Polymerase Chain Reaction With Confronting Two-pair Primers Research Articles

GPX3 rs8177412 Polymorphism Modifies Risk of Upper Urothelial Tumors in Patients with Balkan Endemic Nephropathy.

Current data suggest that aristolochic acid (AA) exposure is a putative cause of Balkan endemic nephropathy (BEN), a chronic kidney disease strongly associated with upper tract urothelial carcinoma. The cellular metabolism of AA is associated with the production of reactive oxygen species, resulting in oxidative distress. Purpose: Therefore, the aim of this study was to analyze individual, combined and cumulative effect of antioxidant gene polymorphisms (Nrf2 rs6721961, KEAP1 rs1048290, GSTP1AB rs1695, GSTP1CD rs1138272, GPX3 rs8177412 and MDR1 rs1045642), as well as GSTP1ABCD haplotypes with the risk for BEN development and associated urothelial cell carcinoma in 209 BEN patients and 140 controls from endemic areas. Experimental method: Genotyping was performed using polymerase chain reaction (PCR) and PCR with confronting two-pair primers (PCR-CTTP) methods. Results: We found that female patients carrying both variant GPX3 rs8177412 and MDR1 rs1045642 genotypes in combination exhibited significant risk towards BEN (OR 1 = 3.34, 95% CI = 1.16-9.60, p = 0.025; OR 2 = 3.79, 95% CI = 1.27-11.24, p = 0.016). Moreover, significant association was determined between GPX3rs8174412 polymorphism and risk for urothelial carcinoma. Carriers of variant GPX3*TC + CC genotype were at eight-fold increased risk of BEN-associated urothelial tumors development. There was no individual or combined impact on BEN development and BEN-associated tumors among all examined polymorphisms. The haplotype consisting of variant alleles for both polymorphisms G and T was associated with 1.6-fold increased risk although statistically insignificant (OR = 1.64; 95% CI = 0.75-3.58; p = 0.21). Conclusions: Regarding GPX3 rs8177412 polymorphism, the gene variant that confers lower expression is associated with significant increase in upper urothelial carcinoma risk. Therefore, BEN patients carrying variant GPX3 genotype should be more frequently monitored for possible upper tract urothelial carcinoma development.

DEVELOPMENT OF A METHOD FOR GENOTYPING THE 𝘔𝘛𝘏𝘍𝘙 RS1801133 POLYMORPHISM IN VIETNAMESE, USING THE POLYMERASE CHAIN REACTION WITH CONFRONTING TWO-PAIR PRIMERS

Aims: To develop a method using polymerase chain reaction with confronting two-pair primers (PCR-CTPP) to genotype MTHFR rs1801133 polymorphism in Vietnamese people. Methods: DNA samples from 15 Vietnamese people were used to evaluate this assay. The Sanger sequencing method was used to identify the standard genotypes of the rs1801133 polymorphism. Some bioinformatic softwares were used to design four a multiplex PCR-CTPP. Experimental procedures were conducted to verify the primers and components of the PCR method. Results: The protocol of the PCR-CTPP was successful developed with optimal inner/outer primers ratio, the melting temperature of primers, the components and the thermal cycling to identify MTHFR rs1801133 polymorphism. Conclusion: The PCR-CTPP protocol should be applied to genotyping MTHFR rs1801133 polymorphism in large cohorts to investigate the association between the polymorphism and metabolic syndrome in Vietnamese population.

Evaluation of novel PCR-CTPP for simultaneous detection of Mycobacterium tuberculosis complex and identification of RpoB H526D point mutation

Background: Tuberculosis (TB) is a chronic and highly contagious disease caused of the acid-fast bacilli, Mycobacterium tuberculosis complex (MTC). Currently, it has been reported that rifampicin-mono resistant M. tuberculosis containing histidine to aspartate replacement at residue 526 (H526D) of the beta-subunit RNA polymerase enzyme (RpoB) increased the cell wall permeability and approximately eight times more susceptible to vancomycin. Objectives: To develop and evaluate the Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) for simultaneous detection of MTC and identification of RpoB H526D mutation. Materials and methods: PCR-CTPP was implemented for TB diagnosis. Reaction and profile were optimized and applied for detection in a total of 308 clinical samples. Sensitivity and specificity of PCR-CTPP was calculated in comparison to the acid-fast bacilli (AFB) staining and standard culture method. In addition, microscopic observation drug susceptibility (MODS) assay was modified for vancomycin susceptibility determination in 15 clinical isolates. Results: Limit of detection of PCR-CTPP was approximately 2×103 bacilli and no cross-detection to other mycobacteria. PCR-CTPP was evaluated in 308 clinical samples. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of PCR-CTPP versus standard culture method were 90.95%, 79.31%, 91.78% and 77.53%, respectively. In addition, comparison of developed PCR-CTPP versus AFB staining were also represented. MODS was performed in fifteen samples, two multidrug-resistant (MDR) strains containing RpoB H526D were susceptible against vancomycin. Conclusion: The established PCR-CTPP is highly sensitive, specific for investigation of MTC and identification of RpoB H526D mutation. This method could be useful for TB diagnosis together with precision medicine application in vancomycin susceptibility determination in TB patients in the future.

Mutant Allele of CD44 (rs8193C>T) and Pum2 Regulatory Element as A Prognosis Factor of Prostate Neoplasms: A Case-Control and In Silico Studies.

Expression of CD44 variant 6 (CD44v6) as a homing-associated cell adhesion molecule (HCAM), has proved to change most cancer cells. Aim of the study is the effect of mutant allele of CD44 (rs8193C>T) and Pum2 regulatory element as a prognosis factor of prostate neoplasms: a case-control and in silico studies in the Mazandaran province-Iran. In a case-control study, CD44-rs8193C>T genotyping of the 420 prostate neoplasms (210 benign prostatic hyperplasia (BPH) patients and 210 prostate cancer patients) and 150 healthy samples are performed by the touchdown polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method. The T mutant allele effects on the mRNA structure and cell pathways were also investigated in silico methods. Our results showed that the increase of T mutant allele frequency was significantly associated with BPH compared with prostate cancer. Furthermore, results showed TT genotype was significantly associated with BPH [odds ratio (OR)=0.572 and P=0.015], and also influenced the CD44v6 transcript secondary structure, miRNA binding, and regulatory element-binding site for Pum2 protein. Attachment of Pum2 to standard CD44 transcript may lead to transcript isoform-switching and shift-expression to a variety of CD44 isoforms, which can trigger some of the cell signaling pathways, such as Nanog-Stat, PKC-Nanog, and PKC-Twist. Based on this, the presence of the T mutant allele of CD44 (rs8193C>T) in the populations may create a regulatory element-binding site for Pum2. So, it could be known as a prognosis factor and prediction of prostate neoplasms. However, more comprehensive studies in different populations (with various ethnicities and large population sizes), and also CD44v6 gene expression studies in protein and transcript levels are required to confirm our data.

The Association of Polymorphisms in Genes Encoding Antioxidant Enzymes GPX1 (rs1050450), SOD2 (rs4880) and Transcriptional Factor Nrf2 (rs6721961) with the Risk and Development of Prostate Cancer.

Background and Objectives: Mounting evidence implicates oxidative damage in prostate carcinogenesis, contributing to modifications of macromolecules that drive cellular malignant transformation. Functional single-nucleotide polymorphisms (SNPs) of enzymes involved in redox homeostasis can disrupt pro-oxidant–antioxidant balance, leading to accumulation of reactive oxygen species and oxidative damage. We investigated the potential role of genetic polymorphisms of antioxidant enzymes glutathione peroxidase 1 (GPX1 rs1050450) and superoxide dismutase 2 (SOD2 rs4880) and regulatory antioxidant protein nuclear factor erythroid 2-related factor 2 (Nrf2 rs6721961) in the susceptibility to prostate cancer development (PC) and prognosis. Materials and Methods: We conducted a case–control study consisting of 235 patients with PC and 240 controls. Gene polymorphisms were determined by quantitative polymerase chain reaction (qPCR) and polymerase chain reaction with confronting two-pair primers (PCR-CTTP) methods. Multiple risk models were composed to inspect the separate and mutual effect of multiple genes and in combination with acquired contributory factors on the risk of PC development. Results: Independently, carriers of at least one SOD2*C allele had increased risk of PC development, which was significantly further amplified in advanced statistical models. When tested in combination, individuals with both SOD2*C allele and Nrf2*C/C genotype were also at increased risk of PC development, which was augmented when combined with acquired contributory factors. During the mean 75 ± 25 months of follow-up, investigated gene polymorphisms did not affect overall survival. Conclusion: Our results suggest that these gene polymorphisms could be used as risk biomarkers of PC evolution.

A Review of Optimization Strategies and the Advantages and Disadvantages of using Polymerase Chain Reaction with Confronting Two-Pair primers (PCR-CTPP) in Genomics Studies

A Review of Optimization Strategies and the Advantages and Disadvantages of using Polymerase Chain Reaction with Confronting Two-Pair primers (PCR-CTPP) in Genomics Studies

A simple genotyping method for CD247 3'-untranslated region polymorphism rs1052231 and characterization of a reference cell panel.

CD247 (or CD3‐ζ chain) is an essential adaptor and signal‐transducing molecule of the T‐cell antigen receptor (TCR) complex, and it also couples to NK‐cell activating receptors such as NKp46, NKp30 and CD16A (FcγRIII). Noncoding sequence polymorphisms and variations in CD247 expression, a tightly regulated process, have been related with an altered immune response in multiple health conditions. A single nucleotide polymorphism (T > A) at nucleotide 844 of the CD247 3′‐untranslated region, rs1052231, has been related with lower CD247 gene expression and it has been investigated as a potential biomarker of autoimmune disease. We present here a simple, accurate, reliable, time‐efficient, and cost‐effective method for CD247‐rs1052231 genotyping. Using this method, based on polymerase chain reaction with confronting two‐pair primers (PCR‐CTPP), we have also characterized the CD247‐rs1052231 genotypes in a panel of worldwide available cell lines, which should facilitate study of the role of this polymorphism in immunity and human health.

Single Nucleotide Polymorphisms (SNPs) of OGG1 (Ser326Cys) and APE1 (Asp148Glu; –141T/G) Genes and Breast Cancer Risk in Filipino Women

Base excision repair (BER) pathway involves repair of damaged DNA caused by spontaneous decay of DNA, reactive oxygen species, and ionizing radiation. Polymorphisms of genes involved in the pathway have been reported to be associated with cancer risk. In this study, the association of BER gene polymorphisms with breast cancer risk in Filipino women was assessed. The polymorphisms studied included X-ray repair cross-complementing group 1 (XRCC1, Arg399Gln), 8-oxoguanine DNA glycosylase (OGG1, Ser326Cys), and apurinic/apyrimidinic endonuclease 1 (APE1, Asp148Glu; –141T/G). A total of 186 participants (93 breast cancer cases and 93 breast cancer-free control) were recruited for the study. The genotyping of samples was performed using polymerase chain reaction with confronting two-pair primers (PCR-CTPP). The association of polymorphisms of BER genes with breast cancer risk and gene-environment interaction was determined using the unconditional logistic regression model. Distributions of OGG1 and APE1 genotypes were in Hardy-Weinberg equilibrium (HWE); however, XRCC1 genotype distribution deviated from HWE and was not further analyzed. The analysis showed that OGG1 Ser326Cys, APE1 Asp148Glu, and APE1 –141T/G had no significant association with breast cancer risk. Also, there is no significant interaction between the three BER gene variants and family history of cancer. Lastly, no significant increased risk was observed when the combined effects of risk alleles of the three BER gene variants were determined. In conclusion, the study suggests that OGG1 Ser326Cys, APE1 Asp148Glu, and APE1 –141T/G are not good indicators of breast cancer risk in Filipino women.

SIRT1 Gen Polimorfizmleri ve Parkinson Hastalığı Arasındaki İlişkinin Araştırılması

Aim: Parkinson’s disease is a disorder caused by insufficient dopamin production due to the loss of dopaminergic neurons concentrated in the substantia nigra of the brain. Oxidative stress and mitochondrial dysfunction play a central role in the pathogenesis. The Sirtuin1 (SIRT1) gene, shown to protect cells against oxidative stress, has been reported to be associated with predisposition to Parkinson’s disease. In this study, we aimed to investigate the relationship between Parkinson’s disease and the SIRT1 gene polymorphisms rs7895833 and rs2273773. Materials and Methods: The study included 40 patients with Parkinson’s disease (the patient group) and 50 healthy individuals (the control group). The polymerase chain reaction with confronting two-pair primers (PCR-CTPP) and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) methods were used for the rs7895833 and rs2273773 polymorphisms, respectively. Results: For the rs7895833 polymorphism, the genotype distribution for the patient and control groups respectively was as follows: AA (62.5%–53.1%), AG (27.5%–40.8%), GG (10.0%–6.1%). For the rs2273773 polymorphism, the genotype frequencies for the patient and control groups were as follows: TT (90.0%–98.0%), CT (10.0%–2.0%). No statistically significant difference was found between the patient and control groups in terms of rs2273773 and rs7895833 polymorphisms (p>0.05). Discussion and Conclusion: Our findings indicated that the SIRT1 gene polymorphisms investigated did not play a predisposing role in the development of Parkinson’s disease.

Polymorphisms in CPT1B and CPT2 have no significant effect on plasma carnitine levels in Japanese cancer patients.

ABSTRACTTreatment of cancer patients undergoing chemotherapy with L-carnitine (LC) supplementation is becoming increasingly popular in the clinic. The present study aimed to examine the possible effects of polymorphisms in CPT1B and CPT2 (CPT1B G320D, S427C, c.282-18 C>T, and p.E531K, and CPT2 V368I) on the plasma concentration of carnitine in humans. The subjects were the 218 participants of the Iga Cohort Study. Differences in plasma-free carnitine levels by genotype were examined. Genotyping was conducted by polymerase chain reaction with confronting two-pair primers (PCR-CTPP). The plasma carnitine levels were significantly higher in males (P<0.001; Student’s t-test), and there was no significant difference in plasma carnitine levels between the age groups (P=0.202; ANOVA). One-way ANOVA revealed the plasma levels of carnitine were neither significantly different by CPT1B G320D, S427C, c.282-18 C>T, or p.E531K, nor by CPT2 V368I genotypes (P=0.133, P=0.538, P=0.636, P=0.509, and P=0.398, respectively). When analysis of covariance (ANCOVA) adjusted for age and sex was applied, the plasma levels of carnitine were not statistically significantly different according to these genotypes (P=0.299, P=0.715, P=0.980, P=0.851, and P=0.674, respectively). The present study did not identify any statistically significant differences in plasma carnitine levels between subjects with different CPT1 and CPT2 genotypes, suggesting that there may be no need to tailor treatments to patients’ genotypes when determining the dose/amount of LC to be administered to cancer patients undergoing palliative care.

A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

Abstract The amylose content (AC) of rice is a key determinant of the grain cooking and eating quality. The Waxy (Wx) gene, which encodes granule-bound starch synthase I (GBSSI), is the major gene controlling AC in rice. The A - C substitution in exon 6 (Ex6A/C) alters the amino acid codon from serine to tyrosine and is associated with intermediate-AC rice (Wx-in). In this paper, we reported a perfect functional marker for the SNP Ex6A/C of Wx-in based on polymerase chain reaction with confronting two-pair primers (PCR-CTPP) in a single-tube PCR assay. Specificity and applicability of the PCR assay were verified in a Chinese mini core collection (MCC) of Oryza sativa L. and a breeding population. Were commend the use of the simple, inexpensive assay for routine genotyping for intermediate AC in the breeding population or discrimination of Wx-in genotypes in rice germplasm.

Association of Helicobacter pylori infection with Toll-like receptor-4 Thr399Ile polymorphism increased the risk of peptic ulcer development in North of Iran.

Toll-like receptor-4 (TLR4) polymorphisms may influence host immune response against Helicobacter pylori (H.pylori). This study aimed to investigate whether TLR4 polymorphisms are associated with H.pylori susceptibility and risk of peptic ulcer development or not. The TLR4+3725G/C polymorphism was studied using polymerase chain reaction with confronting two-pair primers (PCR-CTPP). In addition, TLR4 Asp299Gly and Thr399Ile polymorphisms were evaluated by PCR-restriction fragment length polymorphism (RFLP). There was no significant difference in TLR4+3725G/C and Asp299Gly genotype frequencies between non-peptic ulcer (NPUD) and peptic ulcer (PUD) individuals in the context of peptic ulcer development and susceptibility to infection with H.pylori. Nevertheless, a significant association with increased risk for PUD development was observed for polymorphism TLR4 Thr399Ile [odds ratio (OR)=4.2; 95% confidence interval (CI)=1.35-13.26; p=0.01]. Correspondingly, TLR4 Thr399Ile polymorphism was associated with H.pylori susceptibility (OR=0.27; 95% CI=0.08-0.88; p=0.04). In addition, TLR4 Thr399Ile polymorphism increased 4.2-fold, the risk of peptic ulcer development in individuals infected by H.pylori carrying CT+TT genotype. Our results showed that TLR4 Thr399Ile polymorphism along with H.pylori infection may play critical roles in peptic ulcer development in North of Iran.

An improved PCR-CTPP assay for the detection of ADH1B Arg48His polymorphism.

ADH1B Arg48His polymorphism is associatedwith the development of alcohol-related diseases. In this study, we aimed to explore an improved polymerase chain reaction with confronting two-pair primers (PCR-CTPP) assay for the detection of ADH1B Arg48His polymorphism. A mismatch was introduced at the 3' end of each of the two allele-specific to increase the specificity of the reaction. But beyond that, a new mismatch at-3 positions of outer primers was designed to decrease the efficiency of the aforementioned primers and depresses the amplification of an internal nonspecific DNA control. A total of 180 samples from healthy volunteers Han Chinese were tested to evaluate this new assay. The protocol of PCR-CTPP was successful for genotyping of ADH1B Arg48His. The results from the improved PCR-CTPP assay were confirmed by Sanger sequencing, and correct genotyping rates were 100%.The genotype frequencies were 49.44% (89 cases) for His/His, 46.67% (84 cases) for Arg/His, and 3.89% (seven cases) for Arg/Arg respectively. This improved PCR-CTPP assay is simple, rapid, cost-effective, and reliable, specific for the detection ofADH1B Arg48His polymorphism in most clinical diagnostic laboratories.

Clinical Impact of the AKT1 rs1130233 SNP in Japanese Gastrointestinal Cancer Patients with Palliative Care

Objective: Cancer patients often suffer from chronic inflammation, anorexia and the resultant decrease of nutrient intake, followed by weight loss and muscle wasting called “sarcopenia”. Such conditions are known as “cachexia”. In this study, we examined the associations between genetic polymorphisms of AKT1 rs1130233, ICAM1 rs281432, SELP rs6128 and TNSRSF1A rs4149570, which are reportedly associated with cachexia in Caucasians, together with LIF rs929271, in Japanese gastrointestinal cancer patients with palliative care. Methods: The study subjects were 59 patients (37 males and 22 females) with gastrointestinal cancers who visited the outpatient clinic at Iga General Hospital from December 2011 till August 2015. Genotypings for AKT1 rs1130233, ICAM1 rs281432, SELP rs6128, TNSRSF1A rs4149570 and LIF rs929271 were conducted with polymerase chain reaction with confronting two-pair primers (PCR-CTPP) or the Taqman SNP Genotyping assay. Associations of these SNPs with patients’ prognosis as well as weight loss defined as weight loss more than 5 percent during 6 months after the initiation of chemotherapy were evaluated. Results: A significant increase in the risk of 5% weight loss was observed in those with A/G genotype AKT1 rs1130233 polymorphism (AKT1 A/G vs. G/G, adjusted odds ratio [aOR]=7.11; 95%CI: 1.41-35.7), or in those with at least one A allele of AKT1 rs1130233 (AKT1 A/G+A/A vs. G/G, aOR=4.57; 95% CI: 1.14-18.3) when adjusted for age, sex and UICC clinical stage 4. There was no statistically significant correlation of the polymorphisms examined with patients’ survival. Conclusion: The present study revealed that AKT1 rs1130233 A allele may play a key role in the development of cancer cachexia. Given the involvement of AKT1 in the development of cancer as well as in apoptosis, it would be worth studying the roles of this molecule in human cancers further from clinical, epidemiological and biological viewpoints in the near future.

The Association between Prolonged Jaundice and UGT1A1 Gene Polymorphism (G71R) in Gilbert's Syndrome.

Jaundice is a common condition during the neonatal period. Prolonged jaundice occurs in a large number of breastfed infants. Considering the impact of genetic factors on the incidence of jaundice present study was conducted. The aim of this study was to determine the association between prolonged jaundice and G71R polymorphism in Gilbert's syndrome. This case-control study was conducted at Taleghani Children's Hospital of Gorgan, Iran. The study group consisted of 87 icteric patients (aged more than 2 weeks) with an indirect bilirubin level higher than 10mg/dL. The control group consisted of 81 newborns without jaundice. The two groups were matched in terms of age and gender. DNA extraction was performed by "phenol-chloroform" method. Polymerase Chain Reaction with Confronting Two-Pair Primers (PCR-CTPP) was applied to amplify G71R polymorphism. Overall, 84% and 64% of subjects in the study and control groups were male, respectively. The distribution of Gilbert genotype was not significantly different between the two groups (p=0.772). There was a correlation between prolonged jaundice in males and UGT1A1 G71R polymorphism (p =0.03). In the study group, 5(5.7%) subjects were homozygous (for A/A), 73 (83.9%) were heterozygous (for A/G), and 9(10.3%) were normal (for G/G). In the control group, 3(3.7%) participants were homozygous (A/A), 68(84%) were heterozygous (A/G) and 10 (12.3%) were normal (G/G). There was no association between prolonged jaundice and G71R polymorphism, even though a relationship was revealed between male gender and the mentioned polymorphism.

Association between a p73 gene polymorphism and genetic susceptibility to non-small cell lung cancer in the South of China.

This study aimed to identify any association between the p73 gene G4C14-to-A4T14 polymorphism and risk of non-small cell lung cancer (NSCLC) in the south of China. We genotyped the p73 gene polymorphism of peripheral blood DNA from 168 patients with NSCLC and 195 normal controls using HRM (high resolution melting) and PCR-CTPP (polymerase chain reaction with confronting two-pair primers). The results of genotyping by HRM and PCR-CTPP were consistent with direct sequencing, the p73 genotype distribution in 168 lung cancer patients being as follows: GC/GC 101 cases (60.1%), GC/ AT 59 cases (35.1%), AT/AT 8 cases (4.8%). The carriers of AT/AT genotype had a significantly reduced risk of NSCLC (OR=0.370; 95%CI: 0.170-0.806; p=0.010) as compared with non-carriers. However, we found no relations between p73 genotypes and histological type (p=0.798, x2=0.452), tumor stage (p=0.806, x2=0.806), or lymph node metastasis (p=0.578, x2=1.098). Our findings suggest that the p73 G4C14-to-A4T14 polymorphism may be a modifier of NSCLC susceptibility in the Chinese population.

PCR-CTPP design for enzyme-free SNP genotyping using memetic algorithm.

In recent years, many single nucleotide polymorphisms (SNPs) have been successfully genotyped by polymerase chain reaction with confronting two-pair primers (PCR-CTPP). However, computation experiments of feasible CTPP primers are still challenging. The melting temperatures between four primers must be within a very narrow range, and many primer constraints need to be conformed to. PCR-CTPP is a simple, time- and cost-effective SNP genotyping method applied in molecular biology and biomedical fields. In this study, an MA (memetic algorithm)-based method is proposed to enable the design of feasible CTPP primer sets. Overall, 288 SNPs which exclude the deletion/insertion polymorphisms (DIPs) and multi-nucleotide polymorphisms (MNPs) in the SLC6A4 gene were tested in silico. The results were compared with a GA (genetic algorithm)-based method and indicate that the proposed method provides more feasible CTPP primers than the GA-based method. The MA-based CTPP primer design method provides critical melting temperatures and all kinds of evaluation of the common primer constraints. It could conceivably assist biologists and other researchers in obtaining feasible CTTP primer sets. The MA-CTPP algorithm is implemented in JAVA and a user-friendly input interface is freely available at http://bio.kuas.edu.tw/ma-ctpp/.

DEVELOPMENT OF PCR-BASED SNP MARKER OF RICE Waxy GENE WITH CONFRONTING TWO-PAIR PRIMERS.

Rice amylose content (AC) is a key determinant for grain end-use quality attributes. The base substitution (G --> T) at +1 loci of the first intron (In1) of Waxy (Wx), a major gene controlling AC in rice, results in decreased AC. A new SNP typing method of Wx In1 based on polymerase chain reaction with confronting two-pair primers (PCR-CTPP) was reported here: first its practicability was confirmed by 23 varieties with known SN P and AC; and then the segregation ratio at target SN P loci were checked and it fitted well for 1 :2: 1 single gene segregation; at last SNP typing and AC assay with 150 mini core collections (MCC) in China showed that average AC of 53 G type varieties (22.5%) was significantly higher than that of 97 T type varieties (13.7%) (p < 0.01) and the target SNP loci explained 77.8% AC variation. So this method could be used to estimate AC of rice variety roughly or in marker-assisted-breeding, that is, using variety with known and desired AC as Wx allele donor parent and aided with crossbreed, backcross and marker-assisted selection (MAS) reported here rice breeders could improve AC of varieties with comprehensively excellent performance to meet special end-products.

ATP-binding cassette transporter A1 (ABCA1) R219K (G1051A, rs2230806) polymorphism and serum high-density lipoprotein cholesterol levels in a large Japanese population: cross-sectional data from the Daiko Study.

Among polymorphisms in ATP-binding cassette transporter A1 (ABCA1) gene, the available evidence demonstrates that the ABCA1 R219K polymorphism (G1051A, rs2230806) K allele is associated with a higher high-density lipoprotein cholesterol (HDL- C) level and may play a protective role against coronary artery disease (CAD) risk in Asians and Caucasians. The findings from many underpowered studies from Asian countries (n=71-597), however, still remain inconsistent. The objective of this study was to overcome the limitations of previous studies in Asia and provide solid epidemiologic evidence. Subjects were participants of a cohort study, who visited the Daiko Medical Center in Nagoya, Japan. The cohort study belongs to the Japan Multi-Institutional Collaborative Cohort Study (J-MICC Study). In the Daiko Study, 5,133 participants (1,458 men and 3,675 women) aged 35-69 years enrolled from 2008 through 2010 were eligible for the analyses. The ABCA1 polymorphism was genotyped by the polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method. Among all the subjects, the genotype frequencies were 23.9% (n=1,225) for RR, 49.3% (n=2,532) for RK, and 26.8% (n=1,376) for KK, which was in Hardy-Weinberg's equilibrium (P =0.36). Background characteristics did not significantly differ among the genotypes including alcohol and tobacco use. The mean ± SD of HDL-C concentration was higher in men and women with RK or KK genotype than those with RR, although the difference between these genotypes was not statistically significant in both sexes (P =0.31 in men and 0.26 in women by ANOVA). In the multiple linear regression analysis to estimate the independent effects of the R219K polymorphism on HDL-C level, however, the number of K allele was significantly correlated with an increased level of HDL-C (trend P=0.033). Those with the KK genotype showed a significantly higher HDL-C concentration compared with those with the RR genotype by a mean of 1.18 mg/dL. The R219K polymorphism of ABCA1 independently associated with serum level of HDL-C in a large Japanese population.

A PCR method for VKORC1 G-1639A and CYP2C9 A1075C genotyping useful to warfarin therapy among Japanese.

Warfarin is widely prescribed for patients with the risk of thromboembolism around the world. The inter-individual and inter-racial differences in appropriate dosage depend highly on age, body weight, and genetic factors. A lot of studies including genome-wide association studies revealed that vitamin K epoxide reductase complex, subunit 1 (VKORC1) G-1639A and Cytochrome P450 (CYP) 2C9 A1075C are the most strong genetic factors for determining warfarin effects in Asians and Africans. Since we developed a quick and inexpensive genotyping method, polymerase chain reaction with confronting two-pair primers (PCR-CTPP), the method was applied for these genotypes to examine the possibility to clinical use. Subjects were 436 examinees (117 males and 319 females, aged 32 to 85 years) who attended a health checkup program in Japan. The PCR-CTPP for VKORC1 G-1639A and CYP2C9 A1075C was conducted for the subjects, as well as the samples genotyped by DigiTag2 method. The allele frequencies of VKORC1 G-1639A were 0.085 for G and 0.915 for A, and those of CYP2C9 A1075C were 0.979 for A and 0.021 for C, being in Hardy-Weinberg equilibrium (p = 0.658 and p = 0.514, respectively). These frequencies were similar to those reported in the HapMap project. Genotyping for both SNPs by PCR-CTPP was replicated by DigiTag2 method. Our results indicated that the PCR-CTPP could be one of the alternative methods for genotyping VKORC1 G-1639A and CYP2C9 A1075C for Asians and Africans with similar allele frequencies to Japanese.