Polymerase Chain Reaction-denaturing High-performance Liquid Chromatography Research Articles

The prevalence of BRCA1/2 mutations of triple-negative breast cancer patients in Xinjiang multiple ethnic region of China.

BackgroundThe screening of BRCA1 and BRCA2 mutations is now an established component of risk evaluation and management of familial breast cancer, early-onset breast cancer and bilateral breast cancer patients. There is still some controversy about whether this screening should be done in triple-negative breast cancers. Therefore, we evaluated the BRCA mutation prevalence in patients with triple-negative breast cancer in a multi-ethnic region of China.MethodsA total 96 women who were diagnosed with triple-negative breast cancer in the Xinjiang region of China were enrolled in this study. BRCA1 and BRCA2 screening was performed by polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC) sequencing analysis. All mutations were confirmed with direct sequencing.ResultsThe prevalence of a BRCA1/2 germline mutation was about 25% (24/96) in the Xinjiang region of China. Among 35 selected cases with a family history and/or bilateral breast cancers, the BRCA1/2 mutation prevalence was 25.7% (9/35). Of the remaining 61 patients with unselected triple-negative breast cancer, the BRCA1/2 mutation prevalence was 24.6% (15/61), and all 15 individuals with these mutations were premenopausal patients.ConclusionsThese results suggest that premenopausal women with triple-negative breast cancer may be candidates for genetic testing for BRCA1/2 in the Xinjiang region of China, even in the absence of a family history or bilateral breast cancer.

Association of sterol regulatory element binding protein-1c genetic polymorphisms rs2297508 and rs11868035 with type 2 diabetes mellitus in Gansu Han and Dongxiang population

To assess the association between single nucleotide polymorphisms (SNP) rs2297508 and rs11868035 of sterol regulatory element binding protein-1c (SREBP-1c) gene and type 2 diabetes mellitus (T2DM) in Han and Dongxiang populations in Gansu. A total of 342 patients with T2DM and 343 healthy controls of Han ethnics and 218 patients with T2DM and 238 healthy controls of Dongxiang ethnics were enrolled during 2006 and 2009. Genotypes of rs2297508 and rs11868035 were determined by polymerase chain reaction-denaturing high performance liquid chromatography (PCR-DHPLC). Plasma levels of lipid, glucose and insulin in all subjects were assayed by biochemical techniques. Chi-square test was used for data analysis. The genotypic and allelic frequencies of rs2297508 and rs11868035 polymorphisms did not differ significantly in the control groups of Han and Dongxiang ethnics (P> 0.05). But those of T2DM patients were significantly higher than in the controls (P< 0.01). Plasma low density lipoprotein cholesterol (LDL-C) levels for carriers of C allele for rs2297508 were significantly higher than those of non-carriers from the control group of Han ethnics (P<0.05). That of carriers of CC genotypes for rs11868035 was significantly higher than carriers of GG genotype in the control group of Dongxiang ethnics (P<0.05). SNP rs2297508 and rs11868035 of SREBP-1c gene may be associated with T2DM, and C allele appears to be a risk factor for T2DM in Gansu Han or Dongxiang ethnics. Han and Dongxiang ethnics did not differ significantly in terms of genotypic and allelic frequencies for the two SNPs. SNP rs2297508 of SREBP-1c gene may be associated with increased plasma levels of LDL-C in both Han or Dongxiang ethnics.

Molecular alterations of isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) metabolic genes and additional genetic mutations in newly diagnosed acute myeloid leukemia patients

BackgroundIsocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) metabolic genes encode cytosolic and mitochondrial enzymes that catalyze the conversion of isocitrate to α-ketoglutarate. Acquired somatic mutations of IDH1 and IDH2 have recently been reported in some types of brain tumors and a small proportion of acute myeloid leukemia (AML) cases.MethodsTwo-hundred and thirty newly diagnosed AML patients were analyzed for the presence of IDH1 and IDH2 heterozygous mutations by polymerase chain reaction-denaturing high performance liquid chromatography (PCR-DHPLC) followed by direct sequencing. Clinical and biological characteristics were analyzed and correlated to the IDH mutational status. Coexisting mutations such as FLT3, PML-RARA, RAS, AML1, and NPM1 mutations were additionally explored.ResultsThe prevalence of IDH1 and IDH2 mutations was 8.7% (20/230) and 10.4% (24/230), respectively. Six missense mutations were identified among IDH1-mutated cases; p.R132H (n = 8), p.R132C (n = 6), p.R132S (n = 2), p.R132G (n = 2), p.R132L (n = 1), and p.I99M (n = 1). Two missense mutations were found in IDH2-mutated cases; p.R140Q (n = 20) and p.R172K (n = 4). No patients had dual IDH1 and IDH2 mutations. About 18% of AML with normal cytogenetics and 31% of acute promyelocytic leukemia had IDH mutations. Half of the IDH-mutated cohort had normal karyotype and the major FAB subtype was AML-M2. Interestingly, IDH1- and IDH2-mutated cases predominantly had NPM1 mutations (60-74%) as compared to the wild type (P < 0.001). Very few IDH-mutated cases had FLT3 and/or RAS abnormalities and none of them had AML1 mutations. Older age and higher median platelet counts were significantly associated with IDH2 mutations although the clinical impact of either IDH1 or IDH2 mutations on patients' overall survival could not be observed.ConclusionOverall, 19% of newly diagnosed AML patients had alterations of IDH genes. No patients concurrently carried both IDH1 and IDH2 mutations suggesting that these mutations were mutually exclusive. NPM1 mutation appears as a major coexisting genetic mutation in IDH-mutated patients. Our present data failed to support the prognostic relevance of IDH mutations although alterations of these metabolic genes potentially have an important role in leukemia development.

The CRISPLD2 gene is involved in cleft lip and/or cleft palate in a Chinese population

Nonsyndromic cleft lip and/or cleft palate (NSCLP) are common congenital anomalies in humans, the etiologies of which are complex and associated with both genetic and environmental factors. Previous data suggested single nucleotide polymorphisms (SNPs) of rs1546124, rs4783099, and rs16974880 of the CRISPLD2 gene were associated with an increased risk of NSCLP; however, subsequent studies have yielded conflicting results. This study aims to evaluate the associations of the aforementioned polymorphisms with NSCLP in a Northwestern Chinese population. Three CRISPLD2 SNPs were genotyped in a case-control study (n = 907), including 444 NSCLP patients and 463 healthy individuals, using polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC). The genotype and allele frequencies of rs1546124 (odds ratio [OR], 2.30; 95% confidence interval [CI], 1.58-3.34; p = 1 × 10(-5) ) and rs4783099 (OR, 0.73; 95% CI, 0.54-1.00; p = 0.05) were different in NSCLP patients compared with controls. Furthermore, the CC genotype at rs1546124 was associated with increased risk for cleft lip with or without cleft palate (CL/P; OR, 2.11; 95% CI, 1.41-3.15; p(correct) = 1.5 × 10(-4) ) and for cleft palate only (CPO; OR, 2.93; 95% CI, 1.69-5.07; p(correct) = 5.4 × 10(-4) ), whereas the T allele of rs4783099 was associated with decreased risk for CPO. Further gender stratification showed that the statistical association of these two loci is mainly in the male patients, and not in female patients. Our results suggest that the CRISPLD2 gene contributes to the etiology of NSCLP in the Northwestern Chinese population. SNP rs1546124 is significantly related to NSCLP, associated with both CL/P and CPO groups, and SNP rs4783099 is significantly associated with CPO.

A new familial gastric cancer-related gene polymorphism: T1151A in the mismatch repair gene hMLH1

We designed to understand the effects of the T1151A gene polymorphism in the hMLH1 gene on the pathogenesis of familial gastric cancer. Peripheral blood DNA from 113 patients with familial gastric cancer or suspected familial gastric cancer that were newly identified in the same year, along with 180 healthy subjects, was subjected to polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC) and DNA sequencing of exon 12 in the hMLH1 gene. Our results as following, the T1151A detection rate was remarkably higher in patients with familial gastric cancer or suspected familial gastric cancer compared to normal control patients (P < 0.05). Stratified analysis showed that there was a significant difference in the detection rate between the control group and elderly patients whose age of onset was greater than 50 years old (P < 0.05). The detection rate of patients from high-risk families were relatively high (P < 0.05). An especially significant distribution was observed in patients who had suffered precancerous diseases related to gastric cancer (P < 0.01). In conclusion, familial gastric carcinoma families in China carrying the T1151A polymorphism may have a higher risk of suffering from gastric cancer. This gene polymorphism can be used as a candidate screening index for high-risk populations.

Mutation spectrum of the fibrillin‐1 (FBN1) gene in Taiwanese patients with Marfan syndrome

The aim of this study was to establish a national database of mutations in the fibrillin-1 (FBN1) gene that cause Marfan syndrome (MFS) in the Taiwanese population. In this study, we screened 294 patients from 157 families for the presence of FBN1 mutations using polymerase chain reaction/ denaturing high performance liquid chromatography (PCR/DHPLC). We identified 56 mutations in 62 of the 157 (40%) families including 49 single-base substitutions (36 missense mutations, seven nonsense mutations, and six splicing sites), one small insertion, four small deletions, one small indel (insertion and deletion), and one exonic deletion (Exon 36). When family history was taken into consideration, the mutation detection rate rose to 91% (29 of 32). We further investigated the phenotypic data and found that one third (47 of 157) of the families fit the Ghent criteria for MFS. Based on that data, the mutation rate was 98% (46/47). That finding implies that family history and the Ghent criteria play a more important role than clinical manifestations in establishing a clinical diagnosis of Marfan syndrome. Among the 56 mutations found in this study, 40 (71%) have not been registered in the Human Gene Mutation Database (HGMD) or in the Universal Mutation Database (UMD). This is the first study of the mutation spectrum of MFS in a cohort of patients in Taiwan. The database is expected to considerably improve genetic counseling for and medical care of MFS families.

Association of sterol regulatory element-binding protein-1c gene polymorphism with type 2 diabetes mellitus, insulin resistance and blood lipid levels in Chinese population

Aims The sterol regulatory element-binding protein (SREBP)-1c gene has been identified as a susceptibility gene in metabolic diseases such as type 2 diabetes mellitus (T2DM), obesity, dyslipidemia and insulin resistance. Previous studies suggest that SNP17 (rs2297508, exon18c and G952G) of SREBP-1c gene and a common SREBP-1c SNP6 (rs11868035) are associated with an increased risk of T2DM. The present study aimed to confirm the previously reported association in a Chinese population and to examine the two SREBP-1c SNPs for their associations with insulin resistance and blood lipid. Methods We genotyped two SREBP-1c SNPs in a case–control study ( n = 327) from Chinese, including 156 patients with T2DM and 171 healthy controls, using polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC) and tested for association with type 2 diabetes, insulin resistance and blood lipid, respectively. Genotype and allele distributions and haplotype construction were analysed. Results The genotype and allele distributions of rs2297508 and rs11868035 polymorphisms were significantly different in type 2 diabetic patients compared to controls ( P = 0.002 and P = 0.013; 0.00 and 0.001, respectively). Haplotype analyses showed significant association with diabetes risk and confirmed the results of the single SNP analyses. The plasma levels of LDL-c of the minor allele-C carriers of the two SNPs were both significantly higher than the noncarriers in the control group ( P < 0.05). Furthermore, insulin resistance index (HOMA-IRI) of the rare homozygotes C/C of rs11868035 was significantly lower than that of T/T in the T2DM group ( P < 0.05). Conclusions These findings indicate that the SREBP-1c SNPs rs2297508 and rs11868035 are associated with a significantly increased risk of T2DM and dyslipidemia in the Chinese population. Moreover, the SNP (rs11868035) is closely related to insulin resistance (IR) in diabetic patients.

Genotype–phenotype correlations analysis of mutations in the phenylalanine hydroxylase (PAH) gene

The aims of our research were to define the genotype-phenotype correlations of mutations in the phenylalanine hydroxylase (PAH) gene that cause phenylketonuria (PKU) among the Israeli population. The mutation spectrum of the PAH gene in PKU patients in Israel is described, along with a discussion on genotype-phenotype correlations. By using polymerase chain reaction/denaturing high-performance liquid chromatography (PCR/dHPLC) and DNA sequencing, we screened all exons of the PAH gene in 180 unrelated patients with four different PKU phenotypes [classic PKU, moderate PKU, mild PKU, and mild hyperphenylalaninemia (MHP)]. In 63.2% of patient genotypes, the metabolic phenotype could be predicted, though evidence is also found for both phenotypic inconsistencies among subjects with more than one type of mutation in the PAH gene. Data analysis revealed that about 25% of patients could participate in the future in (6R)-L: -erythro-5, 6, 7, 8-tetrahydrobiopterin (BH4) treatment trials according to their mutation genotypes. This study enables us to construct a national database in Israel that will serve as a valuable tool for genetic counseling and a prognostic evaluation of future cases of PKU.

PCR-DHPLC를 이용한 한국인 제2형 당뇨환자의 GCK와 HNF-1α의 유전자다형성 분석

MODY는 일반적으로 제 2 형 당뇨의 특수형으로 25세 이전에 발병하며 상염색체 우성으로 유전되 며 인슐린 분비장애를 특징으로 한다. GCK와 HNF-1α의 유전자 돌연변이는 제 2 형 당뇨에서 가장 큰 원인 중에 하나이다. 따라서 이들 유전자다형성의 연관성을 다양한 분석 방법으로 연구할 필요성이 대두되고 있다. GCK와 HNF-1α 유전자의 exon과 exon에 근접한 intron을 실험하였고, 또한 promotor까지 PCR-DHPLC (Polymerase Chain Reaction - Denaturing High Performance Liquid Chromatography) 방법과 direct sequencing 방 법을 사용하였다. 시료는 11명의 환자와 20명의 정상인에서 DNA를 추출하였고 GCK와 HNF-1α의 단일 염기 다형성을 PCR-DHPLC 방법으로 확인하였다. 결과적으로 GCK 유전자에서는 1개(R135G)를 검출하였고 HNF-1α 유전자에서는 2개(I27L, S487N)를 검출하였으며 intron 8에서도 돌연변이를 검출할 수 있었다. Maturity-onset diabetes of the young (MODY) is a genetically heterogeneous subtype of Type 2 diabetes characterized (non-insulin-dependent) by early onset, usually before 25 years of age, autosomal dominant inheritance and a primary defect in insulin secretion. Mutations in the glucokinase (GCK) and hepatocyte nuclear factor (HNF)-1α genes are the major causes of monogenic forms of Type 2 diabetes mellitus. Therefore it is need to study relation with these polymorphisms by diverse analysis methods. The promotor and coding regions inclusive intron exon boundaries of the GCK, HNF-1α genes were examined by PCR-DHPLC (Polymerase Chain Reaction - Denaturing High Performance Liquid Chromatography) and direct sequencing. We extracted DNA from 11 patients and 20 normals. Then we confirmed a single-nucleotide polymorphism using PCR-DHPLC. As results, we identified one mutation (R135G) in GCK gene and two mutations (I27L, S487N) in HNF-1a and at the same time detected mutation in intron 8.

Vascular endothelial growth factor gene polymorphisms and risk of colorectal cancer

4123 Background: Angiogenesis is closely related to the development, growth, and metastasis of solid tumors, including colorectal cancer (CRC), and the vascular endothelial growth factor (VEGF) is known to be a potent pro-angiogenic factor. Accordingly, the present study was conducted to evaluate the potential association between two VEGF polymorphisms (+405G &gt; C, and 936C &gt; T) and the risk of CRC. Methods: The VEGF genotypes were determined using fresh colorectal tumor tissue from 477 patients with CRC who underwent surgical resection and peripheral blood lymphocytes from 413 healthy controls based on a polymerase chain reaction/denaturing high-performance liquid chromatography (PCR/DHPLC) assay. The incidence of genotypes and haplotypes of two VEGF polymorphisms was compared between the patients with CRC and the controls. Results: The distribution of genotypes and allele frequencies of the 936C &gt; T polymorphism in the CRC group did not differ from those in the control group. However, compared with the combined GC and CC genotype, the GG genotype of +405G &gt; C polymorphism was significantly associated with an increased risk of CRC [odds ratio (OR), 1.575; 95% confidence interval (CI), 1.178–2.104; P = 0.002]. In the haplotype analyses, haplotype +405G / 936C was also associated with a significantly increased risk of CRC (OR, 1.264; 95% CI, 1.043–1.531; P = 0.017), whereas haplotype +405C / 936C was associated with a decreased risk of CRC (OR, 0.818; 95% CI, 0.677–0.989; P = 0.038). None of the VEGF polymorphisms studied significantly influenced the clinical or pathologic features of CRC. Conclusions: These findings suggest that the VEGF +405G &gt; C polymorphism may be associated with the risk of CRC in the Korean population. No significant financial relationships to disclose.

Vascular endothelial growth factor (VEGF) gene polymorphisms associated with prognosis for patients with colorectal cancer

4125 Background: Vascular endothelial growth factor (VEGF) or its family may be considered to play an important role in lymphangiogenesis and lymphatic tumor spread, thereby affecting prognosis of colorectal cancer. Accordingly, the present study analyzed VEGF gene polymorphisms and their impact on the prognosis for patients with colorectal cancer. Patients and Methods: Four hundred and sixty-five consecutive patients with surgically treated colorectal adenocarcinoma were enrolled in the present study. The genomic DNA was extracted from fresh colorectal tumor tissue and 3 VEGF (-2578C &gt; A, -634G &gt; C, and +936C &gt; T) gene polymorphisms determined using a PCR/DHPLC (Polymerase chain reaction/Denaturing high-performance liquid chromatography) assay. Results: The median age of the patients was 64 years (range, 21–89), and 264 (56.7%) patients had colon cancer and 201 (48.2%) patients rectal cancer. Pathologic stages evaluable (n=464) after surgery were as follows: stage I (n=79, 17.0%), stage II (n=157, 33.8%), stage III (n=157, 33.8%), and stage IV (n=71, 15.3%). Multivariate survival analysis including stage, differentiation, and CEA level showed that survival for patients with the -634CC (overall survival [OS]: hazard ratio [HR]=0.175, P&lt;0.001; progression-free survival [PFS]: HR=0.554, P=0.040) or GC genotype (OS: HR=0.158, P&lt;0.001; PFS: HR=0.630, P=0.044) were better than for patients with the -634GG genotype, whereas the +936TT (OS: HR=65.959, P&lt;0.001; PFS: HR=2.823, P=0.016) or CT genotype (OS: HR=16.116, P&lt;0.001; PFS: HR=3.507, P&lt;0.001) were associated with a worse survival compared to the CC genotype. In haplotype analysis, the -2578A/-634G/+936T haplotype exhibited a significantly worse survival when compared to the wild -2578C/-634G/+936C haplotype (OS: HR=4.670, P&lt;0.001; PFS: HR=3.624, P&lt;0.001). Conclusions: VEGF gene polymorphisms were found to be an independent prognostic marker for patients with colorectal cancer. Accordingly, the analysis of VEGF gene polymorphisms can help identify patient subgroups at high risk of a poor disease outcome. No significant financial relationships to disclose.

Germline mutations and polymorphic variants in MMR, E‐cadherin and MYH genes associated with familial gastric cancer in Jiangsu of China

Germline mutations in MSH2, MLH1, E-cadherin and MutY (MYH) genes have been implicated in the occurrence of gastric cancer (GC). Epidemiological investigation was performed by recruiting patients with GC onset during 2002 in Jiangsu province, China. We identified suspected hereditary GC patients based on either the GC family history or GC onset at early ages. We have screened germline variations in 101 suspected hereditary GC patients at the coding sequences of MSH2, MLH1, E-cadherin and MYH genes with polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC) analysis and DNA sequencing. The result showed that about 40% of patients carried germline variations, predominantly with missense mutations. Of the variations detected are 2 base pair substitutions, c.53C > T and c.74G > A, which is predicted to generate missense mutations of p.Pro18Leu and p.Gly25Asp, respectively, and occurred at the same allele of MYH gene. The frequency of variant haplotype T/A in patients was higher than that in the control group (p = 0.021, odds ratio [OR] = 4.43, 95% confidence interval [95% CI] = 1.33-14.72). Difference in the frequency of the silent mutation p.Asn751Asn in E-cadherin gene was also found between patients and controls (p = 0.009, OR = 2.54, 95% CI = 1.30-4.95). Moreover, 6 types of variations were detected in MSH2 and MLH1 genes in 14 of 101 patients. Most of them occurred at exon7 of MSH2, frequently c.1168C > T, resulting in mutation of p.Leu390Phe. In summary, germline mutation at MSH2, MLH1, E-cadherin and MYH genes is a frequent event in the familial GC. They may form a genetic basis for the familial GC susceptibility in Chinese population.

DHPLC의 화학적 특성을 이용한 질병 유전자의 분석 시스템 개발

종양억제유전자(tumor-suppressor gene)는 유방암종과 관련하여 높은 돌연변이 비율로 나타나고 있는 것으로 보고되어지고 있다. p53 유전자는 20kb의 크기를 갖는 유전자로써 인간 염색체의 17p13.1에 위치하고 있다. 본 실험에서는 유방암으로 진단 받고 수술한 환자의 조직 100개와 환자와 전혀 상관없는 정상 조직 103개를 대상으로 DNA를 추출하고 PCR-DHPLC(polymerase chain reaction-denaturing high performance liquid chromatography) 방법으로 단일 염기 다형성을 검출하였다. 또한 컬럼의 충진물질과 DNA의 결합에 의한 분리능을 확인하기 위해 충진물이 다른 컬럼의 단일 염기 다형성을 실험하였다. 그 결과 100개의 유방암 조직 중 exon 5에서 11개(11%)의 C/A, C/G genotype을, exon 8에서 42개(42%) T del genotype을 확인하였다. 103개의 정상 조직에서 exon 5에서 2개(2.9%), exon 8에서 9개(8.7%)의 polymorphism을 확인하였다. 컬럼의 분리능 실험에서는 PS-DVB(poly styrene - divinylbenzene)으로 충진된 컬럼이 C18으로 충진된 컬럼보다 더 좋은 분리능을 보였다. In this study we extracted DNA from 100 tissues of breast cancer patients and 103 normals. Then we confirmed single-nucleotide polymorphism(SNP) using PCR-DHPLC(polymerase chain reaction-denaturing high performance liquid chromatogrphy).Also, we studied SNP of samples using several columns to identify relation between packing materials of column and resolution.As a result, we identified 4 C/A, C/G genotypes(4%) in exon 5 and 37 T del genotypes(37%) in exon 8 among 100 breast cancer tissues and 2 in exon 5, 9 in exon 8 among 103 normal samples.In resolution test, we confirmed that PS-DVB(poly styrene-divinylbenzen) column is more efficient than C18 column.