Novel mutation in SCO2 of patients with high myopia from Enshi Tujia and Miao Autonomous Prefecture of China / 国际眼科杂志(Guoji Yanke Zazhi)

AIM: To evaluate the pathogenic variants of the SCO2(OMIM 604272)gene in patients with high myopia from Enshi Tujia and Miao Autonomous Prefecture of China.METHODS: A total of 384 patients with high myopia whose spherical refractive error was ≤ -6.00 D and whose axial length was ≥26.00 mm in at least one eye were recruited. DNA was extracted by the phenol-chloroform method from 5 mL of peripheral venous blood. Sanger sequencing was performed to identify pathogenic variants in exon 2 of SCO2. The detected variants were evaluated via in silico prediction software. A total of 288 people from the same district were included as the normal control cohort.RESULTS: Seven variants were detected, namely, four synonymous variants(c.201C>T/p.=, c.576C>T/p.=, c.633A>C/p.=, c.780T>C/p.=.), two missense variants(c.187A>G/p.Ile63Val, c.59G>C/p.Arg20Pro)and one nonsense variant(c.544C>T/p.Gln182*). The two missense variants were not damaging, as predicted by PolyPhen2, SIFT and Provean. The novel nonsense variant(c.544C>T/p.Gln182*)cannot be found in the 1000 Genomes Project and was not identified in 288 normal controls. Variant Taster suggested that the nonsense variant site was conserved.CONCLUSION: The newly identified nonsense mutation may be responsible for high myopia of the patients in our cohort. SCO2 is associated with high myopia, while the incidence of SCO2 variants in high myopia in this cohort was as low as 1/384; the nonsense mutation may be a scarce variant of high myopia in the Enshi Tujia and Miao Autonomous Prefecture of China.

Identification of mixed medicinal powder of Epimedii Folium with different origins based on pyrosequencing technology / 药学学报

There are many multi-original medicinal materials in Chinese Pharmacopoeia, and the mixed use of medicinal materials from different sources is common, which has certain influence on the stability of clinical medication. In this study, pyrosequencing technology was used to screen species-specific single nucleotide polymorphisms (SNP) from commonly used DNA barcode sequences, and a rapid and accurate molecular identification method for original species in mixed medicinal powder of Epimedii Folium was established. Multiple sequence alignment analysis showed that the 176th (C/T) mutation and the 196th (A/G) mutation of ITS, the 123rd (C/G) mutation of matK and the 892nd (A/C) mutation of rbcL could be used as the unique SNPs of E. sagittatum, E. koreanum, E. brevicornu and E. pubescens, respectively. In this study, the applicability of pyrosequencing and Sanger sequencing methods in the sequencing of mixture samples was investigated from the perspective of sensitivity and stability. Pyrosequencing method has higher detection sensitivity than Sanger sequencing method for low content samples in the mixed samples. Stability analysis showed that pyrosequencing technology could still obtain effective sequencing results for the amplified products of template DNA after 45 min of 95 ℃ high temperature water bath, while the critical point of Sanger sequencing method was 30 min. In this study, a new identification technology of Epimedii Folium mixed powder primordial species based on pyrosequencing and specific SNP was developed, which can quickly and accurately identify the mixed use of Epimedii Folium with high sensitivity and stability, and can also support the identification of different primordial species and mixed powder primordial herbs, which is conducive to ensuring the consistency and stability of clinical medication.

Clinical laboratory genetic diagnosis of Marfan syndrome / 中华检验医学杂志

Objective:To establish the clinical laboratory genetic diagnosis procedures for Marfan syndrome (MFS) and carry out clinical laboratory genetic diagnosis for MFS families.Methods:The second generation high-throughput sequencing was used to sequence and analyze the FBN1 gene of two MFS families who visited to Fuwai Central China Cardiovascular Hospital (Heart Center of Henan People′s Hospital) from January to December 2020, and then Sanger sequencing was used to verify the second generation high-throughput sequencing results. At the same time, the sanger sequencing of mutation sites was performed on normal family members and 100 healthy people to identify the pathogenic mutations of FBN1 gene in the MFS families. The pregnant women of two families were guided for prenatal diagnosis in the second trimester of pregnancy.Results:The clinical laboratory diagnosis of MFS showed that two MFS patients had the pathogenic mutation of c.2560T>C heterozygous mutation and c.6772T>C heterozygous mutation in FBN1 gene, respectively. The mutation was not observed in 100 healthy people and normal members in two families. The prenatal diagnosis showed that there was a heterozygous mutation of FBN1 gene c.2560T>C in the first fetus of the MFS family, which was MFS. There was no mutation in the FBN1 gene in the second fetus of the MFS family, so it was recommended to continue the pregnancy. The results of postpartum follow-up were consistent with the results of clinical laboratory diagnosis.Conclusion:The clinical laboratory genetic diagnosis procedures for MFS have been established successfully, which provides an important reference for clarifying the clinical diagnosis of MFS.

Preliminary study of familial nonsyndromic tooth agenesis caused by ectodysplasin A mutation / 口腔疾病防治

Objective@# To explore the pathogenic genes in a Chinese family affected by nonsyndromic tooth agenesis so as to study the pathogenesis of oligodontia.@*Methods @# Hospital ethical approval and informed consent of the patients and family members were obtained. Clinical data of the proband and close family members were collected, peripheral venous blood was collected, and DNA was extracted. Gene sequencing was performed through whole-exome sequencing, and then the screened pathogenic genes were verified by Sanger sequencing. The three-dimensional structure of the mutant proteins was analyzed and compared with the wild-type using bioinformatics tools.@*Results@#The two patients with congenital majority tooth loss in this family were cousins, and there were no other patients with congenital majority tooth loss in the family. Besides congenital multiple tooth loss, the two patients had no obvious hair abnormalities, finger/toe abnormalities, sweating abnormalities or other abnormal manifestations of ectodermal tissue. We found a mutant gene that in this family by carrying out gene sequencing of the patients and their close family members. A novel EDA (ectodysplasin A) missense mutation c.983C>T (p. Pro328Leu) was identified, which changed the encoded amino acid from proline (Pro) to leucine (Leu). Analysis of the mutation site showed that the site was highly conserved, and three-dimensional structure modeling also found that it changed the structure of EDA. @* Conclusion@#A novel EDA missense variant (c.983C>T, p.Pro328Leu) was first identified in a Chinese family with nonsyndromic tooth agenesis, extending the mutation spectrum of the EDA gene.

Novel mutations identified in the WNT10A gene and implant rehabilitation of patients with severe tooth agenesis / 口腔疾病防治

Objective@#To detect WNT10A gene mutations in patients with oligodontia or anodontia (≥6 teeth missing) and analyze their dental phenotype. @*Methods@#Patients with oligodontia or anodontia were enrolled from the clinic for oral examination, genetic history collection and whole exon sequencing, and patients with WNT10A gene mutations were included. Sanger sequencing was utilized to validate the WNT10A gene variations in probands and family members compared with the normal sequence. The pathogenicity of WNT10A mutations was evaluated by functional prediction, conservation analysis and structure prediction of protein mutants. Implant rehabilitation was applied to restore the patients' oral function.@*Results@# Five WNT10A gene mutations were detected in six unrelated patients, and c.26G>A (p. Trp9X) and c.1036delT (p. Cys346fs) were novel mutations with pathogenic potential. The mean number of missing teeth was (15.33±8.64) per case. The most frequently missing permanent teeth were maxillary canines (100%), and the least frequently missing teeth were mandibular first molars (25%). Implant rehabilitation was applied in five patients, and patients were found to have ideal implant osseointegration and functional restoration.@*Conclusion @# This study identified novel WNT10A gene pathogenic variants, enriching the WNT10A gene spectrum and providing new evidence for genetic diagnosis and prenatal consultation. Implant rehabilitation was also proven to be a treatment option for these patients.

Identification of microbial agents in culture-negative brain abscess samples by 16S/18S rRNA gene PCR and sequencing

@#Despite clinical suspicion of an infection, brain abscess samples are often culture-negative in routine microbiological testing. Direct PCR of such samples enables the identification of microbes that may be fastidious, non-viable, or unculturable. Brain abscess samples (n = 217) from neurosurgical patients were subjected to broad range 16S rRNA gene PCR and sequencing for bacteria. All these samples and seven formalin-fixed paraffin-embedded tissue (FFPE) samples were subjected to species-specific 18S rRNA PCR for neurotropic free-living amoeba that harbour pathogenic bacteria. The concordance between smear and/or culture and PCR was 69%. One-third of the samples were smear- and culture-negative for bacterial agents. However, 88% of these culture-negative samples showed the presence of bacterial 16S rRNA by PCR. Sanger sequencing of 27 selected samples showed anaerobic/fastidious gram negative bacteria (GNB, 38%), facultative Streptococci (35%), and aerobic GNB (27%). Targeted metagenomics sequencing of three samples showed multiple bacterial species, including anaerobic and non-culturable bacteria. One FFPE tissue revealed the presence of Acanthamoeba 18S rRNA. None of the frozen brain abscess samples tested was positive for 18S rRNA of Acanthamoeba or Balamuthia mandrillaris. The microbial 16/18S rRNA PCR and sequencing outperformed culture in detecting anaerobes, facultative Streptococci and FLA in brain abscess samples. Genetic analyses of 16S/18S sequences, either through Sanger or metagenomic sequencing, will be an essential diagnostic technology to be included for diagnosing culture-negative brain abscess samples. Characterizing the microbiome of culture-negative brain abscess samples by molecular methods could enable detection and/or treatment of the source of infection.

Identify pathogenic mutations of <i>CYP4V2</i> gene in Bietti crystalline corneoretinal dystrophy / 国际眼科杂志(Guoji Yanke Zazhi)

@#AIM: To identify pathogenic mutations of <i>CYP4V2</i> gene in two Chinese families with Bietti crystalline corneoretinal dystrophy(BCD)by Sanger sequencing. <p>METHODS: The relevant clinical examination of BCD patients were collected. Peripheral blood of patients and their family members was collected. Then DNA was extracted from peripheral blood, and Sanger sequencing was used to identify mutation sites.<p>RESULTS: Two probands of BCD from different families were collected. All the probands showed progressive decrease of visual acuity and typical crystal-like material deposition could be seen in the fundus. Sanger sequencing showed that proband 1 and her brother and sister all had homozygous mutation of c.802-8_810del17insGC in <i>CYP4V2</i> gene. On the other hand, proband 2 had a compound heterozygous mutation of c.219T>A(p.F73L)and c.802-8_810del17insGC in <i>CYP4V2</i> gene. <p>CONCLUSION: The most common mutation was c.802-8_810del17insGC in Chinese BCD patients. The homozygous c.802-8_810del17insGC mutation was the cause of BCD in the proband 1 family. On the other hand, proband 2 had c.802-8_810del17insGC heterozygous mutation and c. 219T>A(p.F73L)heterozygous missence mutation, all of which affected the normal coding of <i>CYP4V2</i> gene and led to disease.

Complete screening of exons 2, 3, and 4 of kras and nras genes reveals a higher number of clinically relevant mutations than food and drug administration quantitative polymerase chain reaction-based commercial kits

Abstract Background: The presence of clinically relevant mutations in KRAS and NRAS genes determines the response of anti-epidermal growth factor receptor antibody therapy for metastatic colorectal cancer (mCRC). The only quantitative polymerase chain reaction (qPCR)-based diagnostic tests approved by the Food and Drug Administration (FDA) screen merely for mutations in codons 12 and 13 of KRAS. Objective: The objective of the study was to study the frequency of clinically relevant mutations in KRAS and NRAS genes that are not included in FDA-approved qPCR tests. Methods: Formalin-fixed paraffin-embedded tumor specimens from 1113 mCRC Mexican patients from different health institutions across the country were analyzed by Sanger sequencing for KRAS mutations in exons 2, 3, and 4. Furthermore, 83 were analyzed in exons 2, 3, and 4 of NRAS. Results: From the specimens tested for KRAS, 33.69% harbored a mutation. From these, 71.77% were in codon 12 and 27.69% in codon 13 (both located in exon 2). Codons 59 (exon 3) and 146 (exon 4) accounted for the remaining 0.54%. From the 83 specimens, in which NRAS was analyzed, three mutations were found in codon 12 (3.61%). Approximately 6% of RAS mutated specimens would have been falsely reported as RAS wild type if an FDA-approved qPCR diagnostic test had been used. Conclusions: While these kits based on qPCR can be very practical and highly sensitive, their mutation coverage ignores mutations from poorly genetically characterized populations.

Clinical and Genetic Heterogeneity of Familial Early-Onset Diabetes: Case of Six Tunisian Patients Suspected of Maturity-Onset Diabetes of the Young 12

Background and objective: Maturity-onset diabetes of the young 12 (MODY12) is a form of early-onset type 2 diabetes, which is transmitted in an autosomal dominant mode. It has clinical features similar to MODY1 and MODY3. The aim of this study is to screen for mutations in ABCC8 gene in six Tunisian patients suspected of MODY12 using Sanger sequencing. Methods: Six probands, with diabetes in 2-3 generations and found previously negative for mutations in HNF1A, HNF4A, INS, IPF1 and NEUROD1, were screened for known mutations in ABCC8 gene using Sanger sequencing. A comparison of the clinical features of our patients with MODY12 cohorts of other studies was also performed using ANOVA test. Results: The six patients were diagnosed with overt diabetes (fasting glycemia: 12.85 ± 3.5 mmol/l, HbA1c: 12.51 ± 2.58%) at mean age of 25.16 ± 5.11 years. They had a BMI mean equal to 26.7 ± 5.9 kg/m2. The majority of the patients were initially treated with OHA or on diet. Some of them converted to insulin therapy. Although, the comparison of our cohort with other MODY12 cohorts showed no significant difference in age at diagnostic and HbA1c, molecular analysis showed only two synonymous non-pathological polymorphisms rs1799857 and rs1805036. Conclusion: Our study highlighted the clinical and genetic heterogeneity of familial earlyonset diabetes in the Tunisian population, which is concordant with previous studies Thus, the need for using nextgeneration sequencing technologies to determine the aetiology of these forms of diabetes.

Genetic analysis of a mosaic case with low proportion mutation of / 浙江大学学报·医学版

OBJECTIVE@#To perform gene mutation analysis in a patient with atypical clinical manifestations of tuberous sclerosis (TSC) for definite diagnosis.@*METHODS@#Peripheral blood DNA was obtained from a patient with clinically suspected TSC and her parents, and all exons and their flanking sequences of @*RESULTS@#A heterozygous nonsense mutation c.1096G>T (p.E366*) was identified in the exon 11 of the @*CONCLUSIONS@#The somatic mosaic mutation c.1096G>T (p.e366*) may be responsible for the phenotype of TSC in this patient. And the drop digital PCR is expected to be a diagnostic method for somatic cells mosaicism.

Somatic Mutations in Circulating Cell-Free D-Loop Region of Mitochondrial DNA: A Study from North-East India

Head and neck Squamous cell carcinoma (HNSCC) is highly prevalent in Northeast India. The widespread use of tobacco exposure is a known risk factor, makingmitochondrial DNA (mtDNA) more susceptible to damage by oxidative stress incomparison to nuclear DNA. Mitochondrial dysfunction being a hallmark of cancer, thestudy aims to evaluate liquid biopsy involving circulating cell-free mitochondrial DNA(cfmtDNA) as an early diagnostic marker by reducing the dependability over tumor tissuebiopsy specimen. A total of 50 HNSCC cases reported at Cancer Hospital, Guwahati MedicalCollege from January 2018 to August 2018 were included in this study. Cell-free DNA wasisolated using QIAamp Circulating Nucleic Acid Kit. PCR based amplification ofmitochondrial D-loop, followed by direct sequencing. Our result indicated the presence ofsomatic mutations (73(A/G), 93(G/A), 146(T/C) and 207 (G/A)). Polymorphism was alsoobserved in the sequences (263A>G, 275G>A, 318T>C, 16034T>C, 16257C>A and16519T>C) upon comparison with reference sequence. Analysis of c-tract region showedthe presence of an additional cytosine nucleotide at position 309.Identifying somaticmutations in cfmtDNA using liquid biopsy approach will certainly minimize thedependency of clinicians and molecular biologist over the availability of tumor tissuespecimens. The identified somatic variations from our study will help in theimplementation of preventive measure. Therefore, our study provides an early mtDNAdiagnostic marker using liquid biopsy approach.

Identification of ATP7B gene variant by combined use of Sanger sequencing, array CGH and quantitative PCR / 中华医学遗传学杂志

Objective@#To identify the type and origin of ATP7B gene mutation in a family affected with Wilson disease by combined use of multiple methods.@*Methods@#Peripheral blood samples were collected from the proband, her parents and her brother. Sanger sequencing were used to detect point mutation and small deletion/insertion of the 21 exons and flanking sequences of the ATP7B gene in all family members. Array-based comparative genomic hybridization (aCGH) was performed to identify copy number variations (CNVs) of the ATP7B gene in the proband. The result was validated by quantitative PCR (qPCR) in other 3 members.@*Results@#Sanger sequencing indicated that the proband carried a heterozygous variation c. 2668G>A (p.V890M) derived from her mother. In addition, 5 common SNPs were detected in her mother, three of which were also identified in her father and brother. The 5 SNPs in the proband were of the wide type. aCGH analysis demonstrated that the proband was heterozygous for a 4 kb deletion, which encompassed exons 2 and 3 of the ATP7B gene and 2 SNPs. qPCR showed that the copy number in her father and brother was about half of the control, indicating heterozygous loss of exons 2 and 3.@*Conclusion@#The combined Sanger sequencing, array CGH and qPCR has identified a novel CNV involving the ATP7B gene. The strategy can improve the diagnostic rate for hereditary or rare diseases.

Molecular Testing of MECP2 Gene in Rett Syndrome Phenotypes in Indian Girls

Objective: To assess yield of MECP2 gene sequence variationsanalysis and large deletions in suspected cases of Rettsyndrome.Design: Descriptive study.Setting: Tertiary-care medical genetics center.Patients: Girls with neuroregression, postnatal microcephaly andsigns and symptoms suggestive of classical and atypical Rettsyndrome were classified into two groups. Group I consisted ofgirls with Classical and atypical Rett syndrome on basis on theRevised Rett Syndrome diagnostic criteria, 2010. Group II includedgirls with neuroregression and postnatal microcephaly and otherRett like features but not fulfilling the above criteria.Procedure: Sanger sequencing of coding regions and largedeletional analysis of MECP2 gene.Outcome measure: Identification of mutation in MECP2 gene.Result: Mutation in MECP2 gene was identified in 74% (14/19) ingroup I and none (0/17) in group II. The mutation detection ratewas 93% (13/14) in group I classical Rett syndrome girls (2 withlarge deletions identified with Multiplex ligation dependent probeamplification) and 20% (1/5) in group I atypical Rett syndromegirls. One novel MECP2 sequence variation was identified ingroup I classical Rett syndrome.Conclusion: The yield of the mutation detection in MECP2 ishigher in classical Rett syndrome. In girls with some Rett likefeatures, but not fulfilling revised Rett syndrome diagnosticcriteria, mutation testing for MECP2 gene has a low yield

Simple protocol for population (Sanger) sequencing for Zika virus genomic regions

BACKGROUND A number of Zika virus (ZIKV) sequences were obtained using Next-generation sequencing (NGS), a methodology widely applied in genetic diversity studies and virome discovery. However Sanger method is still a robust, affordable, rapid and specific tool to obtain valuable sequences. OBJECTIVE The aim of this study was to develop a simple and robust Sanger sequencing protocol targeting ZIKV relevant genetic regions, as envelope protein and nonstructural protein 5 (NS5). In addition, phylogenetic analysis of the ZIKV strains obtained using the present protocol and their comparison with previously published NGS sequences were also carried out. METHODS Six Vero cells isolates from serum and one urine sample were available to develop the procedure. Primer sets were designed in order to conduct a nested RT-PCR and a Sanger sequencing protocols. Bayesian analysis was used to infer phylogenetic relationships. FINDINGS Seven complete ZIKV envelope protein (1,571 kb) and six partial NS5 (0,798 Kb) were obtained using the protocol, with no amplification of NS5 gene from urine sample. Two NS5 sequences presented ambiguities at positions 495 and 196. Nucleotide analysis of a Sanger sequence and consensus sequence of previously NGS study revealed 100% identity. ZIKV strains described here clustered within the Asian lineage. MAIN CONCLUSIONS The present study provided a simple and low-cost Sanger protocol to sequence relevant genes of the ZIKV genome. The identity of Sanger generated sequences with published consensus NGS support the use of Sanger method for ZIKV population studies. The regions evaluated were able to provide robust phylogenetic signals and may be used to conduct molecular epidemiological studies and monitor viral evolution.

Applicable Value of AMSS-PCR in Lung Cancer Gene Mutation Detection / 中国肺癌杂志

BACKGROUND@#The detection of driver oncogenes of lung cancer is of great importance. There are various gene detection techniques nowadays which are different from each other. We carried out this study to investigate the specificity and sensitivity of assay panels based on an Amplification Refractory Mutation System-polymerase chain reaction (ARMS-PCR) technique of Amplification Mutation Specific System (AMSS) in detection of lung cancer gene mutation. To estimate the applicable value of assay panels in clinical settings.@*METHODS@#We collected cancer tissue specimens or fluid specimens from 309 patients. Mutation results were presented for those samples previously detected by ARMS-PCR. In comparison, we carried out AMSS-PCR using (epidermal growth factor receptor, EGFR) assay panel and Six-Alliance assay panel as well as Sanger sequencing. Software SPSS 22.0 (SPSS IBM) was used for statistical analysis.@*RESULTS@#The rates of consistency between the results by assay panels and Sanger sequencing or ARMS-PCR were 97.41% and 97.73%, respectively. Besides, EGFR assay panel had higher consistency rates with other detection methods than Six-Alliance assay panel. As for consistency test, the Kappa values of assay panels with Sanger sequencing, assay panels with ARMS-PCR, and ARMS-PCR with Sanger sequencing were 0.946, 0.953, and 0.913, respectively. The receiver operating characteristic curve (ROC) area under curve (AUC) of assay panels was 0.976 referring to Sanger sequencing, and 0.975 as ARMS-PCR was referred to.@*CONCLUSIONS@#AMSS-PCR can make an optimal cancer gene mutation detection method for clinical settings.

Study on application of next-generation sequencing technology in diagnosis of cardio-facio-cutaneous syndrome / 重庆医学

Objective To explore the role of next-generation sequencing(NGS)technology in the assisted diagnosis of RA-Sopathies.Methods Peripheral blood was extracted from 1 child patient with suspected Noonan syndrome and her parents,and the gene mutations were detected by adopting the aCGH and NGS.The results were verified by Sanger sequencing.Results The NGS results revealed that the heterozygous mutation of c.1406G>A existed in BRAF gene,and the results of Sanger sequencing in this child case was consistent with the NGS results.The Sanger sequencing results in her parents showed the locus was G/G wild type. Conclusion This child case was diagnosed as CFC.NGS plays a good auxiliary role in the differentiation diagnosis of RASopathies.

Detection of Rare Mutations in EGFR-ARMS-PCR-Negative Lung Adenocarcinoma by Sanger Sequencing

PURPOSE: This study aimed to identify potential epidermal growth factor receptor (EGFR) gene mutations in non-small cell lung cancer that went undetected by amplification refractory mutation system-Scorpion real-time PCR (ARMS-PCR). MATERIALS AND METHODS: A total of 200 specimens were obtained from the First Affiliated Hospital of Guangzhou Medical University from August 2014 to August 2015. In total, 100 ARMS-negative and 100 ARMS-positive specimens were evaluated for EGFR gene mutations by Sanger sequencing. The methodology and sensitivity of each method and the outcomes of EGFR-tyrosine kinase inhibitor (TKI) therapy were analyzed. RESULTS: Among the 100 ARMS-PCR-positive samples, 90 were positive by Sanger sequencing, while 10 cases were considered negative, because the mutation abundance was less than 10%. Among the 100 negative cases, three were positive for a rare EGFR mutation by Sanger sequencing. In the curative effect analysis of EGFR-TKIs, the progression-free survival (PFS) analysis based on ARMS and Sanger sequencing results showed no difference. However, the PFS of patients with a high abundance of EGFR mutation was 12.4 months [95% confidence interval (CI), 11.6−12.4 months], which was significantly higher than that of patients with a low abundance of mutations detected by Sanger sequencing (95% CI, 10.7−11.3 months) (p < 0.001). CONCLUSION: The ARMS method demonstrated higher sensitivity than Sanger sequencing, but was prone to missing mutations due to primer design. Sanger sequencing was able to detect rare EGFR mutations and deemed applicable for confirming EGFR status. A clinical trial evaluating the efficacy of EGFR-TKIs in patients with rare EGFR mutations is needed.

Comparison of Immunohistochemistry and Direct Sanger Sequencing for Detection of the BRAF(V600E) Mutation in Thyroid Neoplasm

BACKGROUND: The BRAF V600E mutation is the most common genetic alteration identified in papillary thyroid carcinoma (PTC). Because of its costs effectiveness and sensitivity, direct Sanger sequencing has several limitations. The aim of this study was to evaluate the efficiency of immunohistochemistry (IHC) as an alternative method to detect the BRAF V600E mutation in preoperative and postoperative tissue samples. METHODS: We evaluated 71 patients who underwent thyroid surgery with the result of direct sequencing of the BRAF V600E mutation. IHC staining of the BRAF V600E mutation was performed in 49 preoperative and 23 postoperative thyroid specimens. RESULTS: Sixty-two patients (87.3%) had PTC, and of these, BRAF V600E was confirmed by direct sequencing in 57 patients (91.9%). In 23 postoperative tissue samples, the BRAF V600E mutation was detected in 16 samples (70%) by direct sequencing and 18 samples (78%) by IHC. In 24 fine needle aspiration (FNA) samples, BRAF V600E was detected in 18 samples (75%) by direct sequencing and 16 samples (67%) by IHC. In 25 core needle biopsy (CNB) samples, the BRAF V600E mutation was detected in 15 samples (60%) by direct sequencing and 16 samples (64%) by IHC. The sensitivity and specificity of IHC for detecting the BRAF V600E mutation were 77.8% and 66.7% in FNA samples and 99.3% and 80.0% in CNB samples. CONCLUSION: IHC could be an alternative method to direct Sanger sequencing for BRAF V600E mutation detection both in postoperative and preoperative samples. However, application of IHC to detect the BRAF V600E mutation in FNA samples is of limited value compared with direct sequencing.

Application of Sanger sequencing technology in detection of gemcitabine resistance sensitive gene CDA / 国际检验医学杂志

Objective To analyze the polymorphic site mutation of gemcitabine resistant sensitive gene cytidine deaminase (CDA),and to investigate the applicability of the Sanger detection technology in clinical sample detection with the real-time fluores-cence quantitative PCR as the reference.Methods The peripheral blood samples from 255 cases of stage ⅢB to Ⅳ non small-cell lung cancer(NSCLC)were randomly selected for extracting DNA.The G208A and A79C mutation situation of CDA gene was re-spectively detected by qPCR and Sanger sequencing technology.Results The success rate for detecting the CDA gene mutation in peripheral blood sample in 255 cases of stage ⅢB and Ⅳ NSCLC were 98.04%(250/255)by the Sanger sequencing method and 97.25%(248/255)by qPCR.With the qPCR as the reference,the sensitivity and specificity of Sanger sequencing method was 92.50% and 99.52% respectively.All mutation types detected by two methods were fully consistent.Conclusion Adopting the Sanger sequencing method can effectively detect drug resistance gene CDA mutation,realizes the mutation typing,can accurately, high throughput and efficiently detect CDA mutation site,which provides an effective detection method for gemcitabine sensitive medication of NSCLC.