Polymerase Chain Reaction-ligase Detection Research Articles

Histopathological Correlations of Islet Amyloidosis With Apolipoprotein E Polymorphisms in Type 2 Diabetic Chinese Patients

Islet amyloidosis and arteriosclerosis are histopathological hallmarks in type 2 diabetes. Apolipoprotein E (ApoE) is a common component of amyloidosis. ApoE [Latin Small Letter Open E]4 allele is associated with arteriosclerosis and cerebral amyloidosis in Alzheimer disease. We examined the correlations of ApoE polymorphisms with islet amyloidosis in type 2 diabetes. Genomic DNA samples were obtained from 117 autopsy cases with type 2 diabetes and 209 nondiabetic cases. ApoE genotypes and amylin gene mutations were determined by polymerase chain reaction-ligase detection reaction analysis. Islet amyloidosis and arteriosclerosis were evaluated by staining of thioflavin T, amylin, ApoE, and amyloid P component. In the diabetic group, 33.3% in group [Latin Small Letter Open E]2 ([Latin Small Letter Open E]2[Latin Small Letter Open E]2, [Latin Small Letter Open E]2[Latin Small Letter Open E]3), 23.6% in group [Latin Small Letter Open E]3 ([Latin Small Letter Open E]3[Latin Small Letter Open E]3), and 62.5% in group [Latin Small Letter Open E]4 ([Latin Small Letter Open E]4[Latin Small Letter Open E]4, [Latin Small Letter Open E]3[Latin Small Letter Open E]4) had islet amyloidosis. After adjustment for confounders, group [Latin Small Letter Open E]4 had an odds ratio of 7.0 (95% confidence interval, 1.3-38.0; P = 0.023) in having islet amyloidosis compared to group [Latin Small Letter Open E]3. Diabetic cases with islet amyloidosis had more severe arteriosclerosis (P = 0.0111), arteriolar hyalinosis (P = 0.0369), and interstitial fibrosis (P = 0.0188) than those without amyloidosis. Immunoreactivity of both ApoE and amyloid P component was detected in islet amyloid deposits and arteriosclerotic lesions. In type 2 diabetes, islet amyloidosis and arteriosclerosis share common pathophysiological features with ApoE [Latin Small Letter Open E]4 as a probable linking factor.

Single‐nucleotide polymorphisms of IRF8 gene are associated with systemic lupus erythematosus in Chinese Han population

Interferon regulatory factor 8 (IRF8) has been shown to have diverse roles in the regulation of the immune system. Two recent studies had revealed the association between the single-nucleotide polymorphisms (SNPs; rs11644034 and rs2280381) of IRF8 and systemic lupus erythematosus (SLE) in a multiethnic population. The purpose of this study was to evaluate whether the association could be replicated in a Chinese Han population. Genotypes were determined by a multiplex polymerase chain reaction-ligase detection reaction (PCR-LDR) in 358 patients and 357 geographically matched healthy controls. Significant differences in genotype frequency were found between SLE and control individuals (rs11644034: AA vs. GG, P = 0.014, odds ratio (OR) = 0.980, 95% confidence internal (CI): 0.964-0.996; rs2280381: CC vs. TT, P = 0.005, OR = 0.150, 95% CI: 0.033-0.676). Conditional logistic regression analysis showed that the association of rs2280381 remained significant (P adjusted = 0.028) after adjustment for rs11644034, but not vice versa (P adjusted = 0.361).When stratifying patients with SLE according to clinical subtypes, SNP rs2280381 was found to be associated with low complement in patients with SLE. However, SNP rs11644034 was not found to be associated with SLE clinical subgroups. Analysis of the haplotypes revealed that haplotype G-T and G-C were also significantly associated with SLE (P = 0.002 and P = 0.012, respectively). Our study indicated that the IRF8 gene polymorphisms might be associated with susceptibility to SLE and with disease-related clinical manifestations in Chinese Han population.

Toll-like receptor 9 promoter polymorphism is associated with decreased risk of Alzheimer’s disease in Han Chinese

BackgroundToll-like receptors (TLRs), as major innate immune mediators, may be involved in clearance of cerebral amyloid-β (Aβ) deposits. Recently, a novel TLR9 signaling pathway has been uncovered, which is functionally associated with the immune inflammatory response and reducing Aβ burden in Alzheimer’s disease (AD) mice. Therefore, TLR9 might represent a reasonable functional candidate gene for AD.FindingsOur study investigated 1,133 sporadic late-onset AD (LOAD) and 1,159 healthy controls matched for sex and age in a large Han Chinese population. One selected functional rs187084 polymorphism within the TLR9 gene was genotyped by polymerase chain reaction-ligase detection reaction in a case–control associated study. The TLR9 rs187084 variant homozygote GG was significantly associated with a decreased LOAD risk after adjusting for age, gender, and ApoE ϵ4 status by logistic regression analysis (P = 0.035). Our result showed significant evidence of the interaction of ApoE ϵ4 with rs187084. When we further stratified our data by the ApoE ϵ4 status, we detected significant differences in the genotype and allele distributions of rs187084 between LOAD patients and controls in ApoE ϵ4 carriers (P < 0.001, P = 0.003, respectively). Moreover, we examined TLR9 expression in peripheral blood monocytes by flow cytometry, and the GG genotype of the TLR9 rs187084 polymorphism was associated with a higher TLR9 expression than two other genotypes in LOAD patients.ConclusionOur findings support the hypothesis that the TLR9 polymorphism may modify LOAD risk in the Han Chinese population.

The relationship between single nucleotide polymorphisms of the NTRK2 gene and sporadic Alzheimer's disease in the Chinese Han population

Alzheimer's disease (AD) is characterized by the degeneration of basal forebrain cholinergic neurons, whose survival and function are affected by neurotrophins and their receptors. The impaired signaling pathway of brain-derived neurotrophic factor/tropomyosin-related kinase B (BDNF/TrkB) is considered to play an important role in AD pathogenesis. To explore the association of polymorphisms within the NTRK2 gene (encoding TrkB) and sporadic AD (sAD), a case–control study was conducted in a Chinese Han cohort including 216 sAD patients and 244 control participants. Five single nucleotide polymorphisms (SNPs), with four of them within the promoter region and one in intron, were selected and genotyped with a polymerase chain reaction-ligase detection reaction (PCR-LDR) method. No association was revealed between these SNPs or the haplotypes containing four promoter SNPs and the risk of sAD. The results of this study indicate that polymorphisms in the selected regions of the NTRK2 gene are unlikely to confer the susceptibility of sAD in the Chinese Han population.

Relationship between Glutathione S-Transferase P1 (GSTP1), X-Ray Repair Cross Complementing Group 1 (XRCC1) and 5,10-Methylenetetrahydrofolate Reductase (5,10-MTHFR) Gene Polymorphisms and Response to Chemotherapy in Advanced Gastric Cancer

Background: Our study aimed to investigate the relationship between glutathione S-transferase P1 (GSTP1), 5,10-methylenetetrahydrofolate reductase (5,10-MTHFR) and X-ray repair cross complementing group 1 (XRCC1) gene polymorphisms and the response to chemotherapy in advanced gastric cancer. Patients and Methods: 59 cases of advanced gastric cancer were enrolled. All patients were treated with the DCF regimen comprising docetaxel, cisplatin, and 5-fluorouracil. All patients' genotypes regarding GSTP1, XRCC1, and 5,10-MTHFR were analyzed by polymerase chain reaction/ligase detection reaction (PCR-LDR). Results: There were 15 (25.42%) cases of G/G genotype, 21 (35.59%) of G/A genotype, and 23 (38.98%) of A/A genotype for GSTP1, 16 (27.12%) cases of A/A genotype, 18 (30.51%) of G/A genotype, and 25 (42.37%) of G/G genotype for XRCC1, and 21 (35.59%) cases of C/C genotype, 22 (37.29%) of C/T genotype, and 16 (27.12%) of T/T genotype for 5,10-MTHFR. After 2 cycles of chemotherapy, there were 4 cases of complete remission, 14 of partial remission, 19 of stable disease, and 22 of advanced disease, with a total effective rate of 30.51%. Better survival was shown for GSTP1 G/G genotype, XRCC1 A/A genotype, and 5,10-MTHFR T/T genotype (p < 0.05). Conclusion: The gene polymorphisms of GSTP1 G/G, XRCC1 A/A, and 5,10-MTHFR T/T have clinical value for predicting the response to the DCF regimen for advanced gastric cancer.

Plasma Levels of Interleukin 18, Interleukin 10, and Matrix Metalloproteinase-9 and -137G/C Polymorphism of Interleukin 18 Are Associated with Incidence of In-stent Restenosis After Percutaneous Coronary Intervention

This study aims to investigate the relationship between the levels of IL-18, IL-10, and MMP-9 and -137G/C polymorphism of interleukin 18 with the risk of in-stent restenosis (ISR). The study population consisted of 68 patients with ISR, 173 in non-ISR group, treated with drug-eluting stent and evaluated by coronary angiography post-procedure and at follow-up, and also 109 without angiographic evidence of coronary artery disease (CAD) which formed a reference control group (non-CAD group). The sequential plasma IL-18, IL-10, and MMP-9 levels were assessed at admission, 24 h, and 2 weeks after percutaneous coronary intervention. The -137G/C polymorphism of IL-18 was genotyped by the ligase detection reaction-polymerase chain reaction. Plasma IL-18 and MMP-9 increased significantly from admission, peaking after 24 h and fall after 2 weeks. Compared with the non-ISR group, the ISR group had higher levels of IL-18 and MMP-9, but IL-10 level was the opposite. The -137GG genotype of IL-18 was significantly higher than of the CG and CC genotypes. A significant higher frequency of -137G allele or GG genotype of IL-18 was observed in patients with ISR group compared with the non-ISR group. There is correlation between the changes of IL-18, IL-10, MMP-9, and ISR. IL-18 promoter -137G/C polymorphism influences IL-18 levels and the susceptibility to ISR, suggesting that IL-18-mediated pathways are causally involved in the process of ISR.

SLC26A4 gene polymorphism and late-onset Alzheimer's disease in a Han Chinese population from Qingdao, China.

In a recent genome-wide association study, the SLC26A4 gene rs2072064 polymorphism was found to be associated with late-onset Alzheimer's disease in Caucasians. Here, we investigated this association in a large Northern Han Chinese cohort consisting of 599 sporadic late-onset Alzheimer's disease patients and 598 healthy controls matched for sex and age in a Northern Han Chinese population from Qingdao, China. Genotyping by the polymerase chain reaction-ligase detection reaction revealed that there were significant differences in the genotype (P = 0.017) and allele (P = 0.007) frequencies of the rs2072064 polymorphism between late-onset Alzheimer's disease patients and controls. The A allele of this polymorphism was significantly associated with a reduced risk of late-onset Alzheimer's disease (odds ratio (OR) = 0.792, 95% confidence interval (CI) = 0.670–0.937, P = 0.007). When the data were stratified by the apolipoprotein E ε4 status, there was a significant difference only among apolipoprotein E ε4 non-carriers (genotypic P = 0.001, allelic P = 0.001). Furthermore, the association between rs2072064 and late-onset Alzheimer's disease remained significant by logistic regression analysis after adjustment for age, gender, and the apolipoprotein E ε4 carrier status (dominant model: OR = 0.787, 95% CI = 0.619–1.000, P = 0.050; recessive model: OR = 0.655, 95% CI = 0.448–0.959, P = 0.030; additive model: OR = 0.792, 95% CI = 0.661–0.950, P = 0.012). These findings suggest that SLC26A4 is a susceptibility gene for late-onset Alzheimer's disease in a Northern Han Chinese population from the Qingdao area.

Genetic polymorphisms in the Fas and FasL genes are associated with epithelial ovarian cancer risk and clinical outcomes

AimIn this study, we evaluated whether functional polymorphisms within the Fas and FasL genes were associated with the risk of developing epithelial ovarian cancer (EOC) and survival of patients with EOC. MethodsA case–control study was performed in 342 EOC patients and 344 control women. The genotypes of three promoter region polymorphisms (Fas −1377G/A, −670A/G and FasL −844T/C) were determined using ligase detection reaction-polymerase chain reaction (LDR-PCR). The clinical outcomes in 202 EOC patients were compared across genotypes. ResultsThe genotype frequencies of the FasL −844 T/C polymorphism were significantly different between the case and control groups (P=0.034). Compared to the T/T and T/C genotypes, the C/C genotype significantly increased the risk of developing EOC (OR=1.46, 95% CI=1.08–1.99). The survival analysis showed that the Fas −1377G/A and −670A/G polymorphisms were related to prognosis in EOC patients. Compared with patients with the G/G genotype of the −1377G/A polymorphism, patients carrying the A allele had a shorter PFS and OS, as determined by univariate and multivariate analysis (HR=1.81, 95% CI=1.26–2.62 and HR=1.86, 95% CI=1.15–3.00, respectively). Similarly, Kaplan–Meier and Cox proportional hazard model analyses indicated that patients carrying the G allele of Fas −670A/G polymorphisms had shorter PFS and OS than those carrying the AA genotype (HR=1.67, 95% CI=1.15–2.42 and HR=1.80, 95% CI=1.10–2.94, respectively). ConclusionsFunctional polymorphisms in the Fas and FasL genes may be involved in epithelial ovarian cancer development and progression in northern Chinese women.

Association of HLA-DRB1 Single Nucleotide Polymorphisms with Left Ventricular Remodelling in Elderly Patients with Essential Hypertension

To investigate the associations between human leucocyte antigen DRβ1 (HLA-DRB1) gene polymorphisms and cardiovascular remodelling (left ventricular dilatation [LVD]) in Han Chinese patients ≥ 60 years old, with essential hypertension. LVD was diagnosed via echocardiographic measurements. Multiplex polymerase chain reaction-ligase detection reaction was used to determine the genotypes of three HLA-DRB1 single nucleotide polymorphisms (SNPs; rs2308765, rs9269186 and rs3135388). HLADRB1 rs2308765 wild-type (G) allele and genotype (GG) were associated with decreased risk of LVD. HLA-DRB1 rs9269186 and rs3135388 were not associated with LVD risk. Mean waist and abdominal circumferences were significantly larger in patients with, compared with those without, LVD. Multivariate logistic regression analyses found that rs2308765 was associated with LVD (GT + TT versus GG; odds ratio 7.958; 95% confidence interval 1.935, 32.723). Mutation in HLA-DRB1 rs2308765 was associated with increased risk of LVD in elderly patients with hypertension. Genotype analysis may allow identification of patients at high risk of cardiovascular events such LVD.

Analysis of the genetic effects of prolactin gene polymorphisms on chicken egg production

Chicken prolactin (PRL) is a physiological candidate gene for egg production. Variations of T8052C and G8113C in exon 5 of PRL gene may associate with chicken egg production. The objective of the study was to investigate the association of these two single nucleotide polymorphisms in PRL gene with egg production of Recessive White chickens and Qingyuan Partridge chickens. Genotyping was performed by polymerase chain reaction-ligase detection reaction (PCR-LDR) method. The T8052C and G8113C of PRL were significantly associated with age at first egg (AFE) and total egg number at 300 days of age (EN 300). A significant association was also found between T8052C-G8113C haplotypes and AFE as well as EN300, the H2H3 was the most advantageous diplotype for egg production. We putatively drew the conclusion that these two SNPs in PRL gene as well as their haplotypes could be used as the potential molecular markers for egg production traits in chicken.

PLC-ε1 Gene Polymorphisms Significantly Enhance the Risk of Esophageal Squamous Cell Carcinoma in Individuals with a Family History of Upper Gastrointestinal Cancers

Phospholipase C epsilon 1 (PLCε1) may regulate cell growth, differentiation, apoptosis and angiogenesis and play an important role in carcinogenesis and the progression of several cancers. This study was designed to validate the association of the PLCε1 rs2274223 single nucleotide polymorphism (SNP) with esophageal squamous cell carcinoma (ESCC) as identified by genome-wide association studies (GWAS) and further assess whether the rs11599672 SNP could affect an individual's susceptibility to ESCC. These two SNPs were genotyped by polymerase chain reaction ligase detection reaction (PCR-LDR) in 527 ESCC patients and 527 controls. Compared with the rs2274223 SNP AA genotype, other genotypes or combined genotypes all enhanced the risk of ESCC. Further analyses showed that AG/GG genotype carriers with a family history of upper gastrointestinal cancers (UGIC) had an increased risk of ESCC than those AA genotype carriers without UGIC family history (OR = 2.10, 95% CI = 1.46-3.10). Overall, rs11599672 SNP had no influence on ESCC susceptibility. However, UGIC family history elevated the risk of ESCC for subjects with the TT genotype (OR = 1.59, 95% CI = 1.13-2.24). These results highlighted the role of a genetic factor in ESCC and suggested that the PLCε1 rs2274223 SNP might be an effective genetic marker to assess the risk of ESCC in individuals with a UGIC family history from a region of high incidence in northern China.

Association of P213S polymorphism of the L-selectin gene with type 2 diabetes and insulin resistance in Chinese population

AimsL-selectin belongs to selectin family of adhesion molecule and participates in the generation and development of type 2 diabetes (T2D). In this study, we evaluated the relationship between the P213S polymorphism of L-selectin gene and T2D and insulin resistance in the Chinese population. MethodsWe genotyped P213S polymorphism in 801 patients with T2D and 834 healthy controls in the Chinese population using polymerase chain reaction–ligase detection reaction (PCR–LDR) technique. Plasma glucose, insulin, lipid, blood urea nitrogen, creatinine and uric acid levels were measured by biochemical technique. ResultsThe frequency of 213PP genotype and P allele of the L-selectin gene in patients with T2D was significantly higher than that in controls (P=0.007; P=0.019, respectively). The relative risk of allele P suffered from T2D was 1.191 times higher than that of allele S. Moreover, the levels of FPG and HOMA-IR of PP and PS genotype carriers were significantly higher than those of SS genotype carriers in the T2D group (P<0.05). ConclusionThese findings indicated that the P213S polymorphism of L‐selectin gene may contribute to susceptibility to T2D and insulin resistance in the Chinese population, and P allele appears to be a risk factor for T2D.

Study on the relationship between TagSNPs and haplotype of hCHK2 and esophageal cancer in Kazakh and Han in Xinjiang

Aim of the studyTo determine the association of hCHK2 rs2278022, rs2602431, and rs2970077 polymorphisms and haplotypes with susceptibility to esophageal cancer in Kazakh and Han in Xinjiang Uygur Autonomous Region.Material and methodsMolecular epidemiology was carried out on 239 cases of esophageal cancer (132 Kazakh, 107 Han) and 513 controls (309 Kazakh, 204 Han) of Xinjiang. Polymorphisms of hCHK2 at rs2278022, rs2602431 and rs2970077 were analyzed by polymerase chain reaction-ligase detection reaction (PCR-LDR). Haplotypes were estimated by the SHEsis software. Statistical differences in genotype/haplotype frequencies, and frequencies between the case group and the control group were estimated.Results1) No significant difference was observed in the frequency of hCHK2 at rs2278022, rs2602431 and rs2970077 between the cases and controls in Kazakh and Han (P > 0.05); 2) In Kazakh and Han, the distribution of haplotypes was not significantly different between esophageal cancer cases and controls (P > 0.05).ConclusionsPolymorphisms of hCHK2 at rs2278022, rs2602431 and rs2970077 and haplotypes are unlikely to be associated with the susceptibility to esophageal cancer in Kazakh and Han.

ERCC1 Gene +262A/C Polymorphism Associated with Risk of Gastric Cardiac Adenocarcinoma in Nonsmokers

Polymorphisms in DNA repair gene may alter an individual's DNA repair capacity and be associated with the risk of various cancers. This study was designed to investigate whether ERCC1 +262A/C and XPF -357A/C polymorphisms affect individual susceptibility to esophageal squamous cell carcinoma (ESCC) and gastric cardiac adenocarcinoma (GCA). In 389 ESCC patients vs. 778 healthy controls and 262 GCA patients vs. 524 healthy controls in a high incidence region of northern China, ERCC1 +262A/C polymorphism and XPF -357A/C polymorphism were genotyped by the method of polymerase chain reaction ligase detection reaction (PCR-LDR) and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis, respectively. Family history of upper gastrointestinal cancers (UGIC) may increase the risk of ESCC and GCA. Allelotype and genotype distributions of ERCC1 +262A/C and XPF -357A/C polymorphisms in ESCC and GCA patients were not significantly different from that in their respective controls (p >0.05). Compared with ERCC1 +262C/C genotype, A/A genotype decreased the risk of GCA in nonsmokers (age, gender and family history of UGIC adjusted odds ratio [OR] = 0.30, 95% confidence interval [CI] = 0.13-0.70). Neither the A/C nor the C/C genotype was associated with the overall risk of ESCC and GCA when compared with the XPF -357A/A genotype. ERCC1 +262A/A genotype may reduce the risk of GCA for nonsmokers. XPF -357A/C polymorphism was not associated with the risk of ESCC and GCA in a population of a high-incidence region in northern China.

Interleukin-10 Genotype Correlated to Deficiency Syndrome in Hepatitis B Cirrhosis

Traditional Chinese medicine (TCM) syndrome is an important basis for TCM diagnosis and treatment. As Child-Pugh classification as well as compensation and decompensation phase in liver cirrhosis, it is also an underlying clinical classification. In this paper, we investigated the correlation between single nucleotide polymorphisms (SNPs) of Interleukin-10 (IL-10) and TCM syndromes in patients with hepatitis B cirrhosis (HBC). Samples were obtained from 343 HBC patients in China. Three SNPs of IL-10 (−592A/C, −819C/T, and −1082A/G) were detected with polymerase chain-reaction-ligase detection reaction (PCR-LDR). The result showed the SNP-819C/T was significantly correlated with Deficiency syndrome (P = 0.031), but none of the 3 loci showed correlation either with Child-Pugh classification and phase in HBC patients. The logistic regression analysis showed that the Excess syndrome was associated with dizzy and spider nevus, and the Deficiency syndrome was associated with dry eyes, aversion to cold, IL-10-819C/T loci, and IL-10-1082A/G loci. The odds ratio (OR) value at IL-10-819C/T was 4.022. The research results suggested that IL-10-819C/T locus (TC plus CC genotype) is probably a risk factor in the occurrence of Deficiency syndrome in HBC patients.

Four new single nucleotide polymorphisms (SNPs) of toll-like receptor 7 gene discovered in Chinese ducks

In order to reveal the single nucleotide polymorphisms (SNPs), genotypes and allelic frequencies of each mutation site of TLR7 gene in Chinese native duck breeds, SNPs of duck TLR7 gene were detected by DNA sequencing. The genotypes of 465 native ducks from eight key protected duck breeds were determined by polymerase chain reaction ligase detection reaction (PCR-LDR) method. The results show that four new SNPs (T2606C, T2739C, C2820T and A3284G) were discovered and three genotypes were all found in each mutation site. The first and the fourth SNPs resulted in two amino acid changes of Methionine (M) → Threonine (T) and Glutamine (Q) → Arginine (R), respectively. Allele C frequency of TLR7 T2606C mutation site in Gaoyou (GY) duck breed was significantly higher than the corresponding allelic frequency in the other duck populations, and allele T frequency of TLR7 C2820T mutation site in GY duck breed was also significantly higher than the corresponding allelic frequency in the other duck populations except Putian (PT) duck breed. In conclusion, the four new SNPs and the genetic differences among different duck breeds will promote duck disease resistance research. Key words : TLR7, duck, single nucleotide polymorphism (SNP), polymerase chain reaction ligase detection reaction (PCR-LDR).

Simultaneous detection of hepatitis B virus genotypes and mutations associated with resistance to lamivudine, adefovir, and telbivudine by the polymerase chain reaction-ligase detection reaction

OBJECTIVES: Detection of mutations associated to nucleos(t)ide analogs and hepatitis B virus (HBV) genotyping are essential for monitoring treatment of HBV infection. We developed a multiplex polymerase chain reaction-ligase detection reaction (PCR-LDR) assay for the rapid detection of HBV genotypes and mutations associated with lamivudine, adefovir, and telbivudine resistance in HBV-infected patients. METHODS: HBV templates were amplified by PCR, followed by LDR and electrophoresis on a sequencer. The assay was evaluated using plasmids that contained wild-type or mutant HBV sequences and 216 clinical samples. RESULTS: The PCR-LDR assay and sequencing gave comparable results for 158 of the 216 samples (73.1%) with respect to mutation detection and genotyping. Complete agreement between the two methods was observed for all the samples (100%) at codon 180 and codon 204. Concordant results were observed for 99.4% of the 158 samples at codon 181 and 98.7% at codon 236. The genotyping results were completely concordant between the PCR-LDR assay and sequencing. The PCR-LDR assay could detect a proportion of 1% mutant plasmid in a background of wild-type plasmid. CONCLUSION: The PCR-LDR assay is sensitive and specific for detection of HBV genotypes and drug resistance mutations, and could be helpful for decision making in the treatment of HBV infection.

Simultaneous detection of hepatitis B virus genotypes and mutations associated with resistance to lamivudine, adefovir, and telbivudine by the polymerase chain reaction-ligase detection reaction

ObjectivesDetection of mutations associated to nucleos(t)ide analogs and hepatitis B virus (HBV) genotyping are essential for monitoring treatment of HBV infection. We developed a multiplex polymerase chain reaction-ligase detection reaction (PCR-LDR) assay for the rapid detection of HBV genotypes and mutations associated with lamivudine, adefovir, and telbivudine resistance in HBV-infected patients. MethodsHBV templates were amplified by PCR, followed by LDR and electrophoresis on a sequencer. The assay was evaluated using plasmids that contained wild-type or mutant HBV sequences and 216 clinical samples. ResultsThe PCR-LDR assay and sequencing gave comparable results for 158 of the 216 samples (73.1%) with respect to mutation detection and genotyping. Complete agreement between the two methods was observed for all the samples (100%) at codon 180 and codon 204. Concordant results were observed for 99.4% of the 158 samples at codon 181 and 98.7% at codon 236. The genotyping results were completely concordant between the PCR-LDR assay and sequencing. The PCR-LDR assay could detect a proportion of 1% mutant plasmid in a background of wild-type plasmid. ConclusionThe PCR-LDR assay is sensitive and specific for detection of HBV genotypes and drug resistance mutations, and could be helpful for decision making in the treatment of HBV infection.

Mitochondrial nt3010G-nt3970C haplotype is implicated in high-altitude adaptation of Tibetans

Tibetans are well adapted to living and thriving in high-altitude environments. Mitochondria are central links to oxygen consumption, and variations in mitochondrial DNA (mtDNA) could play a role in high-altitude adaptation. Alleles at several polymorphic sites in mtDNA define common haplotypes, or haplogroups, including some that have been implicated in the risk of developing certain diseases. However, few reports have determined whether relationships exist between haplogroups and high-altitude adaptation in the Tibetan population. The D4 haplogroup is a major haplogroup of the Han Chinese. In the present study, genotypes of 12 polymorphisms were determined in members of a Tibetan population (n = 72), low altitude-Han (la-Han, n = 144), and high altitude-Han (ha-Han, n = 227) populations using polymerase chain reaction–restriction fragment length polymorphism and polymerase chain reaction–ligase detection reaction assays. The mitochondrial haplogroup D4 was negatively associated with high-altitude adaptation in Tibetans (P = 0.001 vs. la-Han, OR = 0.166, 95% CI = 0.048–0.567; P = 0.009 vs. ha-Han OR = 0.232, 95% CI = 0.069–0.778). The frequency of the nt3010G-nt3970C haplotype was significantly higher in Tibetans than in la-Han (P = 0.000) and ha-Han (P = 0.001) subjects. Findings in the present study suggest that unique mitochondrial variations determine a genetic background that is associated with high-altitude adaptation in the Tibetan population.

Identification of susceptibility genes loci associated with type 2 diabetes

In this study, we selected 10 susceptible SNPs loci to investigate their contribution to susceptibility to type 2 diabetes in Han Chinese among Hubei population. We genotyped SNPs rs5219, rs1801282, rs1470579, rs1111875, rs1081661, rs7754840, rs4506565, rs13266634, rs4402960, and rs5643981 by using the method of polymerase chain reaction-ligase detection reaction (PCR-LDR). In a case-control study, we have genotyped the 10 candidate susceptibility SNP loci, and here, we reported that the SNP rs5219 in KCNJ11 was strongly associated with type 2 diabetes in Han Chinese in Hubei China. There were significant differences in the TT genotype frequency (OR=1.6, 95%CI 1.1-2.3, p=0.01) and T allele frequency (OR=1.3, 95%CI 1.1-1.6, p=0.03) of SNP rs5219 between cases and controls. The other nine SNP loci did not show significant association with type 2 diabetes in Han Chinese in Hubei. The result suggests that KCNJ11 gene is a susceptibility gene of type 2 diabetes among this population.