一种检测kras基因突变的新型TB-ARMS qPCR方法的建立

在荧光定量PCR基础上建立一种简单有效并且高度灵敏的TB-ARMSkras基因突变检测方法,并对其检测性能进行评估,探讨其临床应用价值。针对kras基因8种常见的点突变类型,通过设计并优化突变特异性引物、野生型特异性封闭引物并综合应用突变富集扩增反应条件等多种手段,提高点突变检测的灵敏度和特异性,采用已知野生型基因组样品和构建的突变质粒作为标准品,进行方法学评价;通过对临床样本的检测及与现有商品化试剂盒的比较进行性能验证;通过对术前血浆和配对组织样品的对比检测,评估方法是否适用于血液样本的检测。建立了TB-ARMS kras突变检测的新方法,能检测的最低突变率可达到0.01%。通过综合采用野生型特异性封闭引物和突变富集扩增条件等方法证明了其0.01%的突变检测灵敏度。检测准确性优于现有商品化试剂盒,血浆DNA TB-ARMS qPCR检测结果与配对组织DNA测序结果相符合。因此,TB-ARMS kras基因突变检测方法具有广泛的临床应用价值,既适用于临床组织样品的检测,也可应用于液体活检。     

Suitability of Surgical Tumor Tissues,Biopsy, or Cytology Samples for Epidermal Growth Factor Receptor Mutation Testing in Non–Small Cell Lung Carcinoma Based on Chinese Population

BACKGROUND: Epidermal growth factor receptor (EGFR) mutation status is crucial in treatment selection for non–small cell lung cancer (NSCLC) patients; however, the detection materials’ availability remains challenging in clinical practice. In this study, we collected surgical resection tissues, lymph node biopsy, and cytological samples for EGFR mutation testing and investigated the associations between gene mutation and clinical characteristics. METHODS: Two hundred and seventy-six NSCLC adenocarcinoma specimens were collected, and highly sensitive amplification refractory mutation system method was implemented for EGFR mutation detection, with clinicopathologic characteristics involved in the final analysis. RESULTS: In the total of 276 samples, 96% (265/276) of tumors obtained evaluable EGFR mutation status, the frequency of mutation was 55.8% (148/265) in all specimens, and three different type samples shared a comparable successful testing rate: 97.4% (38/39) in surgical tumor tissues, 100% (108/108) in lymph node biopsy samples, and 92.2% (119/129) in cytological samples. EGFR mutation was significantly associated with sex, smoking history, lymph node metastasis status (N stage), primary tumor size, testing tissues origin, and sample type (P < .05). Multivariate analysis reconfirmed that smoking history and primary tumor size shared significant correlation with EGFR mutation after adjustment. CONCLUSIONS: Both lymph node biopsy and cytological samples were suitable surrogates for EGFR mutation detection in NSCLC compared with tumor tissues, gene status should be detected widely considering the high EGFR mutation rate, and nonsmoking history together with smaller primary tumor size was an independent indicator of EGFR mutation status.     

Correlation exploration among CT imaging,pathology and genotype of pulmonary ground-glass opacity

To analyse the clinical features, imaging manifestation, pathological typing and genetic testing results of patients undergoing surgery for ground-glass opacity (GGO) nodules, and explore the reasonable diagnosis and treatment program for GGO patients as to provide the basis for the establishment of GGO treatment process. This study is an exploratory study. 465 cases with GGO confirmed by HRCT, undergoing surgery and approved by pathologic diagnosis in Shanghai pulmonary hospital were enrolled in this study. All the patients with GGO were cases with single lesion. The relationship between the clinical, imaging, pathological and molecular biological data of single GGO were statistically studied. (1) Among 465 cases, the median age was 58 years and females were 315 (67.7%); there were 397 (85.4%) non-smoking, and 354 cases (76.1%) had no clinical symptoms. There were 33 cases of benign and 432 cases of malignant GGO. Significant differences were observed on the size, vacuole sign, pleural indentation and blood vessel sign of GGO between two groups (p < 0.05). Of 230 mGGO, there were no AAH, 13 cases of AIS, 25 cases of MIA and 173 cases of invasive adenocarcinoma. The probability of solid nodules in invasive adenocarcinoma was higher than that in micro invasive carcinoma, and the difference was statistically significant (p < 0.05). 360 cases were followed up with the average follow-up time of 6.05 months, and GGO of 34 cases (9.4%) increased. (2) In 428 adenocarcinoma samples approved by pathologic diagnosis, there were 262 (61.2%) lesions of EGFR mutation, 14 (3.3%) lesions of KRAS mutation, 1 (0.2%) lesion of Braf mutation, 9 (2.1%) lesions of EML4-ALK gene fusion and 2 (0.5%) lesions of ROS1 fusion. The detection rate of gene mutation in mGGO was higher than that of pGGO. During the follow-up period, genetic testing results of 32 GGO showed that EGFR mutation rate was 53.1%, ALK positive rate of 6.3%, KRAS mutation rate of 3.1% and no ros1 and BRAF gene mutation. No statistically significant difference was observed in comparison with unchanged GGO. (3) EGFR mutation rate of invasive adenocarcinoma was the highest (168/228, 73.7%), mainly in the 19Del and L858R point mutations. No KRAS mutation was found in atypical adenoma hyperplasia. No significant difference was observed on the mutation rate of KRAS between different types of GGO (p = 0.811). EML4-ALK fusion gene was mainly detected in invasive adenocarcinoma (7/9). GGO tends to occur in young, non-smoking women. The size of GGO is related to the degree of malignancy. Pleural depression sign, vacuole sign and vascular cluster sign are all characteristic images of malignant GGO. pGGO and mGGO reflect the pathological development of GGO. During the follow-up, it is found that GGO increases and solid components appear, which is the indication of surgical resection. The detection rate of EGFR mutations in mGGO and invasive adenocarcinoma is high. pGGO has heterogeneity in imaging, pathology and molecular biology. Heterogeneity research helps to formulate correct individualized diagnosis and treatment plans.     

The Prothrombin 20209C>T Sequence Variant: To Test or Not to Test

Only one mutation in the prothrombin gene (Factor II), 20210G>A, has been definitively associated with an increased risk for venous thrombosis. Using hybridization probe analysis for mutation detection on the LightCycler (Roche Molecular Biochemicals), we identified seven patient samples with atypical melt curve patterns. Sequence analyses of each of these samples revealed heterozygosity for a C to T transition at position 20209. As in other reported cases, each of the apparently unrelated patients was of African-American descent, suggesting that the variant is population specific. Two patients were referred for testing due to a history of stroke, one with a right major coronary artery embolic stroke and the other with a right cerebellar stroke. A third patient had chronic renal failure secondary to hypertension with a reported family history of renal failure. Three patients had a history of multiple pregnancy losses. The last patient had a kidney transplant for end stage renal disease secondary to glomerulonephritis. She was being evaluated for a second transplant, but to our knowledge, had a negative history of venous thrombosis. The prevalence and the clinical significance of the prothrombin 20209C>T mutation is unknown. Recently reported functional studies revealed conflicting results. The clinical utility of testing for and reporting this variant remains unresolved.     

From clinical and biochemical to molecular genetic diagnosis of Wilson disease in Latvia

Wilson disease (WD) is an autosomal recessive disorder of copper metabolism characterized by hepatic and/or neurological damage. More than 300 mutations in gene ATP7B causing this defect have been reported. The data on correlation between WD patient genotypes and clinical presentation are controversial. In this paper, the results of ATP7B mutation analysis by testing for mutation H1069Q and direct sequencing of six exons together with the clinical data of 40 Latvian WD patients are presented. Two previously described and two novel mutations as well as one previously reported polymorphism were identified. The H1069Q mutation was present at 52.5% of the disease alleles. One individual among 157 healthy Latvians was also found to be a mutation H1069Q carrier. The estimated incidence of WD in Latvia is ∼1 in 25600. Wide clinical variability was observed among individuals with the same ATP7B genotype, thus supporting the suggestion that modifying factors play an additional role in the pathogenesis of WD. An algorithm for the diagnosis of WD, including testing for mutation H1069Q, is recommended for the populations where mutation H1069Q accounts for 50% of WD alleles or more. The text was submitted authors English.     

Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene.

The amplification refractory mutation system (ARMS) is a simple, rapid and reliable method for the detection of any mutation involving single base changes or small deletions. We have applied ARMS methodology to the detection of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Single ARMS tests have been developed for 11 CFTR mutations found in the northwest of England. ARMS reactions for the most common mutations have been multiplexed to give a test which will detect the presence of the delta F508, G551D, G542X, and 621 + 1G----T mutations in a DNA sample. The multiplex test has been validated by the analysis of over 500 previously genotyped samples and has been found to be completely accurate. The rapid detection of the most common mutations has enabled early molecular confirmation of suspected cystic fibrosis in neonates, rapid typing of cystic fibrosis patients and their relatives, and testing of sperm and egg donors.     

Familial mitochondrial encephalomyopathy (MERRF): genetic, pathophysiological, and biochemical characterization of a mitochondrial DNA disease

A large MERRF pedigree permitted the direct testing of the predictions for a mitochondrial DNA (mtDNA) mutation. A mtDNA mutation was demonstrated by proving maternal inheritance and by identifying specific deficiencies in muscle energetics and mitochondrial respiratory complexes I and IV. mtDNA heteroplasmy (a mixture of mutant and wild-type mtDNAs) was demonstrated by showing variation in the mitochondrial energetic capacity between family members. The phenotypic consequences of differential tissue-specific reliance on mitochondrial ATP was shown by correlating individual respiratory deficiency with the nature and severity of patients' clinical manifestations. The observed spectrum of clinical manifestations resulting from this heteroplasmic mtDNA mutation implies that mtDNA disease may be much more prevalent than previously anticipated.     

Detection of mutations in human DNA

Efficient methods for the detection of mutations are of fundamental importance in research and in diagnostics. By detection of a DNA sequence alteration that cosegregates with a clinical phenotype in an affected family, the gene at fault may be identified and assigned a function. Mutation detection methods are also a rate-limiting factor for the clinical application of DNA diagnostics. Currently a large number of techniques are in use to scan for new mutations and to distinguish among previously established sequence variants. Here, some of the problems connected with mutation detection are discussed together with principles on which current and future mutation detection assays can be based.     

晚期NSCLC患者血液EGFR基因检测研究进展

目的:随着表皮生长因子受体酪氨酸酶抑制剂(epidermal growth factor receptor-tyrosine kinase inhibitor,EGFR-TKI)在非小细胞肺癌(Non-Small Cell Lung Cancer,NSCLC)治疗中的应用,患者的生活质量及生存期均有很大程度的提高,但是,组织表皮生长因子受体(epidermal growth factor receptor,EGFR)检测结果为能否接受EGFR-TKI治疗的先决条件,而晚期肺癌患者却因组织量少、质量不佳、组织异质性无法进行检测,血液EGFR检测便应运而生,本研究将综述晚期非小细胞肺癌(Non-Small Cell Lung Cancer,NSCLC)患者血液EGFR基因检测研究。方法:检索Pub-med、SCI、Medline及中国生物文献数据库中晚期非小细胞肺癌患者血液EGFR基因检测的相关研究。结果:对于晚期NSCLC患者,血液EGFR基因检测有较高的敏感度与特异度,并且能够较好的预测患者对EGFR-TKI的疗效以及进行耐药监测。结论:当组织获取困难及质量不佳时,血液可替代组织行EGFR基因检测。     

Current status and future potential of somatic mutation testing from circulating free DNA in patients with solid tumours

Genetic alterations can determine the natural history of cancer and its treatment response. With further advances in DNA sequencing technology, multiple novel genetic alterations will be discovered which could be exploited as prognostic, predictive and pharmacodynamic biomarkers in the development and use of cancer therapeutics. As such, the importance in clinical practice of efficient and robust somatic mutation testing in solid tumours cannot be overemphasized in the current era of personalized medicine. However, significant challenges remain regarding the testing of genetic biomarkers in clinical practice. Reliance on archived formalin fixed, paraffin embedded tumour, obtained from diagnostic biopsies, for testing somatic genetic alterations could restrict the scientific community in asking relevant questions about a patient’s cancer biology. Problems inherent with using formalin fixed, archival tissue are well recognized and difficult to resolve. It could be argued that to achieve rapid and efficient incorporation of genetic biomarkers into clinical practice, somatic mutation testing in cancer patients should be simpler, less invasive using a readily available clinical sample, whilst maintaining robustness and reproducibility. In this regard, use of circulating free DNA (cfDNA) from plasma or serum as an alternative and/or additional source of DNA to test cancer specific genetic alterations is an attractive proposition. In light of encouraging results from recent studies, this mini review will discuss the current role and future potential of somatic mutation testing from circulating or cell free DNA derived from the blood of patients with solid tumours.     

A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands

Cowden syndrome (CS) and Bannayan-Riley-Ruvalcaba syndrome are allelic, defined by germline PTEN mutations, and collectively referred to as PTEN hamartoma tumor syndrome. To date, there are no existing criteria based on large prospective patient cohorts to select patients for PTEN mutation testing. To address these issues, we conducted a multicenter prospective study in which 3042 probands satisfying relaxed CS clinical criteria were accrued. PTEN mutation scanning, including promoter and large deletion analysis, was performed for all subjects. Pathogenic mutations were identified in 290 individuals (9.5%). To evaluate clinical phenotype and PTEN genotype against protein expression, we performed immunoblotting (PTEN, P-AKT1, P-MAPK1/2) for a patient subset (n = 423). In order to obtain an individualized estimation of pretest probability of germline PTEN mutation, we developed an optimized clinical practice model to identify adult and pediatric patients. For adults, a semiquantitative score-the Cleveland Clinic (CC) score-resulted in a well-calibrated estimation of pretest probability of PTEN status. Overall, decreased PTEN protein expression correlated with PTEN mutation status; decreasing PTEN protein expression correlated with increasing CC score (p < 0.001), but not with the National Comprehensive Cancer Network (NCCN) criteria (p = 0.11). For pediatric patients, we identified highly sensitive criteria to guide PTEN mutation testing, with phenotypic features distinct from the adult setting. Our model improved sensitivity and positive predictive value for germline PTEN mutation relative to the NCCN 2010 criteria in both cohorts. We present the first evidence-based clinical practice model to select patients for genetics referral and PTEN mutation testing, further supported biologically by protein correlation.     

Genetic testing for women previously diagnosed with breast/ovarian cancer: examining the impact of BRCA1 and BRCA2 mutation searching

This study sought to investigate the impact of BRCA1 and BRCA2 mutation searching on women previously diagnosed with breast or ovarian cancer. In-depth interviews were undertaken with 30 women who had undergone a BRCA1 and BRCA2 mutation search within the clinical setting. The main reasons reported for undergoing mutation searching were: to provide genetic information for other family members, general altruism, curiosity about the aetiology of cancer, and to provide information to facilitate risk management decisions. In the main, the process of undergoing genetic testing was not experienced as anxiety provoking. The benefit of receiving a result confirming the presence of a genetic mutation was seen as an end to uncertainty, whereas the costs included difficulties in disclosing information to kin and potentially increased anxiety about one's own or others' cancer risks. Women receiving an inconclusive test result reported a range of emotional reactions. There was evidence that some women misunderstood the meaning of this result, interpreting it as definitive confirmation that a cancer-predisposing mutation was not present within the family. It is concluded that women with cancer who participate in BRCA1 and BRCA2 testing need to receive clear information about the meaning and implications of the different types of test results. Some recommendations for clinical practice are discussed.     

结节性硬化症伴癫痫患儿临床特征和基因型分析

摘要 目的：探讨结节性硬化症（TSC）伴癫痫患儿的临床特征和基因型特点,旨在了解 TSC伴癫痫患儿的临床表现,以及表型与基因型的相关性,为临床诊治提供更有效的方案。方法：回顾性分析 2019年 12月至 2021年 1月安徽省儿童医院神经内科收治的 10例 TSC伴癫痫患儿的临床表现,采用芯片捕获高通量测序以及 Sanger测序验证,对 TSC伴癫痫患儿及父母进行基因检测,分析其临床及遗传变异的特征。结果：10例中男性 4例,女性 6例,首次发作痉挛 3例,局灶性 7例,70.00%首发年龄小于 1岁。临床表现：90.00%皮肤病变,80.00%心脏横纹肌瘤,20.00%眼底异常,未见肾脏、肝脏、肺脏病变。视频脑电图显示 60.00%痫样波位于额颞区,100.00%伴神经影像学皮层 /皮层下异常,90.00%双侧室管膜 /室管膜下异常,10.00%室管膜下巨细胞星形细胞瘤。研究患儿均完善基因检测,3例为 TSC1基因突变,7例为 TSC2突变,包括错义、移码及剪接位点突变,2例检测出家族变异,7例均未检测出家族变异。结论：TSC伴癫痫患儿男女发病无明显差异性,散发病例多见,发病年龄多为 1岁内,首次发作常为局灶性。视频脑电图痫样波额颞区为主,头颅影像学多为皮层 /皮层下及双侧室管膜 /室管膜下异常。TSC2突变较 TSC1突变常见,临床表现严重,痉挛发生率高,发病年龄小,多控制不佳。早期基因检测,对于发病年龄小,疗效欠佳患儿尤为重要。     

A simple PCR-based assay allows detection of a common mutation, IVS8-1G-->C, in DHCR7 in Smith-Lemli-Opitz syndrome

Smith-Lemli-Opitz syndrome (SLOS) is an autosomal recessive multiple malformation disorder. A deficiency of the enzyme 7-dehydrocholesterol delta 7-reductase (DHCR7) is the primary abnormality in SLOS. The gene encoding DHCR7 has been cloned, and we have identified a mutation affecting the splice acceptor site 5' of exon 9 that occurs frequently in affected individuals. We developed a novel PCR-based assay to detect this common mutation in DHCR7. Using this assay, heterozygosity was detected for this mutation in 18 of 26 and homozygosity in 1 of 26 unrelated affected individuals. The high frequency of this mutation is suggestive of either a founder effect in our group of patients or a mutational hotspot. The simplicity and reliability of this assay will allow it to be used as a clinical test to aid in diagnosis of atypical cases, in carrier testing, in prediction of prognosis based on genotype, and in prenatal molecular genetic diagnostic testing.     

Real-time PCR genotyping using displacing probes

Simple and reliable genotyping technology is a key to success for high-throughput genetic screening in the post-genome era. Here we have developed a new real-time PCR genotyping approach that uses displacement hybridization-based probes: displacing probes. The specificity of displacing probes could be simply assessed through denaturation analysis before genotyping was implemented, and the probes designed with maximal specificity also showed the greatest detection sensitivity. The ease in design, the simple single-dye labeling chemistry and the capability to adopt degenerated negative strands for point mutation genotyping make the displacing probes both cost effective and easy to use. The feasibility of this method was first tested by detecting the C282Y mutation in the human hemochromatosis gene. The robustness of this approach was then validated by simultaneous genotyping of five different types of mutation in the human β-globin gene. Sixty-two human genomic DNA samples with nine known genotypes were accurately detected, 32 random clinical samples were successfully screened and 114 double-blind DNA samples were all correctly genotyped. The combined merits of reliability, flexibility and simplicity should make this method suitable for routine clinical testing and large-scale genetic screening.     

The study of mitochondrial A3243G mutation in different samples

Mitochondrial encephalopathy, lactic acidosis and stroke-like episodes syndrome (MELAS) is the most frequent syndromic manifestation of A3243G mutation in mitochondrial DNA. Detection of A3243G mutation in blood is less helpful for the diagnosis of MELAS and the carriers, and the mutation ratio in blood correlates only in a limited extent with the severity of the disease. Here we compared the ratio of A3243G mutation in four easily available samples (blood, urine, hair follicle and saliva) in patients with MELAS carrying A3243G mutation as well as their maternal relatives from 32 families, to find out the samples appropriate for the detection of the patients and carriers and useful for the evaluation of clinical severity from their mutation ratio. In MELAS patients and the carriers with minor symptoms or normal phenotype, A3243G mutation ratio was significantly higher in urine than in blood. A close correlation between A3243G mutation ratio in blood and that in urine, hair follicles and saliva was found in the probands and their relatives. Clinical features closely correlated with the mutation ratio in urine. Measurement of A3243G mutation ratio in urine is a non-invasive, convenient and rapid method with its diagnostic meaning superior to blood testing.     

Evaluation of a mutation test using S49 mouse lymphoma cells and monitoring simultaneously the induction of dexamethasone resistance, 6-thioguanine resistance and ouabain resistance

A test for the detection of chemically induced mutants in S49 mouse lymphoma cells is described. These cells can be plated in parallel in several selective media; the induced frequencies of dexamethasone-resistant, 6-thioguanine-resistant and ouabain-resistant mutants were compared. The first two selection systems permit the detection of all kinds of mutation that result in alteration or partial or complete loss of the gene product concerned, whereas ouabain-resistant mutants can only be induced with strong point mutagens in these cells. Dexamethasone resistance is the marker induced at the highest frequency among these three. Data obtained from this selection system are therefore the most amenable to statistical analysis. Dexamethasone resistance is expressed within a short time after mutagenesis (3 days), and because S49 cells do not display metabolic co-operation, large numbers of cells can be screened. A metabolizing system in vitro with rat-liver homogenate may be included in tests of indirectly acting mutagens. These features make the S49 mutation test system using dexamethasone resistance as the main marker and other markers as internal controls an attractive tool in mutation testing in somatic cells in vitro.     

Development and applications of Bacillus subtilis test systems for mutagens, involving DNA-repair deficiency and suppressible auxotrophic mutations.

A mutagen-tester of Bacillus subtilis was constructed and tested with known carcinogens. The parental strain HA101 of Okubo and Yanagida carrying suppressible nonsense mutations in his and met genes was transformed to carry an excision-repair deficiency mutation. The constructed strain TKJ5211 showed a 20--30-fold higher sensitivity for His+ reversion than the parental strain when treated with UV and UV-mimetic chemicals but unchanged mutation frequency with X-rays and methyl methanesulfonate. The tester strain was used in a spot test of 30 selected chemicals and also for testing with liver homogenate activation. The results showed an almost equivalent but somewhat broader detection spectrum than the Salmonella typhimurium TA100 system. Another test method used a pair of B. subtilis strains differing in their DNA-repair capacity, i.e. the most UV-sensitive mutant HJ-15 and a wild-type strain, to detect repair-dependent DNA damage produced by chemicals. Spores could be used in either test.