PCR-direct Sequencing Method Research Articles

Hysterothylacium amoyense (Nematoda: Raphidascarididae) infecting Trichiurus lepturus (Scombriformes: Trichiuridae) from Demak, Central Java, Indonesia

Abstract. Utami AMR, Murwantoko, Istiqomah I, Triyanto, Setyobudi E. 2022. Hysterothylacium amoyense (Nematoda: Raphidascarididae) infecting Trichiurus lepturus (Scombriformes: Trichiuridae) from Demak, Central Java, Indonesia. Biodiversitas 23: 1030-1037. This study aims to determine parasitic infection and identify the larvae of anisakid nematode found on the hairtail Trichiurus lepturus caught on the northern coast of Demak District, Central Java Province, Indonesia. One hundred seventy-eight hairtail samples were collected from fishermen who caught the fish at the Java Sea north coast of Demak. Fish specimens were measured (length) and weighed, then examined for anisakid larvae examination in the abdominal cavity, internal organs, and muscle. Data analysis included prevalence, mean intensity, and distribution of anisakid larvae on target organs. Selected samples of collected anisakid larvae were identified molecularly using PCR direct sequencing method. The results showed that the hairtail at the northern coast of Demak District was susceptible to anisakid larvae infection, on the category "frequently infected" with the prevalence of 56% and low mean intensity of infection of 2.43 larvae/host. Anisakid larvae were mainly found in the abdominal cavity (67%); followed by the digestive tract (19%), liver (13%), and gonads (1%). There were no anisakid larvae infecting the muscle tissue. Molecular analyses identified the anisakid infecting Trichiurus lepturus as Hysterothylacium amoyense.

Exploring the p53 connection of cervical cancer pathogenesis involving north-east Indian patients.

As per WHO, Cervical cancer (CaCx) is a global issue, being the fourth common cancer in women with incidence rate of 13.1 per 1 lakh women globally and accounting for 311000 deaths in the year 2018 itself globally. The molecular pathogenesis in Human papillomavirus (HPV) infected cases is inconclusive. The detection of molecular factors leading to progression of CaCx can be important in the diagnosis and management of the disease. p53 a known tumor suppressor gene having a regulative role in cell cycle has been highlighted as key factor in the prevention of cancer but its significance in CaCx cases has been variably documented. The present study therefore targeted to evaluate the significance of p53 profile in CaCx cases in ethnically distinct northeast Indian population. Blood and Tissue samples (N = 85) of cervical cancer patients were collected and screening for HPV was performed using PCR. Thereafter the differential mRNA expression(qPCR), Immunohistochemistry, Mutation (PCR direct sequencing method) of p53 was studied. Further p53 epigenetic profiling was done by Methylation specific PCR (MS-PCR) and western blotting by using p53 acetylation specific antibodies. Our findings revealed that the downregulation of p53 was associated with the progression of disease and the variation in downregulation based on p53 polymorphism was observed. Further hypermethylation and deacetylation of p53 was also found to be associated with the pathogenesis of CaCx. The downregulated expression and hypermethylation of p53 in lower grade of CaCx, together established its association with the progression of CaCx from lower to severe grade. Therefore, in CaCx patients of northeast Indian population, malfunctioning of p53 is found to have significant role in cervical cancer progression.

The fluctuation of APC gene in WNT signaling with adenine deletion of adenomatous polyposis coli, is associated in colorectal cancer

Colorectal cancer is one of the most important malignancies in the classification of gastrointestinal cancers. One of the predisposing factors at molecular level for this cancer is via WNT signaling which is associated with the vast numbers of different genes. Thus, in this study, we aimed to investigate whether Adenomatous Polyposis Coli gene (APC) mutation of rs41115in two locations such as 132.002 and 131.989 acts as a trigger or cause of colorectal cancer. Relatively, 30 blood samples of colorectal cancer patients and 30 normal blood samples as control group after colonoscopy and also confirmation of pathology report at Rohani Hospital in Babol (Iran) were investigated. The primers were designed in order to be included the rs41115 to identify the particular polymorphisms of gene. The polymerase chain reaction (PCR direct sequencing method) was used. Conclusively, deletion of adenine in two specific locations such as 131.989 and 132.002 has been identified, but there was no relationship between rs41115 polymorphisms located in adenomatous polyposis coli gene and colorectal cancer.

Characterization of the "a" determinant region of the hepatitis B virus genome in Iranian patients at different clinical phases of chronic infection.

To determine the distribution of important mutations of the "a" determinant region in the HBV genome among patients in different clinical phases of HBV infection. Variations in Hepatitis B infection not only change the outcome of the disease but also the symptoms from which the chronic HBV patients are suffering. We have meticulously selected a total of 40 chronic HBV patients from four different subclasses of chronic HBV clinical phases including immune tolerant (IT), immune active (IA), inactive carrier (IC) and hepatitis B e antigen (HBeAg)-negative (ENEG); 10 samples per each phase. Mutations of the "a" determinant region were identified using PCR-Direct sequencing method. 17 amino-acid substitutions at 12 positions inside the "a" determinant were identified in all forty samples; 3 mutations in the IT group, 6 mutations in the IA phase, 3 mutations in the IC patients and 5 mutations in the ENEG phase. Different substitutions were observed in all four clinical phases. The IA phase was the most variant group with the highest number of amino-acid substitutions. These results did not reveal a strong pattern to distinguish different clinical phases of Chronic HBV infection, but there are some obvious differences regarding the number and position of mutations between these four clinical phases.

Broad Range of Hepatitis B Virus (HBV) Patterns, Dual Circulation of Quasi-Subgenotype A3 and HBV/E and Heterogeneous HBV Mutations in HIV-Positive Patients in Gabon.

Integrated data on hepatitis B virus (HBV) patterns, HBV genotypes and mutations are lacking in human immunodeficiency virus type 1 (HIV-1) co-infected patients from Africa. This survey was conducted in 2010–2013 among 762 HIV-1-positive adults from Gabon who were predominantly treated with 3TC-based antiretroviral treatment. HBV patterns were identified using immunoassays detecting total antibody to hepatitis B core antigen (HBcAb), hepatitis B surface antigen (HBsAg), IgM HBcAb, hepatitis B e antigen (HBeAg), antibody to HBsAg (HBsAb) and an in-house real-time PCR test for HBV DNA quantification. Occult hepatitis B (OBI) was defined by the presence of isolated anti-HBc with detectable serum HBV DNA. HBV genotypes and HBV mutations were analyzed by PCR-direct sequencing method. Seventy-one (9.3%) patients tested positive for HBsAg, including one with acute hepatitis B (0.1%; 95% CI, 0.0%-0.2%), nine with HBeAg-positive chronic hepatitis B (CHB) (1.2%; 95% CI, 0.6%–2.2%), 16 with HBeAg-negative CHB (2.1%; 95% CI, 1.2%–3.3%) and 45 inactive HBV carriers (5.9%; 95% CI, 4.4%–7.8%). Sixty-one (8.0%; 95% CI, 6.2%–10.1%) patients showed OBI. Treated patients showed similar HBV DNA levels to those obtained in untreated patients, regardless of HBV patterns. Around 15.0% of OBI patients showed high (>1,000 UI/mL) viremia. The mutation M204V/I conferring resistance to 3TC was more common in HBV/A (47.4%) than in HBV/E isolates (0%) (P = .04). Our findings encouraged clinicians to promote HBV vaccination in patients with no exposure to HBV and to switch 3TC to universal TDF in those with CHB.

Association study of IL2RA and CTLA4 Gene Variants with Type I Diabetes Mellitus in children in the northwest of Iran.

Introduction: A variety of genetic predisposing factors and environmental factors are known to influence the pathogenesis of type-1 diabetes (T1D). This study intended to investigate the association of cytotoxic T-lymphocyte associated protein 4 (CTLA4) and interleukin 2 receptor subunit alpha (IL2RA) gene polymorphisms with type 1 diabetes in children of northwest of Iran. Methods: Genomic DNA was extracted by salting-out method. PCR amplification and direct sequencing methods were used for genotyping of CTLA4 (exon 1) and IL2RA (intron 1) genes in all patients and controls. SNPStats was used to calculate odds ratios (ORs), 95% confidence intervals (CIs), and p values. Results: In this study, the frequency of G allele and GG genotype of CTLA-4 (+49A/G) polymorphism in T1D patients were significantly different from those in the controls (26% vs. 11%, p = 0.006). Moreover, a significant difference was observed between patients and control group in the allele frequencies of the new SNP (chr2:203868145) that was identified in exon one of CTLA4 (14% vs. 3%, p = 0.006). The results showed that the GG homozygous genotype of +49 A>G was associated with increased glycemic level in T1D patients in the study population (95% CI = 10.47, p = 0.0067). However, no significant association was found between IL2RA (ss52580101C>A) polymorphism and T1D patients (2% vs. 4%, p = 0.41). Conclusion: The results further support the association of T1D with +49A>G SNP in the CTLA4 gene in the population of northwest of Iran. However, no significant relationship was observed between ss52580101C>A polymorphism of IL2RA gene and T1D in this study.

The effect of SIRT1 gene polymorphisms on ambulatory blood pressure of hypertensive patients in the Kazakh population.

To investigate the effect of silent information regulator 1 (SIRT1) gene polymorphisms on ambulatory blood pressure in hypertensive patients. Three hundred forty hypertensive patients were recruited from January 2013 to January 2015. SIRT1 Tag single-nucleotide polymorphisms (SNPs; rs2273773, rs4746720, and rs7896005) were genotyped using a PCR-direct sequencing method, and the association between the SIRT1 gene SNPs and ambulatory blood pressure was analyzed. After adjusting for confounding factors, patients with the rs2273773/CT+CC genotypes had lower 24-h systolic and diastolic blood pressures; there were no associations between rs4746720 and rs7896005 genotypes and blood pressure. The SIRT1 gene polymorphism (rs2273773) is significantly associated with ambulatory blood pressure level in Han Chinese patients with hypertension.

Abstract 809: BrafV637E mutation as an early change in hepatocarcinogenesis induced by neonatal treatment with diethylnitrosamine in B6C3F1 mice

Abstract Neonatal treatment of B6C3F1 mice with diethylnitrosamine (DEN) is often employed as an experimental model for hepatic tumors. In this model, microscopic preneoplastic foci emerge in the early stage and subsequently progress into adenomas, from which hepatocellular carcinoma (HCC) is finally developed. We detected the BrafV637E mutation, that is correspondent to the human BrafV600E mutation, in 4/4 DEN-induced hepatic tumors at 13 months after DEN treatment by whole exome analysis, and further in 16/17 (94.1%) late tumors by the PCR-direct sequencing method. By microdissection, the BrafV637E mutation was also detected in 16/18 (88.8%) and 22/28 (78.5%) microscopic lesions (preneoplastic foci and microadenomas) respectively at 5 and 8-9 months after DEN treatment. Meanwhile, although the BrafV637E mutation was detected in 5/7 (71.4%) hepatic tumors induced by neonatal DEN treatment followed by repeated CCl4 administration, it was not found in 24 hepatic tumors induced by CCl4 alone and 6 spontaneous hepatic tumors in B6C3F1 mice, indicating that the BrafV637E mutation is specific to the DEN-initiated hepatic tumors, presumably being derived from the genotoxic action of DEN. The DEN-induced tumors showed hyperphosphorylation of MEK and ERK1/2, indicating that the BrafV637E mutation activated the downstream MAPK pathway. Furthermore, the DEN-induced tumors overexpressed the pro-survival/pro-proliferative cytokines/chemokines such as complement C5/C5a, soluble intercellular adhesion molecule (sICAM-1), IL-1 receptor antagonist (IL-1ra) and chemokine CXCL9 as well as the oncogene-induced senescence (OIS) markers, p15Ink4b and p19Arf mRNAs, suggesting that the BrafV637E mutation might influence the gene expression that is involved either in cellular growth/survival or OIS. Transgenic mice expressing BrafV637E specifically in the liver under the control of albumin promoter showed enlarged hepatic mass as large as 4-5 times of normal liver, and whole liver was consisted of small basophilic hepatocytes resembling the cells in the early preneoplastic lesions induced by neonatal treatment with DEN. These results indicate that the BrafV637E mutation plays a pivotal role in the DEN-induced hepatocarcinogenesis. Citation Format: Masahiro Yamamoto, Hiroki Tanaka, Xin Bing, Yuji Nishikawa, Kohsuke Yamazaki, Keiko Shimizu, Katsuhiro Ogawa. BrafV637E mutation as an early change in hepatocarcinogenesis induced by neonatal treatment with diethylnitrosamine in B6C3F1 mice. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 809. doi:10.1158/1538-7445.AM2015-809

A common genetic variant of the chromogranin A-derived peptide catestatin is associated with atherogenesis and hypertension in a Japanese population.

Chromogranin A (CHGA) is a major protein in the secretory granules of chromaffin cells. CHGA also gives rise to cardiovascular/metabolism regulatory peptides, such as catestatin (CST) and pancreastatin (PST). While CST is a potent inhibitor of catecholamine secretion, PST is a potent physiological inhibitor of glucose-induced insulin secretion. Recently, several SNPs were identified in the CST and PST domains of CHGA locus in different populations. Among the discovered SNPs, CST variant allele Ser-364 was associated with blood pressure alteration and PST variant allele Ser-297 was associated with significantly higher plasma glucose level. In this study, we examined whether these CST and PST variant alleles exist and influence cardiovascular and metabolic phenotypes in Japanese population. Our study comprised of 343 Japanese subjects aged 45-85 years (143 men and 200 women, mean age 66 ± 8 years). We determined the genotypes of CST and PST by PCR-direct sequencing method and carried out genotype-phenotype association analysis. In 343 participants, the minor allele frequency of CST variant Ser-364 was 6.10%. On the other hand, we did not detect the PST variant Ser-297 in this entire study population. The presence of Ser-364 allele was associated with increased in baPWV (an index of systemic arterial stiffness) that suggests an initiation and/or progression atherogenesis and hypertension. The Ser-364 allele was also associated with elevated systolic blood pressure and pulse pressure, consistent with increased baPWV. In conclusion, the CST Ser-364 allele may increase the risk for cardiovascular diseases in Japanese population.

Rs495828 polymorphism of the ABO gene is a predictor of enalapril-induced cough in Chinese patients with essential hypertension.

ABO genetic polymorphisms have recently been associated with angiotensin-converting enzyme (ACE) activity and inflammation, which play a critical role in the pathogenic mechanism of ACE inhibitor-induced cough. Therefore, the current study determined the association of ABO genetic polymorphisms with enalapril-induced cough in Chinese patients with essential hypertension. A total of 450 essential hypertensive patients treated with 10 mg of enalapril maleate were genotyped for ABO genetic polymorphisms using the PCR-direct sequencing method. Cough was recorded when patients were bothered by cough and respiratory symptoms during enalapril treatment without an identifiable cause. The distribution of rs8176740 and rs495828 was different between the coughers and the controls [P=0.039; odds ratio (OR)=0.70, P=0.018; OR=1.41]. The risk of enalapril-induced cough in the rs495828 TT carriers was increased (P=0.008; OR=2.69), which remained significant after false discovery rate correction. The results for the rs8176740 polymorphism were significant in the female subgroup (P=0.027; OR=0.22). Haplotype analysis of the four ABO polymorphisms (rs8176746/rs8176740/rs495828/rs12683493) showed that the frequency of the GATC haplotype was higher in the coughers than those in the controls (26.6 vs. 18.8%, P=0.033; OR=1.43). The rs495828 polymorphism was associated with enalapril-induced cough and may serve as a useful pharmacogenomics marker of the safety of enalapril in Chinese patients with essential hypertension. The mechanism for the associations may involve the effects of the ABO gene or ABO blood type on ACE activity and inflammation.

Sequence analysis of EBV immediate-early gene BZLF1 and BRLF1 in lymphomas

The immediate-early (IE) genes, BZLF1 and BRLF1, play an important role in switching Epstein-Barr virus from the latent to the lytic state. The functions of the two IE genes and their respective proteins: ZEBRA and Rta have been well studied, but little is known about their DNA coding sequence variations and disease association. In order to investigate the sequence variation patterns and elucidate their association with lymphomas, BZLF1 and BRLF1 were analyzed in 26 and 33 lymphomas using PCR-direct sequencing method respectively. Three sequence variation types of BZLF1 gene were identified. The type BZLF1-A and BZLF1-B was detected in 34.6% (9/26) and 57.7% (15/26) of the tumor specimens, respectively. Among the three functional domains of ZEBRA, the transactivation domain had the most mutations. Three variation types were also identified in BRLF1 gene where type BR1-A and BR1-C were detected in 27.3% (9/33) and 69.7% (23/33) of specimens, respectively. Among the three functional domains of Rta, the dimerization domain was well conserved while multiple mutations were detected in both the DNA binding domain and the transactivation domain. The variation types BZLF1-B and BR1-C were more frequent in the lymphomas, compared with the throat washing samples from the healthy donors. These results suggest that the type BZLF1-B and BR1-C may be associated with the tumorigenesis of lymphoma.

Molecular diagnostic algorithm for epidermal growth factor receptor mutation detection in Asian lung adenocarcinomas: Comprehensive analyses of 445 Taiwanese patients with immunohistochemistry, PCR‐direct sequencing and Scorpion/ARMS methods

Therapeutic responses of lung adenocarcinoma patients to tyrosine kinase inhibitors (TKIs) of epidermal growth factor receptor (EGFR) are closely associated with activating mutations within the EGFR tyrosine kinase domain. Screening activating EGFR mutations prior to selection for therapeutic strategy has been considered extremely valuable for clinical management of lung adenocarcinoma patients in Asian countries including Taiwan, where the EGFR mutation rate is higher than in the rest of the world. Currently there is no consensus on the method of choice to assess EGFR mutations in tumour tissue. We enrolled 445 lung adenocarcinoma patients for analysis of tumour EGFR mutations using polymerase chain reaction (PCR)-direct sequencing, scorpion/amplified refractory mutation system (ARMS) technology and immunohistochemistry with mutation-specific antibodies. Two hundred forty-five patients (245/445; 55%) were found to harbour activating EGFR mutations using PCR-direct sequencing method, with a majority of patients (233/245; 95%) carrying exon 19 deletion or p.L858R point mutations. One hundred three of 200 patients were negative for EGFR mutations from PCR-direct sequencing were further analysed using Scorpion/ARMS technology. Up to 30% of the PCR-direct sequencing negative patients turned out to be positive in the Scorpion/ARMS EGFR mutation tests. For immunohistochemistry analysis of EGFR mutations, the p.E746_A750del specific antibody showed a sensitivity of 57% and a specificity of 100% for exon 19 deletions while the p.L858R point mutation specific antibody showed a sensitivity of 68% and a specificity of 95%. Based on this study, we proposed an algorithm for comprehensive and efficient testing of EGFR mutations on lung adenocarcinoma patients in Asia.

RELATIONSHIP BETWEEN NOVEL POLYMORPHISMS OF THE C5L2 GENE AND CORONARY ARTERY DISEASE

ObjectivesC5L2, a G protein-coupled 7-transmembrane domain complement, has been demonstrated to be a functional receptor of acylation-stimulating protein (ASP), which is a stimulator of triglyceride synthesis or glucose transport. In...

Variability in the Precore and Core Promoter Regions of HBV Strains in Morocco: Characterization and Impact on Liver Disease Progression

BackgroundHepatitis B virus (HBV) is one of the most common human pathogens that cause aggressive hepatitis and advanced liver disease (AdLD), including liver cirrhosis and Hepatocellular Carcinoma. The persistence of active HBV replication and liver damage after the loss of hepatitis B e antigen (HBeAg) has been frequently associated with mutations in the pre-core (pre-C) and core promoter (CP) regions of HBV genome that abolish or reduce HBeAg expression. The purpose of this study was to assess the prevalence of pre-C and CP mutations and their impact on the subsequent course of liver disease in Morocco.Methods/Principal FindingsA cohort of 186 patients with HBeAg-negative chronic HBV infection was studied (81 inactive carriers, 69 with active chronic hepatitis, 36 with AdLD). Pre-C and CP mutations were analyzed by PCR-direct sequencing method. The pre-C stop codon G1896A mutation was the most frequent (83.9%) and was associated with a lower risk of AdLD development (OR, 0.4; 95% CI, 0.15–1.04; p = 0.04). HBV-DNA levels in patients with G1896A were not significantly different from the other patients carrying wild-type strains (p = 0.84). CP mutations C1653T, T1753V, A1762T/G1764A, and C1766T/T1768A were associated with higher HBV-DNA level and increased liver disease severity. Multiple logistic regression analysis showed that older age (≥40 years), male sex, high viral load (>4.3 log10 IU/mL) and CP mutations C1653T, T1753V, A1762T/G1764A, and C1766T/T1768A were independent risk factors for AdLD development. Combination of these mutations was significantly associated with AdLD (OR, 7.52; 95% CI, 4.8–8; p<0.0001).ConclusionsThis study shows for the first time the association of HBV viral load and CP mutations with the severity of liver disease in Moroccan HBV chronic carriers. The examination of CP mutations alone or in combination could be helpful for prediction of the clinical outcome.

Study of the correlation between H-ras mutation and primary hepatocellular carcinoma

The aim of this study was to investigate the correlation between H-ras mutation and primary hepatocellular carcinoma (HCC) and to describe the role of H-ras mutation in carcinogenesis. Clinical samples of 69 patients were collected and the expression levels of H-ras in HCC and the surrounding normal tissues were examined using HotStarTaq PCR. H-ras mutation was further analyzed using the PCR direct sequencing method. The results showed that H-ras mutation was present in 49 samples (49/69, 71.01%), of which 19 had codon 40 mutated from CTA to CTG and 30 had codon 61 mutated from GGC to AGC. By contrast, only 2 mutations were found in the normal tumor-adjacent tissues. The H-ras mutation rate in the high-risk of metastatic recurrence group was markedly higher than that in the low-risk group (P<0.01). The H-ras mutation rate in patients with metastatic recurrence during postoperative follow-up was also significantly higher than that in patients without metastatic recurrence (P<0.01). Based on the above results, the H-ras mutation frequency in cancer tissues is markedly higher compared with that in normal tissues. H-ras mutation may play an important role in the genesis and development of HCC and may serve as a reliable marker for individual comprehensive therapy in HCC.

The Spectrum of α- And β-Thalassemia Mutations in Yunnan Province of Southwestern China

The aim of this study was to investigate the spectrum of thalassemia mutations in Yunnan Province, Southwestern China. We detected 450 thalassemia patients and carriers by multiplex gap polymerase chain reaction (gap-PCR), PCR reverse dot-blot hybridization and direct sequencing methods in 535 suspected patients. Four types of α-thalassemia (α-thal) mutations, – –SEA (59.2%), –α3.7 (rightward) (19.0%), Hb Constant Spring [Hb CS, α142, Term→Gln, TAA>CAA (α2), αCSα] (15.5%), and –α4.2 (leftward) (6.34%) were detected. Six types of β-thal mutations, the most prevalent being Hb E [β26(B8)Glu→Lys, GAG>AAG or codon 26 (G>A)] (30.5%), followed by codon 17 (A>T) (20.8%), codons 41/42 (−TCTT) (17.5%), IVS-II-654 (C>T) (17.2%), −28 (A>G) (6.95%), and codons 71/72 (+A) (2.42%) were also detected. Other rare mutations were codons 27/28 (+C), IVS-I-1 (G>T), Hb New York [β113(G15)Val→Glu, GTG>GAG], Hb D-Los Angeles [β121(GH4)Glu→Gln, GAA>CAA], codon 5 (–CT), Hb G-Taipei [β22(B4)Glu→Glu (GAA>GGA)], Hb J-Lome [β59(E3)Lys→Asn (AAG>AAC)], Hb J-Bangkok [β56(D7)Gly→Asp (GGC>GAC)], IVS-I-2 (T>C), and −31 (A>C). In this study, we provide a complete mutation spectrum of α- and β-thal mutations and a valuable strategy for accurate molecular diagnostic testing in Yunnan Province, People’s Republic of China (PRC).

Mutations within enhancer II and BCP regions of hepatitis B virus in relation to advanced liver diseases in patients infected with subgenotype B3 in Indonesia

Studies on the characteristics of mutations within the hepatitis B virus (HBV) genome, their roles in the pathogenesis of advanced liver diseases, and the involvement of host properties of HBV-infected individuals have not been conducted in subgenotype B3-infected populations. For addressing this issue, 40 cases with HBV surface antigen (HBsAg)-positive advanced liver diseases, including advanced liver cancer and cirrhosis (male 31, female 9, age 54.4 ± 11.6-year-old), were collected and compared with 109 cases with chronic hepatitis B (male 71, female 38, age 38.0 ± 13.4-year-old). Mutations in enhancer II (Enh II) and basal core promoter (BCP)/precore regions were analyzed by PCR-direct sequencing method. HBV viral load was examined by real-time PCR. For all examined regions, the prevalence of mutation was significantly higher in cases with advanced liver diseases. Multivariate analysis showed that, in patients older than 45 years, C1638T and T1753V mutations constituted independent risk factors for the advancement of liver diseases. The presence of C1638T and T1753V mutations may serve as predictive markers for the progression of liver diseases in Indonesia and other countries, where subgenotype B3 infection is prevalent.

Relationship between a novel polymorphism of the C5L2 gene and coronary artery disease

BackgroundC5L2 has been demonstrated to be a functional receptor of acylation-stimulating protein (ASP), which is a stimulator of triglyceride synthesis or glucose transport. However, little is known about the variations...

A Novel Locus for Congenital Simple Microphthalmia Family Mapping to 17p12-q12

To investigate the etiology in a family with autosomal-dominant congenital simple microphthalmia of Chinese origin. A whole-genome scan was performed by using 382 microsatellite DNA markers after the exclusion of reported candidates linked to microphthalmia. Additional fluorescent markers were genotyped for fine mapping. To find out the novel predisposing gene, 14 candidate genes including CRYBA1 and NCOR1 were selected to screen for the mutation by the PCR direct-sequencing method. Genome-wide single-nucleotide polymorphism (SNP) genotyping was performed to find out the pathogenetic copy number variation, as well. The most statistically significant linkage results were obtained at D17S1824 (maximum LOD score, 4.97, at recombination fraction 0.00). Haplotype analyses supported the location of the disease-causing gene to a 21.57-cM interval between loci D17S900 and D17S1872 of chromosome 17, region p12-q12. However, no mutation or CNV (copy number variation) was identified to be responsible for the microphthalmia phenotype of this pedigree. A novel suggestive linkage locus for congenital microphthalmia was detected in a Chinese family. This linkage region provides a target for susceptibility gene identification.

Sequence variation of Epstein-Barr virus (EBV) BZLF1 gene in EBV-associated gastric carcinomas and nasopharyngeal carcinomas in Northern China

Epstein-Barr virus (EBV) BZLF1 gene can trigger EBV from latent infection to lytic replicative phase. The functions of BZLF1 are well known, while little is known about its gene polymorphism. In order to elucidate the sequence variations of BZLF1 and its association with malignancies, we analyzed BZLF1 gene in 24 EBV-associated gastric carcinomas, 41 nasopharyngeal carcinomas and 24 throat washing samples from healthy donors in Northern China using PCR-direct sequencing method. Three types and 8 subtypes of BZLF1 were identified. A dominant type BZLF1-A was found in 67 of 89 (75.3%) isolates. Type BZLF1-B was characterized by a common Ala deletion at residue 127, which was detected in 21 of 89 isolates (23.6%). Type BZLF1-C contained only one isolate (GC103), which had the same sequence with the prototype B95-8. Among 3 functional domains of BZLF1 protein, the transactivation domain had most mutations, followed by the bZIP domains (the DNA binding domain and dimerization domain). No prevalence of any subtypes or mutations in the functional domains among three specimen groups was found ( P > 0.05). Our study indicates that BZLF1 subtypes and amino acid changes in functional domains are not preferentially associated with EBV-associated gastric carcinomas or nasopharyngeal carcinomas in Northern China. BZLF1 gene variations are geographically restricted rather than tumor-specific polymorphisms.