Novel biosensor-based microarray assay for detecting rs8099917 and rs12979860 genotypes

AIM: To evaluate a novel biosensor-based microarray (BBM) assay for detecting rs12979860 and rs8099917 genotypes.METHODS: Four probes specific for rs8099917C/T or rs12979860G/T detection and three sets of quality control probes were designed, constructed and arrayed on an optical biosensor to develop a microarray assay. Two sets of primers were used in a one tube polymerase chain reaction (PCR) system to amplify two target fragments simultaneously. The biosensor microarray contained probes that had been sequenced to confirm that they included the rs8099917C/T or rs12979860G/T alleles of interest and could serve as the specific assay standards. In addition to rehybridization of four probes of known sequence, a total of 40 clinical samples collected from hepatitis C seropositive patients were also tested. The target fragments of all 40 samples were amplified in a 50 μL PCR system. Ten μL of each amplicon was tested by BBM assay, and another 40 μL was used for sequencing. The agreement of the results obtained by the two methods was tested statistically using the kappa coefficient. The sensitivity of the BBM assay was evaluated using serial dilutions of ten clinical blood samples containing 10³-10⁴ white cells/μL.RESULTS: As shown by polyacrylamide gel electrophoresis, two target segments of the interleukin 28B-associated polymorphisms (SNPs) were successfully amplified in the one-tube PCR system. The lengths of the two amplified fragments were consistent with the known length of the target sequences, 137 and 159 bps. After hybridization of the PCR amplicons with the probes located on the BBM array, the signals of each allele of both the rs8099917 SNPs and rs12979860 SNPs were observed simultaneously and were clearly visible by the unaided eye. The signals were distinct from each other, could be interpreted visually, and accurately recorded using an ordinary digital camera. To evaluate the specificity of the assay, both the plasmids and clinical samples were applied to the microarray. First, 30 PCR amplicons of the various SNP alleles were hybridized on the BBM microarray. Full agreement between plasmids and the BBM assay was observed, with 30/30 correct matches (100%). The kappa value for the BBM assay with plasmids was 1.00 (P < 0.05). For the 40 clinical blood samples, the BBM assay hybridization and direct sequencing results were compared for each amplicon. For patient blood samples, agreement was 28/28 for rs8099917T/T, 9/11 for rs8099917T/G, 1/1 for rs8099917G/G, 24/24 for rs12979860C/C, 11/14 for rs12979860C/T, and 2/2 for rs12979860T/T. Only five clinical samples of amplicon assay and direct sequencing results were discordant and heterozygotes: 2/11 rs8099917T/G and 3/14 rs12979860C/T. The agreement of outcomes between BBM assay and direct sequencing for the detection of rs8099917 and rs12979860 was 95% and 92.5%, respectively; and the corresponding kappa values were 0.88 and 0.85 (A kappa value > 0.75 was defined as substantial agreement). The BBM assay and sequencing had similar specificities for detection and identification of the two SNPs and their alleles. The sensitivity evaluation showed that the BBM assay could detect and identify SNP sequences present in blood samples containing as few as 10² white blood cells/μL.CONCLUSION: This biosensor microarray assay was highly specific, sensitive, rapid and easy to perform. It is compatible with clinical practice for detection of rs8099917 and rs12979860.     

Association of IL-13 rs20541 and rs1295686 variants with symptomatic asthma in a Saudi Arabian population

Objective: Interleukin 13 (IL-13) plays a critical pro-inflammatory role in asthma. Several single nucleotide polymorphisms (SNPs) are associated with asthma susceptibility in specific populations; however, further replicative studies in other ethnic groups are mandatory. Methods: The association between IL-13 SNPs rs762534, rs20541, rs1295686, and rs1800925 (risk alleles A, A, T, and A, respectively) and asthma predisposition in a Saudi Arabian cohort was examined via a case–control cross-sectional study. Results: The frequencies of alleles between asthmatics and control populations were significantly different for rs20541 and rs1295686 SNPs (p < 0.001), whereas the frequencies of genotypes between asthmatics and controls were significantly different only for rs20541. The association of the risk (minor) alleles with asthma was examined using the dominant genetic model. Individuals with at least one copy of the risk alleles A (for rs20541) and T (for rs1295686) had significantly greater odds of being asthmatic (OR = 2.13, 95% CI = 1.39–3.26, p < 0.0001; OR = 1.69, 95% CI = 1.12–2.54, p = 0.008) relative to their most common homozygous genotypes. On the other hand, the minor A alleles for rs762534 and rs1800925 were not significantly associated with asthma risk. Regarding haplotype association analysis, individuals with at least one copy of the minor “risk” allele for both rs20541 and rs1295686 (CATG and CATA, respectively) had greater odds of being asthmatic relative to CGCG haplotype; however, this trend was not statistically significant (p > 0.3). Conclusions: IL-13 minor T and A alleles for rs1295686 and rs20541, respectively, were associated with significantly higher risk of asthma in the Saudi Arabian population.     

Association between APE1 rs1760944 and rs1130409 polymorphism with prostate cancer risk: A systematic review and meta-analysis

Background:Recently, some studies have suggested that the association of apurinic/apyrimidinic endonuclease 1 (APE1) gene polymorphism with prostate cancer (PCa) risk, but there are still some controversies. Hence, we elaborated the relationship between APE1 rs1760944 and rs1130409 gene and PCa risk through systematic literature review and meta-analysis.Methods:As of March 2020, EMBASE, PubMed, the Cochrane Library, Science Direct/Elsevier, MEDLINE and CNKI were used for systematic literature retrieval to investigate the correlation between APE1 rs1760944 and rs1130409 gene polymorphism with PCa risk. Meta-analysis was performed using Review Manager and Stata software.Results:Seven studies were distinguished, consists of 1769 cases of PCa patients and 2237 normal controls. Our results illustrated that there are significant correlation between the APE1 rs1760944 gene polymorphism and PCa in all genetic models (P < .05). The combined odds ratios and 95% confidence intervals were as follows: Additive model (ORs 0.62, 95%, CI [0.39, 0.97]); Codominant model (ORs 0.74, 95% CI [0.58, 0.95]); Dominant model (ORs 0.75, 95%, CI [0.59, 0.95]); Recessive model (ORs 0.63, 95% CI [0.41, 0.96]); Allele model (ORs 0.78, 95% CI [0.65, 0.94]). There also have significant associations between APE1 rs1130409 polymorphisms and PCa in all genetic models (P < .05). The combined odds ratios and 95% confidence intervals were as follows: Additive model (ORs 1.37, 95%, CI [1.01, 1.85]); Codominant model (ORs 1.21, 95% CI [1.01, 1.44]); Dominant model (ORs 1.33, 95%, CI [1.02, 1.73]); Recessive model (ORs 1.74, 95% CI [1.06, 2.85]); Allele model (ORs 1.14, 95% CI [1.00, 1.29]).Conclusion:This study suggests that APE1 rs1760944 polymorphisms might be a protective factor of PCa, and APE1 rs1130409 is suggested to be a risk factor of PCa. APE1 rs1760944 and rs1130409 polymorphisms may be used in the risk assessment of PCa.     

The ALDH2 gene rs671 polymorphism is not associated with essential hypertension

Essential hypertension (EH) is a worldwide problem. Acetaldehyde dehydrogenase 2 (ALDH2) gene has been suggested to be correlated with EH. However, the results are inconsistent. This study aimed to investigate the associations of ALDH2 rs671 polymorphism with EH in a Chinese Han population in Shanghai. Genotype of ALDH2 rs671 was analyzed in 1923 EH patients and 1115 control subjects. We found no association between ALDH2 rs671 and EH risk or EH-related quantitative blood chemistry values. Furthermore, a meta-analysis was performed and the summary results from 11220 patients and 8339 control subjects were consistent with our findings. These results indicated that rs671 of ALDH2 may not associate with the risk of EH.     

Association of XPG rs2094258 polymorphism with gastric cancer prognosis

BACKGROUND The xeroderma pigmentosum group G(XPG)gene at chromosome 13q33 consists of 15 exons,which may be related to the occurrence and development of gastric cancer(GC).AIM To examine the association of several common single nucleotide polymorphisms(SNPs)of the XPG gene with GC risk and survival.METHODS Five SNPs of XPG(rs2094258,rs751402,rs873601,rs2296147,and rs1047768)were genotyped by PCR restriction fragment length polymorphism in 956 histologically confirmed GC cases and 1012 controls in North China.GC patients were followed for survival status and,if deceased,cause of death.Logistic regression and Cox regression were used for analysing associations of XPG SNPs with risk of GC and prognosis,respectively.For rs2094258,heterozygous model(CT vs CC),homozygous model(TT vs CC),recessive model(TT vs CT+CC),and dominant model(TT+CT vs CC)were analyzed.RESULTS None of the examined loci were statistically associated with GC risk,although rs2296147 was marginally associated with GC risk(P=0.050).GC patients with the rs2094258 CT+CC genotype showed worse survival than those with the TT genotype(log-rank test,P=0.028),and patients with the CC genotype had a tendency of unfavourable prognosis compared with those with the TT+CT genotype(log-rank test,P=0.039).The increase in C alleles of rs2094258[hazard ratio(HR)=1.19,95%confidence interval(CI):1.02-1.45,P=0.037]were associated with the long-term survival of GC cases.Other risk factors for survival included tumor differentiation(HR=4.51,95%CI:1.99-8.23,P<0.001),lymphovascular invasion(HR=1.97,95%CI:1.44-3.01,P<0.001),and use of chemotherapy(HR=0.81,95%CI:0.63-0.98,P=0.041).CONCLUSION The XPG rs2094258 polymorphism may be associated with overall survival in GC patients.     

Role of MyD88-adaptor-like gene polymorphism rs8177374 in modulation of malaria severity in the Pakistani population

Introduction

The present study was designed to investigate the association between rs8177374 polymorphism and malaria symptoms due to exposure of Plasmodium vivax and Plasmodium falciparum.

Interaction between ALDH2 rs671 and life habits affects the risk of hypertension in Koreans: A STROBE observational study

Aldehyde dehydrogenase-2 (ALDH2) is associated with the risk of hypertension, and the effects of lifestyle factors on blood pressure vary according to genotype. Among the Han Chinese, the risk of hypertension is lower in the group with the rs671 A allele than in the group with the G allele, and there is a significant association between the frequency of fried food consumption and hypertension. However, the A allele significantly increases the risk of hypertension with increased fried food intake. This study aimed to investigate the effect of the relationship between ALDH2 polymorphism and complex lifestyle habits (fried food consumption and exercise) on hypertension.rs671 polymorphisms of ALDH2 were examined using Korean genome and epidemiology data from 8157 hypertensive cases and 9550 controls. Further, we investigated whether the A allele is protective against hypertension in Koreans and explored the effect of the combination of fried food intake and exercise habits on hypertension by genotype.The genotype frequencies of rs671, which is specific to East Asia, were 2.51% AA, 26.66% GA, and 70.83% GG in the Korean population. The group with inactive aldehyde dehydrogenase-2 had a low odds ratio [OR = 0.75 (95% CI:0.69–0.80), P = 4.35 × 10⁻¹⁴] of hypertension, and low metabolism of acetaldehyde. Subjects carrying the A allele exhibited an increased risk of hypertension with increased fried food intake without exercise [OR = 2.256 (95% CI:1.094–4.654), P = .028].ALDH2 polymorphism and complex lifestyle habits (fried food consumption and exercise) are associated with the risk of hypertension. Further, the A allele is associated with a low risk of hypertension, but it increases the risk of hypertension as fried food intake without exercise increases.     

CXCL12 rs1801157基因多态性与乳腺癌易感性关联的Meta分析

目的探讨CXCL12 rs1801157基因多态性与乳腺癌易感性的关系。方法通过计算机检索和手工检索,收集有关CXCL12 rs1801157基因多态性与乳腺癌易感性关系的文献,筛选出符合条件的文献,应用M eta分析软件对各项研究进行异质性检验,计算合并OR值及其95%可信区间,并行敏感性分析和发表偏倚的评估。结果共5篇符合条件文献纳入本研究,病例组1 058例,对照组1023例。Meta分析合并结果显示CXCL12 rs1801157基因A等位基因携带者乳腺癌发生率明显高于G等位基因携带者（OR=1.32,95%CI=1.15~1.51,P〈0.01）;AA∶GG,GA∶GG和AA＋GA∶GG合并OR值及其95%可信区间分别是1.64（95%CI=1.16~2.33）、1.42（95%CI=1.18~1.70）和1.44（95%CI=1.21~1.72）。敏感性分析表明合并结果不受单个研究的影响,未发现发表偏倚,结论可靠。结论 CXCL12 rs1801157基因多态性可能与乳腺癌易感性有关,A等位基因可能增加乳腺癌的发病。     

The association between rs1800872 polymorphism in interleukin-10 and risk of cervical cancer: A meta-analysis

Background:In recent years, several reports have tried to prove this connection between rs1800872 polymorphism in interleukin-10 and cervical cancer among different populations, but the results are debatable. Thus, we collected all the published literature and conducted an integrated meta-analysis, which provided better evidence-based medicine for the relationship between rs1800872 polymorphism in interleukin-10 and risk of cervical cancer.Methods:We systematically performed our search on PubMed, EMBASE, Web of Science, WanFang database, and CNKI for all papers related to this research, published up to August 1, 2020. Summary odds ratios (OR) with 95% confidence interval (95% CI) were calculated in allelic, homozygous, heterozygous, dominant, and recessive model to appraise the association.Results:The meta-analysis included 8 studies containing 1393 cervical cancer cases and 1307 controls. The aggregate data under heterozygous model and dominant inheritance model (OR = 0.66, 95% CI: 0.55--0.80) indicated a significant association between rs1800872 and the low risk of cervical cancer in the entire population. And the aggregated data under the dominant inheritance model shows that rs1800872 is significantly associated with the reduction in the risk of cervical tumors in the entire population.Conclusion:Our conclusion is that the AC/AA + AC variant of Rs1800872 indicates a protective effect in the development of cervical cancer.     

Regulatory polymorphism of CXCL10 rs1439490 in seronegative occult hepatitis C virus infection

AIM To examine the relationship between the single nucleotide polymorphism CXCL10 rs1439490 and seronegative occult hepatitis C virus(HCV) infection(OCI).METHODS One hundred and three cases of seronegative OCI and 155 cases of seropositive chronic HCV infection(CHC) were diagnosed at five Liver Centers in Northeastern China, from 2012 to 2016. CXCL10 rs1439490, rs1440802, and IL-28 B rs12979860 were analyzed by sequencing. Serum CXCL10 was measured by ELISA. Intrahepatic CXCL10 was determined by quantitative PCR and immunohistochemical semi-quantitative scoring. Liver necroinflammation and fibrosis were scored according to the METAVIR system.RESULTS CXCL10 rs1439490 G/G was more prevalent in OCI patients(n = 93/103; 90.3%) than in CHC patients(n = 116/155; 74.8%; P = 0.008). OCI patients had lower serum CXCL10 levels than CHC patients(192.91 ± 46.50 pg/mL vs 354.78 ± 102.91 pg/mL, P 0.0001). Of IL-28 B rs12979860 C/C patients, OCI patients with rs1439490 G/G had lower serum and liver levels of CXCL10 and lower levels of liver necroinflammation and fibrosis than non-G/G patients. OCI patients had higher alanine aminotransferase normalization rates after Peginterferon treatment than CHC patients(P 0.05) and serum CXCL10 decreased significantly(P 0.0001). Liver necroinflammation and fibrosis were alleviated in 8 OCI patients after treatment. Multivariate analysis indicated that rs1439490 G/G significantly influenced the occurrence of OCI in HCV infection(OR = 0.31, 95%CI: 0.15-0.66, P = 0.002).CONCLUSION CXCL10 rs1439490 G/G is positively associated with OCI in HCV infection and antiviral outcome.     

Association of LDLR rs1433099 with the Risk of NAFLD and CVD in Chinese Han Population

Background and AimsRecent genome-wide association studies have shown that low-density lipoprotein receptor (LDLR) rs1433099 polymorphism is associated with cardiovascular disease (CVD) risk in many countries. However, the association of LDLR rs1433099 with CVD in China has not been reported yet. There are no studies on LDLR rs1433099 and non-alcoholic fatty liver disease (NAFLD) as well. The purpose of this study was to investigate whether LDLR rs1433099 is related to CVD or NAFLD in the Chinese population.MethodsLDLR rs1433099 polymorphism was genotyped in 507 individuals, including 140 healthy controls, 79 NAFLD patients, 185 CVD patients, and 103 patients with NAFLD combined with CVD. The expression of LDLR was tested by the sequence detection system, and clinical parameters were assessed by biochemical tests and physical examination.ResultsThe genotype distribution of LDLR rs1433099 was not statistically different among the NAFLD group, the CVD group, the combined group, and the healthy control group (p>0.05). There was no significant correlation of LDLR rs1433099 genotypic distribution or allele frequency and the risk of NAFLD, CVD or NAFLD combined with CVD (p>0.05). In the CVD group, T allele carriers had higher alkaline phosphatase and gamma-glutamyl transpeptidase than non-carriers (p<0.05).ConclusionsOur study demonstrated that the LDLR rs1433099 polymorphism is not a risk factor of NAFLD. The LDLR rs1433099 polymorphism may increase the risk of CVD through a mechanism involving alkaline phosphatase and gamma-glutamyl transpeptidase.     

ALDH2基因rs671位点与中国人群心血管代谢危险因素的关系

目的探讨乙醛脱氢酶2(ALDH2)基因rs671位点与我国人群心血管代谢危险因素的关系。方法利用2000~2001年开展的中国心血管健康多中心合作研究(InterASIA),纳入北方5个省市共计6404例基线未患冠心病和脑卒中个体。分析rs671位点与11种心血管代谢危险因素(腰臀围、血脂和血压等)的关系。结果rs671 A等位基因频率为0.16。rs671与饮酒行为显著相关,携带A等位基因的个体不倾向于饮酒(P<0.001)。rs671与腰围、臀围、甘油三酯和舒张压显著相关(P<0.05),每增加一个A等位基因,分别减少0.61 cm、0.54 cm、4.39 mg/dl和0.68 mmHg。进一步校正饮酒行为后,rs671与臀围的关联仍然显著(P=0.035),但与舒张压的关联不再显著。在饮酒人群中rs671 A等位基因可降低舒张压1.28 mmHg,而在非饮酒人群中没有作用。结论本研究发现rs671位点与中国人群腰围和舒张压显著相关,其中与舒张压的关联主要是通过饮酒发挥作用的。     

The rs7517847 polymorphism in the IL-23R gene is associated with gout in a Chinese Han male population

Abstract

Objectives. Gout is a polygenic auto-inflammatory disease, in which inflammation plays an important role in disease pathogenesis. The cytokine interleukin (IL)-23 promotes inflammation and helps to guide inflammatory cells, while studies have shown that the IL-23R gene is associated with susceptibility to several immune-related diseases. This study aimed to determine whether the IL-23R rs7517847 (G/T) polymorphism is associated with gout in a Chinese Han male population.

Methods. We recruited 400 patients with gout and 582 gout-free controls. After obtaining blood samples for DNA extraction, genotyping of the rs7517847 polymorphism was performed by fluorescence-based quantitative PCR using TaqMan probes. An association analysis was carried out using the χ² test. A genotype–phenotype analysis was also conducted.

Results. Both genotypic and allelic frequencies of rs7517847 differed significantly between gout patients and controls (χ² = 6.792, df = 2, P = 0.034 by genotype; χ² = 4.202, df = 1, P = 0.04 by allele).

Conclusions. IL-23R may be associated with gout in a Chinese Han male population, although our findings should be confirmed using larger sample sizes and other independent populations.