Diagnostic Molecular Pathology最新文献

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The effect of aging of formalin-fixed paraffin-embedded tissues on the in situ hybridization and immunohistochemistry signals in cervical lesions. 福尔马林固定石蜡包埋组织老化对宫颈病变组织原位杂交和免疫组化信号的影响。
Diagnostic Molecular Pathology Pub Date : 2013-09-01 DOI: 10.1097/PDM.0b013e3182823701
Allison J Nuovo, Michela Garofalo, Alexandria Mikhail, Alcina F Nicol, Cecilia Vianna-Andrade, Gerard J Nuovo
{"title":"The effect of aging of formalin-fixed paraffin-embedded tissues on the in situ hybridization and immunohistochemistry signals in cervical lesions.","authors":"Allison J Nuovo,&nbsp;Michela Garofalo,&nbsp;Alexandria Mikhail,&nbsp;Alcina F Nicol,&nbsp;Cecilia Vianna-Andrade,&nbsp;Gerard J Nuovo","doi":"10.1097/PDM.0b013e3182823701","DOIUrl":"https://doi.org/10.1097/PDM.0b013e3182823701","url":null,"abstract":"<p><p>Formalin-fixed, paraffin-embedded tissues are widely used in biomedical research but little is known about the effect of the age of the block or unstained slides on the in situ hybridization or immunohistochemistry signal. We compared the in situ-based and immunohistochemistry-based signals for cervical intraepithelial neoplasia samples that ranged from 0 to 15 years of age. There was a progressive and statistically significant decrease in the strength of the p16 signal when comparing tissues prepared from recent unstained slides (0 to 1 y old, mean score of 92%) to those of intermediate age (5 to 7 y old, mean score of 49%) to old unstained slides (cut 13 to 15 y ago, mean score of 10%). Equivalent, progressive, and significant decreases in the intensity of the signals for microRNAs, CD45, and human papillomavirus DNA were seen in tissues stored on slides from 5 to 7 years and 13 to 15 years, respectively. However, the diminution of signal was much less, although still statistically significant, if the sections from the 13- to 15-year-old paraffin blocks were prepared in 2012. The data likely does not represent degradation of the targets as extraction of several microRNA from the old blocks showed no detectable degradation, despite the markedly weakened in situ hybridization signal. It is concluded that in situ-based signal for DNA, microRNAs, and proteins in paraffin-embedded tissues are significantly reduced over time, especially when stored long term on glass slides which, in turn, can lead to a significant underestimation of the amount and presence of the nucleic acid or protein target. </p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 3","pages":"164-73"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e3182823701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31574553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 21
Prognostic and putative predictive biomarkers of gastric cancer for personalized medicine. 胃癌个体化治疗的预后和推测的预测性生物标志物。
Diagnostic Molecular Pathology Pub Date : 2013-09-01 DOI: 10.1097/PDM.0b013e318284188e
Viktoria S Warneke, Hans-Michael Behrens, Jochen Haag, Katharina Balschun, Christine Böger, Thomas Becker, Matthias P A Ebert, Florian Lordick, Christoph Röcken
{"title":"Prognostic and putative predictive biomarkers of gastric cancer for personalized medicine.","authors":"Viktoria S Warneke,&nbsp;Hans-Michael Behrens,&nbsp;Jochen Haag,&nbsp;Katharina Balschun,&nbsp;Christine Böger,&nbsp;Thomas Becker,&nbsp;Matthias P A Ebert,&nbsp;Florian Lordick,&nbsp;Christoph Röcken","doi":"10.1097/PDM.0b013e318284188e","DOIUrl":"https://doi.org/10.1097/PDM.0b013e318284188e","url":null,"abstract":"<p><p>We investigated various phenotypic and genotypic biomarkers of gastric cancer (GC) testing the following hypotheses: are these biomarkers suitable for the identification of GC subtypes, are they of prognostic significance, and should any of these biomarkers be considered to tailor patient treatment in the future. The study cohort consisted of 482 patients. pTNM-stage was based on surgical pathologic examination. The Laurén and mucin phenotype was assessed. Helicobacter pylori and Epstein-Barr virus infections were documented. The following biomarkers were determined: BRAF, KRAS, NRAS, and PIK3CA genotype, microsatellite instability, mucin 1, mucin 2, mucin 5, and mucin 6, CD10, E-cadherin, β-catenin, and lysozyme. The histologic phenotype correlated with 10/13 (77%) clinicopathologic patient characteristics and 6/13 (46%) immunohistochemical/molecular biological biomarkers. Inversely, immunohistochemical biomarkers (mucin phenotype, E-cadherin, β-catenin, and lysozyme) were unsuitable for subclassification of GC. It showed too much overlap between the different subtypes. Among the genotypes, only microsatellite instability correlated with tumor type being more prevalent in intestinal and unclassified GCs. Patient survival correlated significantly with 8 (62%) clinicopathologic and 5 (36%) immunohistochemical/molecular biomarkers. Interestingly, in proximal GCs, KRAS mutation was associated with worse prognosis, as was persistent H. pylori infection in unclassified GCs. Mucin 2 (all patients, proximal GCs) and PIK3CA (exon 20; intestinal type GC) prognosticated independently patient survival. The biomarkers examined herein are unsuitable to aid histologic classification of GC. However, several of them show a correlation with either phenotype and/or prognosis and may be considered to tailor patient treatment in the future, such as KRAS, PIK3CA, MSI, and H. pylori status. </p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 3","pages":"127-37"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e318284188e","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31573530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 50
Evaluation of a BeadXpress assay for a 151-mutation and variant CFTR screening panel after 11,000 samples: implications for practice. 对11,000个样本后151个突变和变异CFTR筛选小组的BeadXpress检测的评估:实践意义
Diagnostic Molecular Pathology Pub Date : 2013-09-01 DOI: 10.1097/PDM.0b013e318286b4c0
Jay Stoerker, Thomas G Goodman, Heather M Walline, Jeffrey Sugalski, Carol A Holland
{"title":"Evaluation of a BeadXpress assay for a 151-mutation and variant CFTR screening panel after 11,000 samples: implications for practice.","authors":"Jay Stoerker,&nbsp;Thomas G Goodman,&nbsp;Heather M Walline,&nbsp;Jeffrey Sugalski,&nbsp;Carol A Holland","doi":"10.1097/PDM.0b013e318286b4c0","DOIUrl":"https://doi.org/10.1097/PDM.0b013e318286b4c0","url":null,"abstract":"<p><p>We created a 151-mutation and variant screening panel for cystic fibrosis transmembrane regulator (CFTR) using the Illumina Inc. BeadXpress platform (San Diego, CA). The laboratory developed test was validated using a third-party blinding of a set of 450 samples split with an authority laboratory that provides a large panel CFTR screening and 50 diverse controls admixed randomly. The validation proved the test to be 100% sensitive for the mutations tested and >99% specific. A total of 391 mutations in 11,186 samples tested were confirmed by repeat analysis and sequencing, resulting in an overall confirmed positive rate of 3.5%. Of the mutations detected, 348 were part of the American College of Obstetrics and Gynecology (ACOG) panel (89%) and 43 were non-ACOG (11%). A total of 16 of the 23 ACOG panel mutations were discovered in this cohort, along with 21 different non-ACOG mutation genotypes. We confirmed 6 total patients carrying mutations that would not have been identified by any other commercial panel. The role of a large genotyping panel in carrier screening is discussed relative to the ACOG panel and also in relation to comparative efficacy with targeted massive parallel sequencing. </p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 3","pages":"144-8"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e318286b4c0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31574549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Atypical Epstein-Barr viral genomic structure in lymphoma tissue and lymphoid cell lines. 非典型eb病毒在淋巴瘤组织和淋巴样细胞系中的基因组结构。
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e318273fb43
Weihua Tang, Hongxin Fan, Jane Schroeder, Cherie H Dunphy, Ronald J Bryant, Yuri Fedoriw, Margaret L Gulley
{"title":"Atypical Epstein-Barr viral genomic structure in lymphoma tissue and lymphoid cell lines.","authors":"Weihua Tang,&nbsp;Hongxin Fan,&nbsp;Jane Schroeder,&nbsp;Cherie H Dunphy,&nbsp;Ronald J Bryant,&nbsp;Yuri Fedoriw,&nbsp;Margaret L Gulley","doi":"10.1097/PDM.0b013e318273fb43","DOIUrl":"https://doi.org/10.1097/PDM.0b013e318273fb43","url":null,"abstract":"<p><p>Epstein-Barr virus (EBV) DNA is found within the malignant cells of some subtypes of lymphoma, and viral presence is being exploited for improved diagnosis, monitoring, and management of affected patients. Recent work suggests that viral genomic polymorphism, such as partial deletion of the viral genome, could interfere with virus detection in tumor tissues. To test for atypical forms of the EBV genome, 98 lymphomas and 6 infected cell lines were studied using a battery of 6 quantitative polymerase chain reaction assays targeting disparate sections of EBV DNA. Fifty of the lymphomas (51%) had no amplifiable EBV DNA, and 38 lymphomas (39%) had low-level EBV infection that was deemed incidental based on EBV-encoded RNA (EBER) in situ hybridization results. The remaining 10 lymphomas (10%) had high EBV loads and EBER localization to malignant cells by EBER in situ hybridization. All 10 represented lymphoma subtypes were previously associated with EBV (Burkitt, diffuse large B-cell, or T-cell type), whereas no remnants of EBV were detected in other lymphoma subtypes (follicular, small lymphocytic, mantle cell, or marginal zone type). Interestingly, 4 of the 10 infected lymphomas had evidence of atypical viral genomes, including 3 of 4 infected T-cell lymphomas with aberrant loss of LMP2 amplicons, and a single diffuse large B-cell lymphoma lacking the central part of the viral genome spanning BamH1W, BZLF1, and EBNA1 gene segments. A reasonable screening strategy for infected malignancy involves applying EBER1 and LMP1 quantitative polymerase chain reaction assays and confirming that values exceeding 2000 copies of EBV per 100,000 cells have EBER localization to malignant cells.</p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"91-101"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e318273fb43","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31394143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
EGFR promoter methylation detection in cervical cancer by a hybridization-fluorescence polarization assay. 杂交-荧光偏振法检测宫颈癌中EGFR启动子甲基化。
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e31827744ad
Wei Zhang, Yane Gao, Yinghao Jiang, Liang Ping, Hong Cheng, Ju Zhang
{"title":"EGFR promoter methylation detection in cervical cancer by a hybridization-fluorescence polarization assay.","authors":"Wei Zhang,&nbsp;Yane Gao,&nbsp;Yinghao Jiang,&nbsp;Liang Ping,&nbsp;Hong Cheng,&nbsp;Ju Zhang","doi":"10.1097/PDM.0b013e31827744ad","DOIUrl":"https://doi.org/10.1097/PDM.0b013e31827744ad","url":null,"abstract":"<p><p>The methylation status of the epidermal growth factor receptor (EGFR) promoter is of potential predictive value for benefitting from EGFR inhibition therapy. Stratified therapy assignment for cervical cancer patients based on the EGFR promoter methylation status requires a simple detection method in the daily practice of diagnosis. A novel assay detecting the EGFR promoter methylation status in cervical cancer tissue samples using a hybridization-fluorescence polarization (FP) technique was developed. A pair of primers was used to amplify a 156 bp fragment in the promoter region of EGFR. Two probes specific for either methylated or unmethylated EGFR promoter DNA labeled with different fluorophores hybridized, respectively, with their target amplicons. The EGFR promoter methylation status was determined by the FP values. A total of 273 cervical cancer tissue samples were simultaneously analyzed using the new assay technique and combined bisulfite restriction analysis. The new assay was more sensitive compared with the combined bisulfite restriction analysis, and it allowed the discrimination of the EGFR promoter methylation status directly in solution without the restriction enzyme digestion. Sensitivity, specificity, and stability of the hybridization-FP assay had been recorded. The minimum detection level established with the new assay was 50 copies/μL, and it was able to detect the minor population of the EGFR promoter methylation status even when its contents were as low as 10%. No cross-reaction was observed in the assay when the amount of plasmids used accounted for no more than 10(9) copies/μL. The coefficient of variation of the reproducibility for the assay was <10%.</p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"102-6"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e31827744ad","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31395120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Evaluation of 2-year experience with EGFR mutation analysis of small diagnostic samples. 2年小诊断样本EGFR突变分析经验评价
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e31827e6984
Katarina Hlinkova, Pavel Babal, Peter Berzinec, Ivan Majer, Zdenka Mikle-Barathova, Barbora Piackova, Denisa Ilencikova
{"title":"Evaluation of 2-year experience with EGFR mutation analysis of small diagnostic samples.","authors":"Katarina Hlinkova,&nbsp;Pavel Babal,&nbsp;Peter Berzinec,&nbsp;Ivan Majer,&nbsp;Zdenka Mikle-Barathova,&nbsp;Barbora Piackova,&nbsp;Denisa Ilencikova","doi":"10.1097/PDM.0b013e31827e6984","DOIUrl":"https://doi.org/10.1097/PDM.0b013e31827e6984","url":null,"abstract":"<p><p>Mutation analysis of the epidermal growth factor receptor (EGFR) gene is an essential part of the diagnostic algorithm in patients with metastatic or recurrent non-small cell lung cancer (NSCLC). Small biopsies or cytology specimens represent >80% of the available diagnostic material. EGFR mutation analyses were realized on 835 samples (675 cytology specimens, 151 formalin-fixed paraffin-embedded blocks, 5 tumors, and 4 pleural effusions). EGFR mutation analysis was performed by high-resolution melting analysis in combination with mutant-enriched polymerase chain reaction and sequencing analysis. Because of increased risk of inaccuracy in histology diagnosis of small specimens, all subtypes of NSCLC were analyzed. EGFR mutations were detected in 83 cases (10%). EGFR mutation testing failed in 5% (42/835) and was associated with poor cellularity, low percentage of tumor cells, and bad quality of DNA. Although 281 samples were evaluated as insufficient material (poor cellularity and/or unrepresentative tumor content), mutation rates were 7%. Although only adenocarcinomas or NSCLC-not otherwise specified are recommended for EGFR mutation testing, EGFR mutations in 11% of the large cell carcinomas and 4% of the squamous cell carcinomas were observed. Our results indicate that defined algorithm for EGFR testing of small diagnostic samples is sensitive, fast, and suitable even for samples with poor cellularity. The results of this testing should be evaluated depending on tumor content and DNA quality for each sample individually. At the conclusion of our results, we recommend to realize EGFR mutation analysis of small diagnostic samples regardless of the histologic subtypes of NSCLC.</p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"70-5"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e31827e6984","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31394140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 20
High incidence of MYCN amplification in a Moroccan series of neuroblastic tumors: comparison to current biological data. 摩洛哥一系列神经母细胞肿瘤中MYCN扩增的高发生率:与当前生物学数据的比较
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e318277448e
Imane Tabyaoui, Nadia Tahiri-Jouti, Zineb Serhier, Khadija El Maani, Siham Cherkaoui, Mounia Al Zemmouri, Mohamed B Othmani, Soumaya Zamiati
{"title":"High incidence of MYCN amplification in a Moroccan series of neuroblastic tumors: comparison to current biological data.","authors":"Imane Tabyaoui,&nbsp;Nadia Tahiri-Jouti,&nbsp;Zineb Serhier,&nbsp;Khadija El Maani,&nbsp;Siham Cherkaoui,&nbsp;Mounia Al Zemmouri,&nbsp;Mohamed B Othmani,&nbsp;Soumaya Zamiati","doi":"10.1097/PDM.0b013e318277448e","DOIUrl":"https://doi.org/10.1097/PDM.0b013e318277448e","url":null,"abstract":"<p><p>MYCN protooncogene status was assessed for the first time in Morocco in peripheral neuroblastic tumors, including neuroblastoma, ganglioneuroblastoma, and ganglioneuroma. Correlations with age at diagnosis, stage, mitosis-karyorrhexis index, differentiation, and Shimada histology were evaluated. Thirty-six formalin-fixed, paraffin-embedded peripheral neuroblastic tumor tissue specimens collected between 2007 and 2010 from the Pathology Department were assessed for MYCN amplification using fluorescence in situ hybridization. MYCN amplification was found in 27.8% of cases. An association of MYCN amplification with unfavorable Shimada grading, higher mitosis-karyorrhexis index, and undifferentiated morphologic phenotype was found. We found no correlation with older age, advanced stage, or the presence of metastasis. Our results suggested that the presence of MYCN amplification is a strong biological indicator of a poor outcome and aggressive disease in neuroblastoma and nodular ganglioneuroblastoma.</p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"112-8"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e318277448e","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31395122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Gallbladder carcinoma: high rate of mitochondrial D-loop mutations. 胆囊癌:线粒体d -环突变率高。
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e31827a0d5a
Sanjeev K Maurya, Mallika Tewari, Hari S Shukla
{"title":"Gallbladder carcinoma: high rate of mitochondrial D-loop mutations.","authors":"Sanjeev K Maurya,&nbsp;Mallika Tewari,&nbsp;Hari S Shukla","doi":"10.1097/PDM.0b013e31827a0d5a","DOIUrl":"https://doi.org/10.1097/PDM.0b013e31827a0d5a","url":null,"abstract":"<p><p>The molecular mechanisms leading to gallbladder carcinoma (GBC) are poorly understood. Different molecular disorders, including nuclear and mitochondrial genomic alteration, are associated with different cancers. The frequency of mitochondrial genome mutation has remained completely unexplored. In GBC, this is the first report of a mutation analysis in the mitochondrial genome, especially in the D-loop region. For a comprehensive D-loop view in GBC in humans, we sequenced the mitochondrial genome of 35 GBC patients and matched germ-line DNA. A wide range of point mutations and polymorphisms was observed. These variations in the D-loop sequence of human GBC represent good evidence of the mitochondrial role in GB carcinogenesis and may be used as a marker for GBC.</p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"119-22"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e31827a0d5a","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31395123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
High-resolution genome-wide copy-number analyses identify localized copy-number alterations in Ewing sarcoma. 高分辨率全基因组拷贝数分析确定了尤因肉瘤的局部拷贝数改变。
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e31827a47f9
Miriam Lynn, Yuexiang Wang, Jaime Slater, Naisha Shah, Judith Conroy, Sean Ennis, Thomas Morris, David R Betts, Jonathan A Fletcher, Maureen J O'Sullivan
{"title":"High-resolution genome-wide copy-number analyses identify localized copy-number alterations in Ewing sarcoma.","authors":"Miriam Lynn,&nbsp;Yuexiang Wang,&nbsp;Jaime Slater,&nbsp;Naisha Shah,&nbsp;Judith Conroy,&nbsp;Sean Ennis,&nbsp;Thomas Morris,&nbsp;David R Betts,&nbsp;Jonathan A Fletcher,&nbsp;Maureen J O'Sullivan","doi":"10.1097/PDM.0b013e31827a47f9","DOIUrl":"https://doi.org/10.1097/PDM.0b013e31827a47f9","url":null,"abstract":"Ewing sarcoma family tumors are aggressive sarcomas of childhood and adolescence with continuing poor outcomes. Decades of research on the characteristics of the often solitary-known oncogenic-genomic aberration in Ewing sarcoma family tumors, namely a TET-ETS fusion, have provided little advancement in the understanding of the molecular pathogenesis of Ewing sarcoma or treatment thereof. In this study, the high-resolution single-nucleotide polymorphism technology was used to identify additional/secondary copy-number alterations (CNAs) in Ewing sarcoma that might elucidate the aggressive biology of this sarcoma. We compared paired constitutional and tumor DNA samples. Commonly known genomic alterations including gain of 1q and chromosome 8 were the most frequently detected changes in this study. In addition, deletions and loss of heterozygosity were identified in 10q, 11p, and 17p. Furthermore, tumor-specific CNAs were identified not only in genes previously known to be of interest, including CDKN2A, but also in genes not previously associated with Ewing sarcoma, including SOX6 and PTEN. Selected array-based findings were confirmed by fluorescence in situ hybridization, immunohistochemical studies, or sequencing. The results highlight an unexpected level of cytogenetic complexity associated with several of the samples, 2 of which contained TP53 mutations. In summary, our high-resolution genome-wide copy-number data identify several novel CNAs associated with Ewing sarcoma, which are promising targets for novel therapeutic strategies in this aggressive sarcoma.","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"76-84"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e31827a47f9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31394141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 21
Genetic diagnosis in recently transfused patients. 近期输血患者的基因诊断。
Diagnostic Molecular Pathology Pub Date : 2013-06-01 DOI: 10.1097/PDM.0b013e31827630b8
Ana C Mardini, Fabiana Q Mayer, Rodrigo Rodenbusch, Ursula Matte, Maria L Saraiva-Pereira
{"title":"Genetic diagnosis in recently transfused patients.","authors":"Ana C Mardini,&nbsp;Fabiana Q Mayer,&nbsp;Rodrigo Rodenbusch,&nbsp;Ursula Matte,&nbsp;Maria L Saraiva-Pereira","doi":"10.1097/PDM.0b013e31827630b8","DOIUrl":"https://doi.org/10.1097/PDM.0b013e31827630b8","url":null,"abstract":"<p><p>Analysis of recently transfused patients is usually postponed to avoid spurious results because of contamination with donor's cells. However, little is known about the extent of this influence in routine molecular diagnostic tests. To elucidate this question, we tested a mix of blood samples from 2 α-1-antitrypsin-deficient patients diagnosed as Pi*Z homozygous with 1 normal donor at 1:1, 1:10, 1:20, and 1:30 proportions. Human identification panel and Pi*Z allele detection were used to establish the detection limit of a blood mixture. Mixtures of 1:1 and 1:10 were easily detected with both techniques, whereas for 1:30, it was necessary to change the equipment settings to identify the mixture. Moreover, the heterozygous pattern observed for the mixtures on Pi*Z genotyping was weaker at this level of mixture. We further evaluated the degree of mixture detectable in 20 transfused patients who received 1 blood unit (concentrate of irradiated or nonirradiated red blood cells) using the human identification panel. Two days after the transfusion, the presence of the donor's markers was not detected, suggesting that after this time point the levels of admixture are below 1:30. The methods applied in the present study showed adequate sensitivity to identify alleles of the so-called \"smaller population\" of cells up to 3%, approximately. The same result was obtained in a \"diagnostic situation,\" in which the blood mixture was submitted to a PCR-RFLP protocol to detect a mutation.</p>","PeriodicalId":11235,"journal":{"name":"Diagnostic Molecular Pathology","volume":"22 2","pages":"123-6"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1097/PDM.0b013e31827630b8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31395124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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