Cell HE staining smears and paired cell paraffin sections in detection of epithelial growth factor receptor gene of pleural fluid specimens / 中南大学学报(医学版)

OBJECTIVES@#The advanced non-small cell lung cancer (NSCLC) patients with pleural effusion have no opportunity for surgery treatment. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are the first-line drugs for these patients with EGFR-sensitive mutation. However, the disease progression and drug update during or after treatment of EGFR-TKIs bring more challenges and puzzles to clinical diagnosis and treatment, which inevitably requires archived pleural cell samples for EGFR re-examination or comparative study. Understanding the DNA quality of archived pleural fluid samples and effectively using archival data of pleural fluid cells are of great significance for tracing the origin of cases and basic medical research. This study aims to evaluate the consistency of EGFR mutant gene expression between the 2 methods, and to explore a reliable way for preserving cytological data and making full use of cytological archival data via cell HE staining smear and cell paraffin section.@*METHODS@#A total of 57 pleural fluid cytology cases in the Department of Pathology of China Aerospace Center Hospital from October 2014 to April 2021 were selected. Tumor cells were detected by cell HE staining smears and immunohistochemical staining for TTF-1 and Napsin A in the paired cell paraffin sections. There were more than 200 tumor cells in cell HE staining smear and the proportion of tumor cells were ≥70% in matched cell paraffin sections. Patients with 2 cell smears (one for cell data retention and the other for DNA extraction) were selected as the research subjects, and 57 pleural fluid samples were enrolled. EGFR gene mutation was detected by amplification refractory mutation system-polymerase chain reaction in 57 paired cell HE staining smears and cell paraffin sections. DNA concentration was 2 ng/μL. Cell HE smear was amplified side-by-side with DNA samples from paired cell paraffin sections. Result determination was according to the requirements of the reagent instructions. The external control cycle threshold (Ct) value of the No. 8 well of the samples to be tested was between 13 and 21, which was considered as successful and reliable samples. When the Ct value of EGFR gene mutation was <26, it was considered as positive; when the Ct value was between 26 and 29, it was critical positive; when the Ct value was equal or more than 29, it was negative. ΔCt value was the difference between mutant Ct value and externally controlled Ct value. The smaller the ΔCt value was, the better the quality of DNA of the detected sample was.@*RESULTS@#Among the 57 pleural effusion samples, 42 patients were hospitalized with pleural effusion as the first symptom, accounting for 73.7% (42/57). EGFR mutation was detected in 37 samples [64.9% (37/57)]. The mutation rate for 19del was 37.8% (14/37) while for L858R was 48.6% (18/37). Females were 56.7% (21/37) of mutation cases. The mutation consistency rate of cell HE staining smear and matched cell paraffin sections was 100%. The ΔCt values of cell HE staining smears were less than those of matched cell paraffin sections. The mutation Ct values of 37 cytological samples were statistically analyzed according to the preservation periods of the years of 2014-2015, 2016-2017, 2018-2019, and 2020-2021. There were significant differences in cell paraffin section in the years of 2014-2015 and 2016-2017 compared with the years of 2018-2019 and 2020-2021, while no significant differences were found in cell HE staining smear. Statistical analysis of externally controlled Ct values of 57 cytological samples showed that there were significant differences between cell HE staining smears and cell paraffin section in the years of 2014-2015 and 2016-2017, compared with the years of 2018-2019 and 2020-2021. The mutational Ct values of 37 paired cell blocks and smears were all <26, and the externally controlled Ct values of 57 paired cell paraffin sections and HE staining smears were all between 13 and 21.@*CONCLUSIONS@#The DNA quality of cell HE smears and matched cell paraffin section met the qualified requirements. Two methods possess show an excellent consistency in detecting EGFR mutation in NSCLC pleural fluid samples. The DNA quality of cell HE staining smear is better than that of cell paraffin sections, so cell HE staining smear can be used as important supplement of the gene test source. It should be noted that the limitation of cell HE staining smears is non-reproducibility, so multiple smears of pleural fluid are recommended to be prepared for multiple tests.

A duplex probe-directed recombinase amplification assay for detection of single nucleotide polymorphisms on 8q24 associated with prostate cancer

Single nucleotide polymorphisms (SNPs) have important application value in the research of population genetics, hereditary diseases, tumors, and drug development. Conventional methods for detecting SNPs are typically based on PCR or DNA sequencing, which is time-consuming, costly, and requires complex instrumentation. In this study, we present a duplex probe-directed recombinase amplification (duplex-PDRA) assay that can perform real-time detection of two SNPs (rs6983267 and rs1447295) in four reactions in two tubes at 39°C within 30 min. The sensitivity of duplex-PDRA was 2×103-104 copies per reaction and no cross-reactivity was observed. A total of 382 clinical samples (179 prostate cancer patients and 203 controls) from northern China were collected and tested by duplex-PDRA assay and direct sequencing. The genotyping results were completely identical. In addition, the association analysis of two SNPs with prostate cancer risk and bone metastasis was conducted. We found that the TT genotype of rs6983267 (OR: 0.42; 95%CI: 0.23-0.78; P=0.005) decreased the risk of prostate cancer, while the CA genotype of rs1447295 (OR: 1.89; 95%CI: 1.20-2.96; P=0.005) increased the risk of prostate cancer. However, no association between the two SNPs (rs6983267 and rs1447295) and bone metastasis in prostate cancer was found in this study (P>0.05). In conclusion, the duplex-PDRA assay is an effective method for the simultaneous detection of two SNPs and shows great potential for widespread use in research and clinical settings.

Identification of mutations in the pah gene in pku patients in the state of mato grosso / Identificação de mutações no gene da pah em pacientes com fenilcetonúria do estado de mato grosso

ABSTRACT Objective: To identify phenylalanine hydroxylase (PAH) mutations in patients with phenylketonuria (PKU) from the Newborn Screening Service in Mato Grosso, Midwest Brazil. Methods: This is a cross-sectional descriptive study. The sample consisted of 19 PKU patients diagnosed by newborn screening. Molecular analysis: DNA extraction using the "salting-out" method. Detection of IVS10nt-11G>A, V388M, R261Q, R261X, R252W, and R408W mutations by the restriction fragment length polymorphism (RFLP) technique. Results: Two mutant alleles were identified in four patients (21.1%), one allele in five patients (26.2%), and none in the remaining ten patients (52.6%). A total of 13/38 alleles were detected, corresponding to 34.2% of the PAH alleles present. The most prevalent variant was V388M (13.2% of the alleles), followed by R261Q (10.1%) and IVS10nt-11G>A (7.9%). Three variants (R261X, R252W, and R408W) were not found. The most frequent mutation types were: missense mutation in eight alleles (18.4%) and splicing in four alleles (10.5%). The model proposed by Guldberg to determine a genotype/phenotype correlation was applied to four classical PKU patients with two identified mutations. In three of them, the predicted moderate/moderate or moderate PKU phenotype did not coincide with the actual diagnosis. The prediction coincided with the diagnosis of one classic PKU patient. The estimated incidence of PKU for Mato Grosso, Brazil, was 1:33,342 live births from 2003 to 2015. Conclusion: The only mutations found in the analyzed samples were the IVS10nt-11G>A, V388M, and R261Q. The genotype/phenotype correlation only occurred in four (5.3%) patients.

RESUMO Objetivo: Identificar mutações da fenilalanina hidroxilase (PAH) em pacientes com PKU (fenilcetonúria) do Serviço de Triagem Neonatal em Mato Grosso. Métodos: Estudo de corte transversal. Amostra composta de 19 pacientes com PKU através do exame de triagem neonatal biológica. Análise molecular: a) extração de DNA pela metodologia "salting out". B) detecção de mutações IVS10nt-11G>A, V388M, R261Q, R261X, R252W e R408W pela técnica de polimorfismo de comprimento de fragmento de restrição (RFLP). Resultados: Dois alelos foram identificados em quatro pacientes (21,1%), um alelo em cinco pacientes (26,2%) e nenhum nos dez pacientes restantes (52,6%). Um total de 13/38 alelos foram identificados, correspondendo a 34,2% dos alelos PAH presentes. A variante mais prevalente foi a V388M (13,2% dos alelos), seguida de R261Q (10,1%) e IVS10nt-11G>A (7,9%). Três variantes (R261X, R252W e R408W) não foram encontradas. Os tipos de mutações mais frequentes foram: troca de sentido em oito alelos (18,4%) e emenda em quatro alelos (10,5%). O modelo proposto por Guldberg para determinar uma correlação genótipo/fenótipo foi aplicado para quatro pacientes clássicos de PKU, com duas mutações identificadas. Em três, o fenótipo previsto de PKU moderada/moderada ou moderada não coincidiu com o diagnóstico real. A predição coincidiu com o diagnóstico de um paciente PKU clássico. A incidência de PKU estimada para Mato Grosso, Brasil foi de 1:33.342 nascidos vivos para o período de 2003 a 2015. Conclusões: Foram encontradas apenas as mutações IVS10nt-11G>A, V388M, R261Q nas amostras analisadas. A correlação genótipo/fenótipo ocorreu em quatro (5,3%) pacientes.

Hallazgo del virus linfotrópico T humano 1 (HTLV-1) subtipo Cosmopolita subgrupo Transcontinental (Aa) y del HTLV-2 subtipo b en donantes de sangre de Corrientes / Detection of Human T lymphotropic virus 1 (HTLV-1) Cosmopolitan subtype Transcontinental subgroup (Aa) and HTLV-2 subtype b in blood donors of Corrientes

Resumen Se realizó un estudio epidemiológico molecular en una población de 9.422 donantes de sangre de la provincia de Corrientes (noreste de Argentina), con el fin de determinar la prevalencia del virus linfotrópico T del humano tipos 1 y 2 (human T-cell lymphotropic virus: HTLV-1/2), de identificar filogenéticamente a los subtipos/subgrupos de HTLV-1 y 2 encontrados y de realizar el análisis de mutaciones. Sobre la base de los resultados obtenidos, se demostró que tanto el HTLV-1 como el HTLV-2 se encuentran circulando en una población de bajo riesgo de Corrientes, si bien con una prevalencia similar a las de áreas no endémicas. Los estudios filogenéticos identificaron al subtipo Cosmopolita subgrupo Transcontinental (Aa) del HTLV-1 y al subtipo b del HTLV-2. Los donantes infectados no manifestaron antecedentes de riesgo tales como transfusiones, uso de drogas inyectables ni parejas sexuales de riesgo o seropositivas para HTLV-1/2. Estos resultados indican que estos virus fueron transmitidos de madre a hijo, posiblemente de generación en generación, y que estas cepas fueron introducidas en la población caucásica de esta región a partir de ascendientes originarios de áreas endémicas del país o por contacto producido tiempo atrás con individuos infectados de otros países. Nuestros resultados demuestran por primera vez la presencia de HTLV-1 y HTLV-2 en la provincia de Corrientes. Y si bien se puede considerar a esta provincia como área no endémica, se destaca la necesidad de incluir a estos retrovirus en un programa nacional de salud pública, con el fin de contar con profesionales capacitados para realizar su diagnóstico y brindar la información necesaria en relación con la atención primaria y el seguimiento de los pacientes.

Abstract A molecular epidemiological study was conducted in a population of 9422 blood donors in the province of Corrientes, Northeastern Argentina, to determine the prevalence of Human T-cell lymphotropic virus types 1 and 2 (HTLV-1/2), the phylogenetic identification of HTLV-1 and 2 subtypes/subgroups and perform a mutation analysis. Based on the results obtained, it was shown that both HTLV-1 and HTLV-2 are circulating in a low-risk population of Corrientes, although with a similar prevalence to that of non-endemic areas. Phylogenetic studies identified the HTLV-1 Cosmopolitan subtype Transcontinental subgroup (Aa), and the HTLV-2 subtype b. Infected donors reported neither a history of risk factors such as transfusions, intravenous drug use, nor risky or HTLV-1/2 seropositive sexual partners. These results suggest that these viruses were transmitted from mother to child, possibly from generation to generation, and that these strains were introduced into the Caucasian population of this region from ancestors originating from endemic areas of the country either from or through contact with individuals from other countries years ago. Our results demonstrate for the first time the presence of HTLV-1 and HTLV-2 in the province of Corrientes. Moreover, although the province can be considered a non-endemic area, the need to include these retroviruses in a national Public Health program is highlighted, in order to have qualified professionals duly trained to make their diagnosis and provide the necessary information in relation to primary care and patient follow-up.

Mutation Analysis of 19 STR Loci in 20 723 Cases of Paternity Testing / 法医学杂志

OBJECTIVES@#To observe and analyze the confirmed cases of paternity testing, and to explore the mutation rules of STR loci.@*METHODS@#The mutant STR loci were screened from 20 723 confirmed cases of paternity testing by Goldeneye 20A system．The mutation rates, and the sources, fragment length, steps and increased or decreased repeat sequences of mutant alleles were counted for the analysis of the characteristics of mutation-related factors.@*RESULTS@#A total of 548 mutations were found on 19 STR loci, and 557 mutation events were observed. The loci mutation rate was 0.07‰-2.23‰. The ratio of paternal to maternal mutant events was 3.06:1. One step mutation was the main mutation, and the number of the increased repeat sequences was almost the same as the decreased repeat sequences. The repeat sequences were more likely to decrease in two steps mutation and above. Mutation mainly occurred in the medium allele, and the number of the increased repeat sequences was almost the same as the decreased repeat sequences. In long allele mutations, the decreased repeat sequences were significantly more than the increased repeat sequences. The number of the increased repeat sequences was almost the same as the decreased repeat sequences in paternal mutation, while the decreased repeat sequences were more than the increased in maternal mutation.@*CONCLUSIONS@#There are significant differences in the mutation rate of each locus. When one or two loci do not conform to the genetic law, other detection system should be added, and PI value should be calculated combined with the information of the mutate STR loci in order to further clarify the identification opinions.

Prevalence and Phenotypic Expression of Mutations in the MYH7, MYBPC3 and TNNT2 Genes in Families with Hypertrophic Cardiomyopathy in the South of Brazil: A Cross-Sectional Study / Prevalência e Expressão Fenotípica das Mutações nos Genes MYH7, MYBPC3 e TNNT2 em Famílias com Cardiomiopatia Hipertrófica no Sul do Brasil: Um Estudo Transversal

Abstract Background: Mutations in sarcomeric genes are found in 60-70% of individuals with familial forms of hypertrophic cardiomyopathy (HCM). However, this estimate refers to northern hemisphere populations. The molecular-genetic profile of HCM has been subject of few investigations in Brazil, particularly in the south of the country. Objective: To investigate mutations in the sarcomeric genes MYH7, MYBPC3 and TNNT2 in a cohort of HCM patients living in the extreme south of Brazil, and to evaluate genotype-phenotype associations. Methods: Direct DNA sequencing of all encoding regions of three sarcomeric genes was conducted in 43 consecutive individuals of ten unrelated families. Results: Mutations for CMH have been found in 25 (58%) patients of seven (70%) of the ten study families. Fourteen (56%) individuals were phenotype-positive. All mutations were missense, four (66%) in MYH7 and two (33%) in MYBPC3. We have not found mutations in the TNNT2 gene. Mutations in MYH7 were identified in 20 (47%) patients of six (60%) families. Two of them had not been previously described. Mutations in MYBPC3 were found in seven (16%) members of two (20%) families. Two (5%) patients showed double heterozygosis for both genes. The mutations affected different domains of encoded proteins and led to variable phenotypic expression. A family history of HCM was identified in all genotype-positive individuals. Conclusions: In this first genetic-molecular analysis carried out in the south of Brazil, we found mutations in the sarcomeric genes MYH7 and MYBPC3 in 58% of individuals. MYH7-related disease was identified in the majority of cases with mutation.

Resumo Fundamento: Mutações em genes do sarcômero são encontradas em 60-70% dos indivíduos com formas familiares de cardiomiopatia hipertrófica. (CMH). Entretanto, essa estimativa refere-se a populações de países do hemisfério norte. O perfil genético-molecular da CMH foi tema de poucos estudos no Brasil, particularmente na região sul do país. Objetivo: Realizar a pesquisa de mutações dos genes sarcoméricos MYH7, MYBPC3 e TNNT2 numa coorte de CMH estabelecida no extremo sul do Brasil, assim como avaliar as associações genótipo-fenótipo. Métodos: Sequenciamento direto do DNA de todas as regiões codificantes dos três genes sarcoméricos foi realizada em 43 indivíduos consecutivos de dez famílias não-relacionadas. Resultados: Mutações para CMH foram encontradas em 25 (58%) indivíduos de sete (70%) das dez famílias estudadas, sendo 14 (56%) deles fenótipo-positivos. Todas as mutações eram missense, quatro (66%) no gene MYH7 e duas (33%) no gene MYBPC3. Não foram encontradas mutações no gene TNNT2. Mutações em MYH7 foram identificadas em 20 (47%) indivíduos de seis (60%) famílias. Duas delas não haviam sido previamente relatadas. Mutações de MYBPC3 foram detectadas em sete (16%) membros de duas (20%) famílias. Dois (5%) indivíduos apresentaram dupla heterozigose com mutações em ambos os genes. As mutações acometeram distintos domínios das proteínas codificadas e produziram expressão fenotípica variável. História familiar de CMH foi identificada em todos os indivíduos genótipo-positivos. Conclusões: Nessa primeira análise genético-molecular da CMH realizada no sul do Brasil, foram encontradas mutações nos genes sarcoméricos MYH7 e MYBPC3 em 58% dos indivíduos. Doença relacionada ao gene MYH7 foi identificada na maioria dos casos com mutação.

Molecular Genetic Analysis of One Sudden Unexplained Death in the Young by Whole Exome Sequencing / 法医学杂志

OBJECTIVE@#To find the mutation of disease-causing genes of sudden unexplained death syndrome (SUDS) in the young by whole exome sequencing in one case.@*METHODS@#One SUDS case was found no obvious fatal pathological changes after conventional autopsy and pathological examination. The whole exome sequencing was performed with the Ion Torrent PGM™ System with hg19 as reference sequence for sequencing data. The functions of mutations were analyzed by PhyloP, PolyPhen2 and SIFT. A three-step bioinformatics filtering procedure was carried out to identify possible significative single nucleotide variation (SNV), which was missense mutation with allele frequency < 1% of myocardial cell.@*RESULTS@#Four rare suspicious pathogenic SNV were identified. Combined with the analysis of conventional autopsy and pathological examination, the mutation MYOM2 (8_2054058_G/A) was assessed as high-risk deleterious mutation by PolyPhen2 and SIFT, respectively.@*CONCLUSION@#Based on the second generation sequencing technology, analysis of whole exome sequencing can be a new method for the death cause investigation of SUDS. The gene MYOM2 is a new candidate SUDS pathogenic gene for mechanism research.

Evaluation of the Anyplex BRAF V600E Real-Time Detection Assay Using Dual-Priming Oligonucleotide Technology in Fine-Needle Aspirates of Thyroid Nodules

BACKGROUND: Several molecular assays have been developed to detect the BRAF V600E mutation in fine needle aspirates (FNAs) for the diagnosis of papillary thyroid cancer. Using a multiplex PCR technique, we evaluated the Anyplex BRAF V600E Real-time Detection (Anyplex) assay and compared its efficacy with that of the Seeplex BRAF V600E ACE Detection (Seeplex) method. METHODS: We tested 258 consecutive FNA specimens using the Seeplex and Anyplex assays. Any conflicting results between the two assays were confirmed by using mutant enrichment with 3'-modified oligonucleotide (MEMO) sequencing. The limits of detection (LODs) and reproducibility for each assay were evaluated with serially diluted DNA from a BRAF V600E-positive cell line. RESULTS: The BRAF V600E mutation was detected in 36.4% (94/258) FNA specimens by either the Seeplex or Anyplex assay. Results for the two assays showed 93.4% (241/258) agreement, with a kappa value of 0.861 (95% confidence interval, 0.798-0.923). Of the eight specimens that were BRAF V600E-positive by the Anyplex assay but not by the Seeplex assay, five were found to be BRAF V600E-positive by MEMO sequencing. The mutation detection rate of the Seeplex and Anyplex assays was 79.0% and 84.0%, respectively, in the FNA specimens diagnosed as malignant (n=81). The LOD as determined by probit analysis was 0.046% (95% confidence interval, 0.019-0.532%). CONCLUSIONS: The Anyplex assay performed better than the Seeplex assay with respect to the detection of the BRAF V600E mutation.

Identificación de la mutación R579X en el exón 18 del gen RB1, en pacientes con lesiones cervicales asociadas a infección por virus del papiloma humano / Identification of the R579X mutation in exon 18 of the RB1 gene in patients with cervical infection associated with human papilloma virus

Identificar la mutación R579X ubicada en el exón 18 gen RB1, en pacientes con lesiones cervicales asociadas a infección por virus de papiloma humano mediante PCR-SSCP, PCR-RFLP y secuenciamiento. Estudio de 72 muestras de hisopado/cepillado de cuello uterino provenientes de 36 mujeres sanas, y 36 con infección por virus de papiloma humano y con presencia de lesiones cervicales a las cuales se les realizó la extracción de ADN, la amplificación del exón 18 del gen RB1 mediante PCR, y el análisis mediante PCR-SSCP, Secuenciamiento y PCR-RFLP. El análisis por PCR-SSCP reveló dos patrones diferentes de corrida y mediante el secuenciamiento se logró identificar la mutación R579X en el exón 18 del gen supresor de tumores RB1 en el 30,56 por ciento de las muestras experimentales. La mutación R579X encontrada en las muestras experimentales conlleva a la formación de una proteína truncada no funcional, y aunado a esto, el virus de papiloma humano podría estar favoreciendo a la inmortalización de las células que presentan dicha mutación

To identify the mutation R579X in exon 18 located RB1 gene in patients with cervical lesions associated with human papilloma virus infection by PCR-SSCP, PCR-RFLP and sequencing. Study of 72 samples of cervical brushing of the healthy women, infected with human papilloma virus and with cervical lesions that required DNA extraction, PCR amplification of exon 18 of the RB1 gene, PCR-SSCP, Sequencing and PCR-RFLP analysis. PCR-SSCP analysis revealed two different band patterns. We indentified the R579X mutation in exon 18 of the RB1 tumor suppressor gene in 30.56 percent of the experimental samples. The mutation found in the experimental samples leads to the formation of a non-functional truncated protein, in adition, human papilloma virus infection might contributed to the immortalization of cells with this mutation

A Modified Extraction Method of Circulating Free DNA for Epidermal Growth Factor Receptor Mutation Analysis

PURPOSE: Circulating free DNA (cfDNA) in plasma is promising to be a surrogate for tumor tissue DNA. However, not all epidermal growth factor receptor (EGFR) mutations in tumor tissue DNA has been detected in matched cfDNA, at least partly due to inefficient cfDNA extraction method. The purpose of this study was to establish an efficient plasma cfDNA extraction protocol. MATERIALS AND METHODS: The yield of plasma cfDNA extracted by our modified phenol-chloroform (MPC) method from non-small-cell lung cancer (NSCLC) patients was compared with that by QIAamp MinElute Virus Spin kit (Qiagen kit) as control, using the Wilcoxon rank-sum test. TaqMan quantitative polymerase chain reaction (qPCR) assays were used to quantify the plasma cfDNA extracted. Both Mutant-enriched PCR (ME-PCR) coupled sequencing and DxS EGFR mutation test kit were used to evaluate the impact of extraction method on EGFR mutation analysis. RESULTS: MPC method extracted more plasma cfDNA than Qiagen kit method (p=0.011). The proportion of longer fragment (> or =202 bp) in cfDNA extracted by MPC method was significantly higher than by Qiagen kit method (p=0.002). In the sequencing maps of ME-PCR products, a higher mutant peak was observed on plasma cfDNA extracted by MPC method than by Qiagen kit method. In DxS EGFR mutation test kit results, plasma cfDNA extracted by MPC method contained more tumor-origin DNA than by Qiagen kit method. CONCLUSION: An improved plasma cfDNA extraction method of MPC is provided, which will be beneficial for EGFR mutation analysis for patients with NSCLC.

Molecular screening of pointmutation [T3151] using allele specific oligonucleotides-polymerase chain reaction [ASO-PCR]

The development of the BCR-ABL targeted Imatinib Mesylate [IM] represent a paradigm shift in the treatment of chronic myeloid leukemia [CML]. However, a considerable number of CML patients have been reported to show resistance to IM, leading to relapses. The purpose of this paper is to screening for T3151 mutation in patients who are showing criteria of resistance or relapse, using Allele Specific Oligonucleotides Polymerase Chain Reaction [ASO-PCR]. A total of 24 DNA samples related to 18 CML patients of non-responder to IM were analyzed for T3151. They received daily dose of IM [300-400] mg for a mean duration 35 months. They were followed up hematologically, cytogenetically and molecularly every 3-6 months. They had not achieved complete hematological response [CHR], major cytogenetic response [MCyR] or major molecular response [MMR] along the follow up duration and until the end of this study. DNA was extracted from 100 micro l of venous blood [VB] using DNA isolation kit. Screening for the presence of T3151 mutation was done using [ASO-PCR]. PCR products were electrophoresed using 2.5% agarose gel electrophoresis. Agarose gel electrophoresis of ASO-PCR amplified products showed just one band of about [158 bp] in the lanes of wild-type alleles, indicating that non of those patients were harboring such mutation. There was no evidence that the initial lack of CHR, CyR or MMR in CML patients treated with IM due to the presence of T3151 mutation but those patients may have carried other types of mutations result in shift in sensitivity that may allow sufficient kinase activity to initiate disease progression in the presence of IM

[Molecular analysis of alpha globin gene deletions among patients with microcytic hypochromic anemia in Kermanshah-Iran]

The majority of alpha-thalassemi mutations are deletions of one or both alpha- globin genes. Since the Iranian populaion is a mixture of different ethnic groups, frequency and distribution of globin mutations in various regions of the country need to be clarified. The aim of this study was to determine the common alpha globin gene deletions among individuals with hypochromic microcytic anemia in Kermanshah province. Following the initial evaluation, 92 patients [47 women and 45 men] were found as microcytic hypochromic [MCV < 80 fl and MCH< 27 pg] anemia and selected for this study. All samples were analyzed for detection of four alpha-gene deletions [-alpha3.7,-alpha4.2,- [alpha] 20.5 and --MED] by GAP-PCR technique. After amplification, 10microl of PCR product was electrophoresed through 1.2% agarose gel and bands were visualized by staining gel in ethidium bromide solution and photographed under a UV transilluminater. 45 patients had -alpha 3.7 single gene deletion. In patients with -alpha3.7 deletion, in both homozygous and heterozygous states, MCH was lower than normal ranges. However, the percent of HbA2 was in normal range. In this study, other common deletional mutations, including - [alpha]20.5, -alpha4.2 and --MED were not found. The results of persent study showed that the frequency of -alpha3.7 single gene deletion among patients with microcytic hypochromic anemia in Kermanshah province was 48.9%

Use of multiplex ligation-dependent probe amplification (MLPA) for Duchenne muscular dystrophy (DMD) gene mutation analysis.

Background & objectives: Duchenne (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive disorders, caused by mutations in the dystrophin gene. Genetic diagnosis of the proband becomes crucial, and forms the base for carrier analysis, genetic counselling, prediction of natural history and prognosis, and eligibility for therapeutic strategies. Traditional multiplex PCR assay is the common method used in India to detect DMD gene deletions, mainly in the hot-spot region. Deletions of exons outside the usual 18 or 21 exons in the hot-spot, duplications and carrier analysis are often left without precise genetic diagnosis and require efficient dosage/quantitative analysis. In this study we evaluated the efficacy of using multiplex PCR (mPCR) of 30 exons followed by multiplex ligation-dependent probe amplification (MLPA), to study deletions and duplications in the DMD gene in patients clinically diagnosed as BMD/DMD. Methods: Using an algorithm of mPCR and MLPA which was less invasive and cost-effective, we performed retrospective and prospective analysis on 150 male patients. Results: Multiplex PCR could pick up deletions in 103 of the 150 cases. MLPA was able to detect deletions and duplications including nine additional mutations. Further, the borders of the deletions and duplications were more accurately defined by this recent methodology, which enables one to determine the effect of the mutation on the reading frame. In all, including the single exon deletions, MLPA was efficient in accurately confirming mutations in 35 per cent of all cases. Ten novel mutations were identified in this study. Overall, this approach confirmed mutations in 75 per cent of the patients in our study. Interpretations & conclusions: The systematic approach/algorithm used in this study offers the best possible economical mutation analysis in the Indian scenario.

Exon deletions of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemics

A consistent finding of many studies describing the spectrum of mutant phenylalanine hydroxylase (PAH) alleles underlying hyperphenylalaninemia is the impossibility of achieving a 100% mutation ascertainment rate using conventional gene-scanning methods. These methods include denaturing gradient gel electrophoresis (DGGE), denaturing high performance liquid chromatography (DHPLC), and direct sequencing. In recent years, it has been shown that a significant proportion of undetermined alleles consist of large deletions overlapping one or more exons. These deletions have been difficult to detect in compound heterozygotes using gene-scanning methods due to a masking effect of the non-deleted allele. To date, no systematic search has been carried out for such exon deletions in Italian patients with phenylketonuria or mild hyperphenylalaninemia. We used multiplex ligation- dependent probe amplification (MLPA), comparative multiplex dosage analysis (CMDA), and real-time PCR to search for both large deletions and duplications of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemia patients. Four deletions removing different phenylalanine hydroxylase (PAH) gene exons were identified in 12 patients. Two of these deletions involving exons 4-5-6-7-8 (systematic name c.353-?_912 + ?del) and exon 6 (systematic name c.510-?_706 + ?del) have not been reported previously. In this study, we show that exon deletion of the PAH gene accounts for 1.7% of all mutant PAH alleles in Italian hyperphenylalaninemics.

Resistencia a Hormonas Tiroideas (RHT): Descripción de una nueva mutación / Resistance to Thyroid Hormones (RTH): Description of a new mutation

Introducción: La resistencia a hormonas tiroideas (RHT) es un desorden genético de transmisión dominante poco frecuente, caracterizado por una respuesta reducida de los tejidos blanco a las hormonas tiroideas. RHT está ligada al gen del receptor beta de hormona tiroidea (TRβ). El síndrome se identifica por niveles persistentemente elevados de T4 y T3 totales y libres en presencia de TSH no suprimida. Materiales y Métodos: Paciente femenina de 62 años de edad con antecedente de hemitiroidectomía a los 22 años por bocio. Clínicamente, la mujer se encontraba eutiroidea y hemodinámicamente estable. En los exámenes complementarios se constató la presencia de nódulo tiroideo, con estudio citológico benigno y en el laboratorio hormonas tiroideas totales y libres elevadas con TSH no suprimida. La impresión diagnóstica fue RHT, siendo el principal diagnóstico diferencial el tirotropinoma. Se realizó perfil tiroideo completo en el caso índice y en dos familiares de primer grado. Se dosaron gonadotropinas y prolactina, y se realizó RMN de hipófisis en el caso índice. Se estudiaron mutaciones del gen TRβ en ADN genómico en la paciente y en uno de sus familiares. Resultados: Avalando la impresión diagnóstica, tanto el caso índice como los dos familiares mostraron un perfil tiroideo compatible con RHT. El estudio genético identificó una nueva mutación en el exón 10: c.1339C>A que resulta en una sustitución p.P447T. La misma fue observada tanto en el caso índice como en el familiar estudiado. Conclusión: La historia de esta paciente con RHT, al igual que otros casos descriptos en la bibliografía, remarcan la importancia de un diagnóstico adecuado y temprano de esta patología poco frecuente para evitar conductas terapéuticas iatrogénicas y con consecuencias relevantes en la vida de estos pacientes. Paralelamente, se describe una nueva mutación genética en esta familia.

Introduction: Resistance to thyroid hormones (RTH) is an unusual autosomal dominant inherited disorder characterized by a reduced target organ responsiveness to thyroid hormones. RTH is linked to the gene encoding the thyroid receptor β (TR β). This syndrome is characterized by persistent high levels of total and free T4 and T3 while TSH is not inhibited. Materials and Methods: 62 years old female who underwent a partial thyroidectomy because of goiter forty years ago. Clinically, she seemed to be an euthyroid patient and her hemodynamic status was normal. The exams revealed the existence of a benign thyroid nodule, high levels of total and free thyroid hormones and normal values of TSH. Our diagnostic impression was RTH, though differential diagnosis with thyrotropin secreting pituitary adenoma was mandatory. Complete assays of thyroid hormones were performed in the patient and in two first degree relatives. Basal LH, FSH and prolactin were assayed in the patient; and a magnetic resonance imaging of her pituitary gland was obtained. Finally we performed genetic testing in patient's DNA and a relative's DNA to demonstrate gene defect. Results: According to our diagnostic impression, not only the patient's laboratory was compatible with RTH, but so was the laboratory of the two relatives. DNA mutation analisys demonstrated a new mutation in exon 10: c.1339C>A responsible for the substitution p.P447T. This mutation was found in DNA of the patient and DNA of her relative. Conclusion: This patient with RTH, as well as other reported cases, reminds us about the importance of a certain and early diagnosis of this rare disorder in order to avoid iatrogenic treatments. A new mutation is described in this family.

Improved Detection of Germline Mutations in Korean VHL Patients by Multiple Ligation-dependent Probe Amplification Analysis

von Hippel-Lindau (VHL) disease is an autosomal dominant inherited tumor syndrome characterized by the development of tumors in the eye, brain, spinal cord, inner ear, adrenal gland, pancreas, kidney, and epididymis, associated with germline mutations in the VHL gene. We used sequentially sequencing method and multiple ligation-dependent probe amplification (MLPA) analysis and detected germline mutations in the VHL in 15/15 (100%) of VHL patients fulfilling the clinical criteria. Of the 15 distinct mutations detected, large deletions were detected in 5/15 (33.3%) patients, including 4/15 (26.7%) partial deletions and 1/15 (6.6%) deletion of the entire VHL gene by MLPA and the remainder were point mutations detected by sequencing method, of which five mutations were novel. Using MLPA analysis, we detected large deletions including both partial deletions and complete gene deletion, which has not been reported in Korean VHL patients. In conclusion, sequential application of sequencing method and MLPA analysis might make possible to identify germline mutations in most patients with VHL.

Mutational analysis of genes p14ARF, p15INK4b, p16INK4a, and PTEN in human nervous system tumors

The cancer is one of the most common and severe problems in clinical medicine, and nervous system tumors represent about 2% of the types of cancer. The central role of the nervous system in the maintenance of vital activities and the functional consequences of the loss of neurons can explain how severe brain cancers are. The cell cycle is a highly complex process, with a wide number of regulatory proteins involved, and such proteins can suffer alterations that transform normal cells into malignant ones. The INK4 family members (CDK inhibitors) are the cell cycle regulators that block the progression of the cycle through the R point, causing an arrest in G1 stage. The p14ARF (alternative reading frame) gene is a tumor suppressor that inhibits p53 degradation during the progression of the cell cycle. The PTEN gene is related to the induction of growth suppression through cell cycle arrest, to apoptosis and to the inhibition of cell adhesion and migration. The purpose of the present study was to assess the mutational state of the genes p14ARF, p15INK4b, p16INK4a, and PTEN in 64 human nervous system tumor samples. Homozygous deletions were found in exon 2 of the p15INK4b gene and exon 3 of the p16INK4a gene in two schwannomas. Three samples showed a guanine deletion (63 codon) which led to a loss of heterozygosity in the p15 gene, and no alterations could be seen in the PTEN gene. Although the group of patients was heterogeneous, our results are in accordance with other different studies that indicate that homozygous deletion and loss of heterozygosity in the INK4 family members are frequently observed in nervous system tumors.

Screening of RET gene mutations in multiple endocrine neoplasia type-2 using Conformation Sensitive Gel Electrophoresis (CSGE)

Multiple endocrine neoplasia type 2 (MEN2) is an autosomal dominant inherited tumor syndrome caused by RET proto-oncogene germline mutations (RET). Here we tested the Conformation Sensitive Gel Electrophoresis (CSGE) as a screening method for RET hot-spot mutations. Seven MEN2 families were studied by direct sequencing analysis, CSGE and Single Strand Conformational Polymorphism (SSCP). Using CSGE/SSCP, we were able to detect four out of five types of RET mutations verified by sequencing analysis: Cys620Arg, Cys634Arg, Cys634Tyr, and Met918Thr, furthermore a missense substitution at codon 648 (Val648Ile). RET polymorphisms 691 and 769 were also verified. Data obtained using CSGE/SSCP were fully concordant. We conclude that CSGE showed to be a sensitive, fast, low-cost, and simple procedure to detect RET mutations in codons which are reported as the most prevalent RET variants (~ 95 percent) in large MEN2 series. As to the Val804Met mutation, this method still needs to be optimized.

A neoplasia endócrina múltipla tipo 2 (NEM2) é uma síndrome tumoral herdada por mutações germinativas no proto-oncogene RET (RET). Analisamos a aplicação do método Eletroforese em Gel Sensível à Conformação (CSGE) no rastreamento de mutações hot spots do RET. Sete famílias com NEM2 foram rastreadas pelo seqüenciamento gênico, CSGE e análise do Polimorfismo Conformacional de Cadeia Simples (SSCP). Usando ambas as metodologias de rastreamento, identificamos quatro dos cinco tipos de mutações verificadas pelo seqüenciamento: Cys620Arg, Cys634Arg, Cys634Tyr e Met918Thr, além da variação gênica Val648Ile. Das análises englobando mutações hot spots do RET, 90,6 por cento concordaram com o seqüenciamento genético (incluindo a variação gênica Val648Ile). Polimorfismos nos códons 691 e 769 foram documentados. Os dados obtidos por CSGE/SSCP foram totalmente concordantes. Concluímos que o CSGE revelou ser metodologia sensível, rápida, de fácil execução e baixo custo no rastreamento de mutações nos códons associados à grande maioria (~ 95 por cento) dos pacientes com NEM2.

Mutations of short tandem repeat loci in Identifiler system / 法医学杂志

OBJECTIVE@#To explore and analyze the mutations of 15 Short Tandem Repeat (STR) loci using Identifiler system in paternity identification.@*METHODS@#2712 cases of paternity testing were carried out using Identifiler PCR Amplification Kit.@*RESULTS@#Of the 2362 paternity testing cases, mutations of single locus were observed in 51 cases. The mutation loci included D8S1179, D21S11, D7S820, CSF1PO, D3S1358, D13S317, D16S539, D2S1338, D19S433, vWA, D18S51, D5S818 and FGA, with the D21S11 locus having a highest mutation rate (0.369%). Thirty-six of the STR mutations were from paternal source, 7 from maternal source, and the rest (9) were undeterminable. The mutation rates at D21S11 were highest (0.369%).@*CONCLUSION@#Mutations of STR loci are relatively common in human genome. Therefore, retesting of additional relatively stable STR loci with lower mutation rates is necessary when one or two loci exclusions are encountered in paternity testing.