empirically by permutation testing. As to environmental variables, only marginal association was found between sleep quality and AS susceptibility.ConclusionTRAF2 rs3750511 polymorphism may be associated with the susceptibility and severity of AS. Besides, the interaction of TRAF2 and TRAF5 genes may be associated with AS susceptibility, but many open questions remain.

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

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.

scholarly journals LGALS3 +191A and +292C polymorphisms are associated with a reduction in serum gal-3 levels, but not with the clinical events of individuals with sickle cell anemia

2020 ◽  
Vol 9 (9) ◽  
pp. e442997314
Author(s):  
Kleyton Palmeira do Ó ◽  
Taciana Furtado de Mendonça-Belmont ◽  
Isabela Cristina Cordeiro Farias ◽  
Andreia Soares da Silva ◽  
Ana Karla da Silva Freire ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Sickle Cell ◽  
Sickle Cell Anemia ◽  
Serum Levels ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Clinical Events ◽  
Genotype Frequencies ◽  
Galectin 3 ◽  
Taqman Pcr

Objective: This study aimed to evaluate whether the single nucleotide polymorphisms (SNPs) +191 C>A (rs4644) and +292 A>C (rs4652) of the LGALS3 gene and the serum levels of galectin-3 (gal-3) are associated with clinical events in patients with sickle cell anemia (SCA). Methods: SNP +191 and +292 of the LGALS3 gene were detected by the TaqMan PCR system in real time. Gal-3 levels were measured in serum by ELISA. The study included 322 patients, mean age 36 (21-84). Results: AA and CA genotypes of the +191 region were related to lower levels of gal-3 when compared to CC genotype (p=0.0296). Lower level of gal-3 was also associated with the +191/+292 (AA/CC; CA/CC) diplotypes (p=0.0137) compared to the diplotypes (CC/AA; CC/CC; CC/AC; CA/AC). There was no association between serum levels of galectin-3 and genotype frequencies of the LGALS3 +191 and +292 polymorphisms with clinical events in SCA. Conclusion: The polymorphisms +191 and +292 of the LGALS3 are associated to decrease in serum levels of gal-3. However, no association of polymorphisms and levels of gal-3 with clinical events was observed in patients SCA.

scholarly journals E2F1 genetic variants and risk of cervical cancer in Indian women

2018 ◽  
Vol 33 (4) ◽  
pp. 389-394 ◽  
Author(s):  
Sanjay Singh ◽  
Manish Gupta ◽  
Rajeev Kumar Seam ◽  
Harish Changotra
Keyword(s):  
Cervical Cancer ◽  
Cancer Risk ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Indian Women ◽  
Altered Expression ◽  
Cervical Cancer Risk ◽  
Genotype Frequencies ◽  
Pcr Rflp

Introduction: Altered expression of many E2F family members have been reported in various human cancers. In this study, we investigated the role of non-synonymous single nucleotide polymorphisms (rs3213172 C/T, rs3213173 C/T, and rs3213176 G/A) of the gene E2F1 with cervical cancer. Methods: A total of 181 samples including 90 cervical cancer patients and 91 healthy controls were genotyped. The genotype frequencies of these polymorphisms in collected samples were determined by either PCR-RFLP or PCR-ARFLP methods. SHEsis software was used to analyze the haplotypes. Results: Statistically significant differences in the alleles and the genotypes frequencies were observed in rs3213172 (C/T) and rs3213173 (C/T) polymorphisms. The rs3213172 (C/T) polymorphism was a risk factor for cervical cancer in dominant model (odds ratio (OR) 1.96; 95% confidence interval (CI) 1.07, 3.60; P = 0.02) and heterozygous model (OR 1.90; 95% CI 1.01, 3.57; P = 0.04). The rs3213173 (C/T) polymorphism increased the risk of cervical cancer in the homozygous model (OR 2.71; 95% CI 1.11, 6.58; P = 0.02). The rs3213176 (G/A) polymorphism was not associated with cervical cancer risk in any of the genotypic models. In the haplotypes analysis, three haplotypes (CTG, TCG, and TTA) were associated with the cervical cancer risk. Conclusions: These findings revealed that rs3213172 (C/T) and rs3213173 (C/T) polymorphisms and haplotypes (CTG, TCG, and TTA) of the E2F1 gene might play role in the susceptibility of cervical cancer. This is the first report showing an association of these polymorphisms with the cervical cancer risk.

scholarly journals Analysis of Single Nucleotide Polymorphisms within ADAM12 and Risk of Knee Osteoarthritis in a Chinese Han Population

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Lin Wang ◽  
Lin Guo ◽  
Fengde Tian ◽  
Ruihu Hao ◽  
Tiejun Yang
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Population Based ◽  
Recessive Model ◽  
Chinese Han Population ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Han Population ◽  
Genotype Frequencies ◽  
Increased Risk

Objective. Osteoarthritis (OA) is a complex arthritic condition in which the genetic factor plays a major role. One of the candidate genes of is the ADAM12 gene, but no consistency has been reached till now. This study aims to investigate the potential role of four single nucleotide polymorphisms (SNPs) of the ADAM12 gene in susceptibility to knee OA and its progression in Chinese Han population.Methods. The rs1278279, rs3740199, rs1044122, and rs1871054 polymorphisms were genotyped and compared in a population based cohort consisting of 164 OA subjects and 200 age- and gender-matched controls.Results. The SNP rs1871054 was found with increased risk of OA susceptibility in comparing the genotype frequencies between the case and control groups no matter for which model of comparison (allele level, dominant model, recessive model, and extreme genotype model). Additionally, the SNP rs1871054 was found associated with increased OA severity according to the K/L grade.Conclusion. In summary, we have identified that the rs1871054 variant within the ADAM12 gene is a risk factor for increased osteoarthritis susceptibility and severity.

scholarly journals Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes

2020 ◽  
Author(s):  
Bruce A. Williamson-Benavides ◽  
Richard Sharpe ◽  
Grant Nelson ◽  
Eliane T. Bodah ◽  
Lyndon D. Porter ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fusarium Solani ◽  
Root Rot ◽  
Genetic Basis ◽  
Gene Pyramiding ◽  
Interval Mapping ◽  
Differentially Expressed ◽  
Nucleotide Polymorphisms ◽  
Resistance Qtls ◽  
Single Nucleotide

AbstractPisum sativum (pea) yields have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome V explained 14.76 % of the variance with a confidence interval of 10.36 cM. The other four QTLs located on chromosomes II, III, and V, explained 5.26–8.05 % of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

scholarly journals Effects of Single Nucleotide Polymorphisms 869 T/C in the Exon 1 Locus of Transforming Growth Factor-β1 Gene on Susceptibility and Airflow Restriction of Chronic Obstructive Pulmonary Disease

2021 ◽  
Author(s):  
Jie Liu ◽  
Wenjing Zhu
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Single Nucleotide Polymorphisms ◽  
Healthy Volunteers ◽  
Chronic Obstructive ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Obstructive Pulmonary Disease ◽  
Genotype Frequencies ◽  
Copd Patients ◽  
Tgf Β1

Abstract Background: Chronic obstructive pulmonary disease (COPD) is the most common chronic respiratory disease which is expected to become the third leading cause of death worldwide in 2030. Series of susceptibility genes and single nucleotide polymorphism (SNPs) play an important role in the occurrence and development of COPD.Methods: In our study, 98 COPD patients and 90 healthy volunteers were enrolled. The +869 SNP (SNP, Single Nucleotide Polymorphisms) of TGF-β1 was detected in 98 COPD patients and 90 healthy volunteers by PCR-DNA sequencing. The effects of different genotypes of +869 locus on the susceptibility of COPD, pulmonary function and airflow limitation of COPD patients were analyzed.Results: Allele C of +869 locus was associated with the susceptibility of COPD (OR:1.913, 95% CI: 1.251-2.926). The predicted value of FEV1% (FEV1, Forced Expiratory Volume in One Second) in patients with CC of +869 locus was significantly lower than that in patients with TT (P < 0.05). The genotype frequencies of CC, CT and TT were 6.5%, 58.7% and 34.8% in Mild-to-Moderate airflow restriction patients. In severe airflow restriction patients, the genotype frequencies were CC 23.1%, CT 57.7% and TT 19.2%. The distribution of CC genotype in severe airflow restriction COPD patients was significantly higher than that in Mild-to-Moderate airflow restriction COPD patients (P = 0.037). Moreover, the frequency of C allele was significantly higher in patients with severe airflow restriction than that patients with Mild-to-Moderate airflow restriction (P = 0.024).Conclusions: The SNP of +869 T/C in TGF-β1 is closely related to the susceptibility of COPD and the airflow restriction of COPD patients.

scholarly journals Genetic variants in the p53 pathway influence implantation and pregnancy maintenance in IVF treatments using donor oocytes

2021 ◽  
Author(s):  
Arturo R. Palomares ◽  
Adrián Alberto Castillo-Domínguez ◽  
Maximiliano Ruiz-Galdón ◽  
Kenny A. Rodriguez-Wallberg ◽  
Armando Reyes-Engel
Keyword(s):  
Pregnancy Rates ◽  
Gene Variants ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Vitro Fertilization ◽  
Genotype Frequencies ◽  
Nested Case Control ◽  
Donor Oocytes

Abstract Purpose Single-nucleotide polymorphisms (SNPs) in the p53 pathways have shown to play a role in endometrial receptivity and implantation in infertile women undergoing in vitro fertilization (IVF). The present study aimed to assess the influence of these gene variants over pregnancy success through a receptivity model in recipients of egg donation treatments, when factors such as age and quality of the oocytes are standardized. Methods A nested case–control study was performed on 234 female patients undergoing their first fresh IVF treatment as recipients of donor oocytes. Genotyping of TP53 Arg72Pro (rs1042522), LIF (rs929271), MDM4 (rs1563828), and USP7 (rs1529916) SNPs in the recipients allowed comparison of allele and genotype frequencies and their association with the IVF treatment outcome. Results Grouped by genotypes, patients showed differences in IVF outcomes after the embryo transfer. Arg72Pro (rs1042522) gene variant was associated to changes in implantation and clinical pregnancy rates. The polymorphisms USP7 (rs1529916) and MDM4 (rs1563828) were associated to differential ongoing pregnancy rates and variable miscarriage events, respectively. Conclusions This study highlights the association between gene polymorphisms related to P53 function and their influence over IVF reproductive outcomes. Arg72Pro variant may influence early events, as lower implantation rates were found in homozygous for Pro72 allele. By contrast, MDM4 (rs1563828) and USP7 (rs1529916) gene variants were associated with the later maintenance of pregnancy.

scholarly journals Single nucleotide polymorphism within gene in NFKBIA is associated with the risks of nasopharyngeal carcinoma in Chinese Han population.

2019 ◽  
Vol 5 (suppl) ◽  
pp. 67-67
Author(s):  
Hanyi Zhang ◽  
Shun Lu ◽  
Chang Sun ◽  
Siyao Deng ◽  
Jin Yi Lang
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Association Studies ◽  
Sample Size Calculation ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Significance Level ◽  
Genotype Frequencies ◽  
Increased Risk

67 Background: Nasopharyngeal Carcinoma(NPC) is an Epstein-Barr virus(EBV) associated malignancy with remarkable ethnic and geographical distribution. The EBV oncoprotein latent membrane protein 1 (LMP1) is the primary oncogene of EBV infection through the its signaling cascade and its connections to other pathways including NF-κB, TGF-β and JNK signaling, which plays an important role in the pathogenesis of NPC. In GWASs (Genome-wide association studies) associations these pathways were also identified. Single nucleotide polymorphisms (SNPs) in the regulatory regions may regulate the expression of genes in these pathways, or affect the function of the coded protein. Methods: Altogether 149 SNPs were covered by the 15 SNPs in the TRAF2, TRAF3, NFKBIA, MAP2K4, and CHUK genes were genotyped in a hospital-based case-control study of 350 NPC cases and 587 healthy controls from the Chinese Han. The observed genotype frequencies in the controls were tested for Hardy–Weinberg equilibrium (HWE) using the chi-square test. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for associations between genotypes and NPC risk and tumor characteristics were calculated by logistic regression, and they were adjusted for multiple testing using the SNP spectral deposition (SNPSpD) approach for multilocus analyses. Results: We found one NFKBIA SNP was associated with NPC risk after adjustment for multiple comparisons. Minor allele carriers of the NFKBIA had an increased risk of NPC (P 0.05). The analyses were adjusted for age and gender. For a polymorphism with a variant allele frequency between 10 %and 50%, the study had greater than 90% power to detect an OR of 1.50 at a significance level of 0.05 (PS—software for power and sample size calculation, http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/PowerSampleSize). The other genotyped SNPs that we found were not associated with NPC risk. Conclusions: Our data suggests that genetic variation especially in the NFKBIA maybe a useful biomarker for NPC screening and further studies are warranted.

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