Highly recurrent H3F3A mutations with additional epigenetic regulator alterations in giant cell tumor of bone

Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next‐generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin‐fixed paraffin‐embedded (FFPE) samples for clinical diagnosis have not been assessed. To address these issues, we conducted whole‐exome sequencing of 7 GCTBs and integrated the previously published genomic sequencing data of 6 GCTBs. We subsequently performed targeted sequencing of an additional 39 GCTBs, including 2 atypical cases and an extremely rare case of primary malignant transformation of GCTB. We also evaluated the sensitivity of Sanger sequencing for detecting H3F3A mutations in FFPE samples that are usually used for clinical diagnosis. H3F3A glycine hotspot mutations were the most frequently detected mutations (96%) in the 52 GCTBs by NGS. Of the 50 hotspot mutations, p.G34W was observed in 48 cases and p.G34L/G34R was detected in one. One of two atypical GCTB cases with wild‐type H3F3A had a H3F3B mutation (p.G34V). Other mutated genes were not recurrent. Sanger sequencing did not detect H3F3A mutations in 10 of 15 H3F3A NGS mutation‐positive FFPE samples. In conclusion, we confirmed that H3F3A is the most frequently mutated GCTB driver gene, and that H3F3A mutations are not present in atypical GCTBs. Sanger sequencing was much less sensitive than targeted NGS for detecting H3F3A mutations in FFPE samples.     

Comparison of Targeted Next‐Generation Sequencing (NGS) and Real‐Time PCR in the Detection of EGFR,KRAS, and BRAF Mutations on Formalin‐Fixed,Paraffin‐Embedded Tumor Material of Non‐Small Cell Lung Carcinoma—Superiority of NGS

The development of tyrosine kinase inhibitor treatments has made it important to test cancer patients for clinically significant gene mutations that influence the benefit of treatment. Targeted next‐generation sequencing (NGS) provides a promising method for diagnostic purposes by enabling the simultaneous detection of multiple mutations in various genes in a single test. The aim of our study was to screen EGFR, KRAS, and BRAF mutations by targeted NGS and commonly used real‐time polymerase chain reaction (PCR) methods to evaluate the feasibility of targeted NGS for the detection of the mutations. Furthermore, we aimed to identify potential novel mutations by targeted NGS. We analyzed formalin‐fixed, paraffin‐embedded (FFPE) tumor tissue specimens from 81 non‐small cell lung carcinoma patients. We observed a significant concordance (from 96.3 to 100%) of the EGFR, KRAS, and BRAF mutation detection results between targeted NGS and real‐time PCR. Moreover, targeted NGS revealed seven nonsynonymous single‐nucleotide variations and one insertion‐deletion variation in EGFR not detectable by the real‐time PCR methods. The potential clinical significance of these variants requires elucidation in future studies. Our results support the use of targeted NGS in the screening of EGFR, KRAS, and BRAF mutations in FFPE tissue material. © 2012 Wiley Periodicals, Inc.     

Evaluation of DNA and RNA quality from archival formalin‐fixed paraffin‐embedded tissue for next‐generation sequencing – Retrospective study in Japanese single institution

Genetic analysis on formalin‐fixed paraffin‐embedded (FFPE) tissue specimens has become a mainstream method, from conventional direct sequencing to comprehensive analysis using next‐generation sequencing (NGS). In this study, we evaluated the quality of DNA and RNA extracted from FFPE sections, derived from surgical specimens of different tumor types. Electrophoresis was performed using a 4200 TapeStation to evaluate DNA and RNA fragmentation. DNA Ct values were higher and significantly increased over a period of 4 years compared with those from cell lines or frozen tissues. The RNA integrity number equivalent (RIN) ranged from 1 to 4.1 and DV200 ranged from 7.3 to 81%. Twelve of the 108 cases were analyzed by NGS using the AmpliSeq Cancer HotSpot Panel v2 on a Miniseq system. A sufficient number of reads and coverage were obtained in all cases. Our results revealed that NGS analysis was sufficient for FFPE‐derived DNA within 4 years of preservation. Conversely, approximately 20% of the RNA derived from FFPE within 4 years from the collection could be inappropriate for gene analysis based on RIN and DV200. It was suggested that FFPE would be adequate for genetic analysis, although it is desirable to store frozen specimens for the tumor tissues to be subjected to genetic analysis.     

Detection of EGFR mutation in supernatant,cell pellets of pleural effusion and tumor tissues from non-small cell lung cancer patients by high resolution melting analysis and sequencing

To determine epidermal growth factor receptor (EGFR) mutation in advanced non-small cell lung cancer (NSCLC) patients and compare the detection efficiency between different sample resources, both high resolution melting (HRM) analysis and direct sequencing method were used to analyze 36 pleural effusion samples and 22 matched biopsy tumor tissues collected from NSCLC patients. For each pleural effusion sample, the supernatant and the cell pellets were examined separately. Among all the 36 cases of pleural effusion samples, 18 mutations of EGFR were found in cell-free supernatant while 13 mutations were found in the cell pellets as detected by HRM analysis. In the 22 matched samples, 13 cases of EGFR mutations were identified in paraffin-embedded biopsy tissue samples, 12 cases in the cell-free supernatant and 9 cases in the cell pellets of pleural effusion. EGFR mutations in 15 cases out of the total 36 pleural effusion samples detected by direct sequencing were also identified by HRM analysis, giving 100% efficiency for HRM method. The results established the important role of HRM as a reliable and efficient method to determine EGFR mutation status and indicated the feasibility of using pleural effusion in replacement of biopsy tissues in particular clinical cases. Furthermore, the cell-free supernatant of pleural effusion might be a better resource for mutation detection than cell pellets.     

Molecular alterations in endometrial archived liquid‐based cytology

Endometrial cancer is one of the most common gynecological malignancy worldwide and its prevalence is increasing. The introduction of liquid‐based cytology (LBC) and endoflower dispositive in routine practice gives the possibility to examine endometrial cells by cytological diagnosis and may also release the opportunity to study molecular alterations, in endometrioid type cancer in which carcinogenesis is well known. We gathered 72 cases of endometrial LBC samples and corresponding formalin‐fixed paraffin‐embedded (FFPE) blocks, collected from 2004 to 2010. DNA was isolated from both samples using standard protocols. DNA quality and quantity were assessed using Nanodrop and BIOMED2 multiplex PCR. Mutations in exon 5 of PTEN and exon 20 of PI3K were studied using Sanger sequencing. DNA with good quality and amount was isolated from 67/72 FFPE cases. In these samples, two cases were found to harbor mutations in exon 5 of PTEN. No PI3K mutations were identified. LBC samples were then assessed to verify the concordance with the FFPE DNA results. The results obtained were concordant, that is the wild type cases in FFPE were also wild type in LBC and vice versa for the mutated case. Unfortunately, the second case of mutation in PTEN could not be confirmed in LBC due to low amount of DNA obtained. Detection of molecular alterations in LBC will open a new era for the detection in asymptomatic women of precursor lesions that could evolve into cancer and for endometrial cancer diagnosis and screening in selected high‐risk women. Diagn. Cytopathol. 2013. © 2012 Wiley Periodicals, Inc.     

Genotyping of colorectal cancer for cancer precision medicine: Results from the IPH Center for Molecular Pathology

Cancer precision medicine has opened up new avenues for the treatment of colorectal cancer (CRC). To fully realize its potential, high‐throughput sequencing platforms that allow genotyping beyond KRAS need to be implemented and require performance assessment. We comprehensively analyzed first‐year data of 202 consecutive formalin‐fixed paraffin embedded (FFPE) CRC samples for which prospective genotyping at our institution was requested. Deep targeted genotyping was done using a semiconductor‐based sequencing platform and a self‐designed panel of 30 CRC‐related genes. Additionally, microsatellite status (MS) was determined. Ninety‐seven percent of tumor samples were suitable for sequencing and in 88% MS could be assessed. The minimal drop‐out rates of 6 and 25 cases, respectively were due to too low amounts or heavy degradation of DNA. Of 557 nonsynonymous mutations, 90 (16%) have not been described in COSMIC at the time of data query. Forty‐three cases (22%) had double‐ or triple mutations affecting a single gene. Sixty‐four percent had genetic alterations influencing oncological therapy. Eight percent of patients (MSI phenotype: 6%; mutated POLE: 2%) were potentially eligible for treatment with immune checkpoint inhibitors. Of 56% of KRASwt CRC that potentially qualified for anti‐EGFR treatment, 30% presented with mutations in BRAF/NRAS. Mutated PIK3CA was detected in 21%. In conclusion, we here present real‐life routine diagnostics data that not only demonstrate the robustness and feasibility of deep targeted sequencing and MS‐analysis of FFPE CRC samples but also contribute to the understanding of CRC genetics. Most importantly, in more than half of the patients our approach enabled the selection of the best treatment currently available. © 2016 Wiley Periodicals, Inc.     

KRAS mutation analysis on cytological specimens of metastatic colo‐rectal cancer

Recent evidences showed that metastatic colorectal cancer (CRC) patients with tumors harboring a KRAS gene mutation do not derive benefit from the administration of epidermal growth factor receptor‐directed monoclonal antibodies. Typically, the specimens available for KRAS mutational analysis are formalin‐fixed paraffin‐embedded (FFPE) primary tumor tissue blocks. However, in patients with rectal tumours undergoing neoadjuvant therapy, the source of FFPE material is limited. In this setting, CRC cytological samples taken from the metastatic site may be exploited. However, these specimens show at least some degree of necrosis; thus, their suitability for the KRAS assay needs to be tested. Here, we show that 18/19 (94.7%) metastatic CRC smears were perfectly adequate for codon 12 and 13 KRAS mutational analysis by direct gene sequencing. Only one case (5.3%) showing abundant necrotic debris and poor cellular preservation was not informative for KRAS status. Codon 12 gene mutations were found in 4/18 (22.2%) of the adequate cases (c35G>T n = 2; c34G>T n = 1; c35G>A n = 1). Concordance between cytological and FFPE samples, both available in 13 patients, occurred in 92.3% (12/13) of the cases. Thus, whenever histological specimens of CRC are notavailable, KRAS testing may be reliably performed on cytological specimens. Diagn. Cytopathol. 2010;38:869–873. © 2010 Wiley‐Liss, Inc.     

Molecular pathological analysis of sarcomas using paraffin‐embedded tissue: current limitations and future possibilities

Sarcomas of soft tissue and bone are rare neoplasms that can be separated into a large number of different diagnostic entities. Over the years, a number of diagnostic markers have been developed that aid pathologists in reaching the appropriate diagnoses. Many of these markers are sarcoma‐specific proteins that can be detected by immunohistochemistry in formalin‐fixed, paraffin‐embedded (FFPE) sections. In addition, a wide range of molecular studies have been developed that can detect gene mutations, gene amplifications or chromosomal translocations in FFPE material. Until recently, most sequencing‐based approaches relied on the availability of fresh frozen tissue. However, with the advent of next‐generation sequencing technologies, FFPE material is increasingly being used as a tool to identify novel immunohistochemistry markers, gene mutations, and chromosomal translocations, and to develop diagnostic tests.     

非小细胞肺癌患者胸腔积液中EGFR基因突变的检测及临床意义

目的:探讨采用非小细胞肺癌患者胸腔积液标本肿瘤细胞进行表皮生长因子(epidermal growth factor receptor,EGFR)基因突变检测的可行性及其临床意义.方法:采用Sanger测序法检测17例非小细胞肺癌患者胸腔积液及对应的17例手术或肺部穿刺组织标本EGFR基因18～21外显子基因突变,并进行统计分析.结果:胸腔积液标本17例共检出5例突变,检出率29.41％.手术或穿刺组织标本17例共检出7例突变,检出率41.18％.胸腔积液标本EGFR基因突变检出率略低于手术或穿刺组织标本.结论:采用Sanger测序法进行非小细胞肺癌患者胸腔积液中EGFR基因突变的检测,方法可行,尤其适用于无法获取手术或肺部穿刺组织标本的患者.     

Performance of Idylla KRAS assay on extracted DNA and de-stained cytology smears: Can we rescue small sample?

ObjectiveKRAS is a frequently mutated gene in cancers, and with recent FDA-approved targeted therapy for the G12C mutation, testing for KRAS variants is essential. We evaluated the performance of the Idylla KRAS assay on extracted DNA and cytology smears in order to expand the utility of the assay.MethodsIn total, fifty-seven human samples were analyzed. Idylla results from sixteen DNA extracted from formalin-fixed, paraffin-embedded tissues (FFPE DNA) and thirty cytology smears were compared to the reference method. We evaluated the performance of the Idylla assay using corresponding cytology smears to rescue cellblocks or surgical blocks that were quantity not sufficient (QNS) for next generation sequencing (NGS).ResultIn the FFPE DNA cohort, 10 ng DNA input yielded valid results in all 16 samples, with 15 of 16 (93 %) concordant with NGS findings. In the cytology smear cohort, the Idylla KRAS assay demonstrated 100 % concordance with previous NGS results in 30 cases. In the QNS cohort, the assay was valid in all cases and KRAS mutations were identified in 3 of 11 cytology smears, including one G12C mutation.ConclusionThe Idylla KRAS assay is a high-performing, feasible, and convenient option for testing extracted DNA and cytology smears. It rescues QNS samples allowing it to be integrated into the molecular workflow as an initial screening test with remarkably quick turnaround times.     

Targeted RNA sequencing: A routine ancillary technique in the diagnosis of bone and soft tissue neoplasms

The past decade has witnessed remarkable progress in delineating the molecular pathogenesis of many mesenchymal neoplasms. This, in large part, is attributable to the application of next‐generation sequencing. As these techniques decrease in cost, and increasingly support the use of routine clinical specimens—such as formalin‐fixed paraffin‐embedded tissue and cytology samples—they are beginning to be routinely implemented in diagnostic pathology laboratories. The breadth of testing possible by next‐generation sequencing makes this a useful adjunct for pathologists, particularly with the emergence of targeted therapies. The intent of this article is to share our experience, over 2 years, as an early adopter of targeted RNA sequencing as an ancillary diagnostic technique for fusion gene detection in bone and soft tissue neoplasms.     

IDH1 Mutations in Oligodendroglial Tumors: Comparative Analysis of Direct Sequencing,Pyrosequencing, Immunohistochemistry,Nested PCR and PNA‐Mediated Clamping PCR

Mutations in isocitrate dehydrogenase 1 (IDH1) are found in a high proportion of glial tumors and have a significant prognostic impact. Although direct sequencing has been considered to be the gold‐standard method to detect this mutation, the sensitivity of this technique has been questioned especially because specimens from glial tumors may contain large numbers of non‐tumor cells. We screened 141 cases of oligodendroglial tumors for IDH1 mutations using peptide nucleic acid (PNA)‐mediated clamping polymerase chain reaction (PCR) and compared the results with the results of direct sequencing, pyrosequencing, and immunohistochemistry (IHC). Nested PCR was only performed in cases having mutant IDH1 only discovered by clamping PCR. Using dilution experiments mixing IDH1 wild‐type and mutant DNA samples, clamping PCR detected mutations in samples with a 1% tumor DNA composition. Using PNA clamping PCR, we detected 138 of 141 (97.9%) cases with mutant IDH1 in our series, which is significantly higher (P = 0.016; PNA clamping vs. direct sequencing) than those of direct sequencing (74.5%), pyrosequencing (75.2%) and IHC (75.9%). From our results, almost all oligodendroglial tumors have IDH1 mutations, and this suggests that IDH1 mutation is an early and common event especially in the development of oligodendroglial tumors.     

KRAS testing on colo‐rectal carcinoma cytological imprints

Anti‐EGFR monoclonal antibodies, cetuximab, and panitumumab, are administrated under the condition that advanced colo‐rectal cancer (CRC) carries a wild‐type KRAS gene. Thus, clinicians request pathologists to genotype KRAS before treatment. In the near future routine mutation testing at the same time of the surgery may be implemented. The reliability of a rapid KRAS testing on ex vivo cytological samples obtained by direct scraping of the colon tumour tissue is here evaluated. A consecutive series of 20 surgically resected, primary CRC specimens was analysed. Fresh tissue from CRC was scraped with a scalpel blade, smeared on uncoated glass slides, air‐dried and Diff–Quik stained to ensure malignant cell presence. The same tissue area was also histologically processed. Exon 2 KRAS gene mutations were evaluated on both cytological and histological specimens by dideoxy sequencing and by the DxS KRAS Mutation Test Kit (DxS, Manchester, England). Data obtained on on imprint cytology and matched histological samples showed full concordance; however, the mutation frequency was slightly higher (35%) by the DxS KRAS Mutation Test Kit than by the dideoxy sequencing (30%). Thus, colon cancer imprint cytology sample is a reliable biospecimen for both dideoxy‐sequencing and DxS KRAS Mutation Test Kit analysis and it may be useful to abbreviate the KRAS assay turnaround time. Diagn. Cytopathol. 2011;39:274–277. ©2010 Wiley‐Liss, Inc.     

非小细胞肺癌中表皮生长因子受体基因突变直接测序分析及其与临床病理特征的相关性

目的回顾性分析非小细胞肺癌(NSCLC)中采用直接测序法检测的表皮生长因子受体(EGFR)基因突变率、突变分布特征及其与临床病理的相关性。方法收集NSCLC共443例,其中包括手术切除样本299例、粗针穿刺活检标本59例、细针穿刺和胸腔积液细胞学样本85例。所有样本均通过石蜡包埋、切片后确定肿瘤细胞含量,显微切割富集肿瘤细胞后采用聚合酶链反应-直接测序法检测EGFR基因酪氨酸激酶编码区第18至21号外显子的突变。结果(1)在443例NSCLC标本中共检出EGFR基因突变193个,发生在189例患者中(42.7％);EGFR基因第18至21号外显子的突变率分别为2.0％( 4/193)、48.7％ (94/193)、6.7％ (13/193)和42.5％ (82/193);(2)EGFR基因总突变率与年龄无显著相关性,但在年龄大于中位年龄（57岁）的患者中第21号外显子的突变率(50.9％,54/106)高于年龄小于或等于中位年龄者(32.2％,28/87;P＜0.01);(3)女性患者中EGFR基因突变率(53.5％,107/200)高于男性患者突变率(33.7％,82/243;P ＜0.01);(4)腺癌中的突变率(46.5％,161/346)高于鳞癌(13.3％,4/30;P＜0.01)和低分化癌者(24.1％,7/29;P＜0.05),而与腺鳞癌(7/13)差异无统计学意义(P＞0.05);(5)在手术切除、粗针穿刺活检以及细针穿刺和胸腔积液细胞学样本中EGFR突变检出率有逐渐下降的趋势,分别为49.5％( 148/299)、35.6％ (21/59)和23.5％ (20/85),其中细针穿刺和胸腔积液的细胞学样本中的检出率较手术标本中的检出率为低(P＜0.01)。结论直接测序法是检测NSCLC中EGFR基因突变的有效方法,特别对未知突变类型的检出具有优势;NSCLC中EGFR基因突变在女性和腺癌中多见,以第19号外显子的缺失突变和第21号外显子的点突变为主;EGFR基因突变分布特征可能与年龄有一定关系;EGFR基因突变检出率与样本类型密切相关,活检组织及细胞学样本是检测EGFR基因突变的有用材料,但可能会漏检部分患者中EGFR基因的突变。     

Use of the Ion AmpliSeq Cancer Hotspot Panel in clinical molecular pathology laboratories for analysis of solid tumours: With emphasis on validation with relevant single molecular pathology tests and the Oncomine Focus Assay

Targeted application of next-generation sequencing (NGS) technology allows detection of specific mutations that can provide treatment opportunities for cancer patients. We evaluated the applicability of the Ion AmpliSeq Cancer Hotspot Panel V2 (CHV2) using formalin-fixed, paraffin-embedded (FFPE) tissue of clinical specimens.Thirty-five FFPE tumour samples with known mutational status were collected from four different hospitals and sequenced with CHV2 using an Ion Chef System and Ion S5 XL system. Out of 35 cases, seven were sequenced with Oncomine focus Assay Panel for comparison. For the limit of detection test, we used an FFPE reference standard, a cell line that included an engineered 50% EGFR T790?M in an RKO cell line background. Coverage analysis results including number of mapped reads, on target percent, mean depth, and uniformity were not different according to hospitals. Sensitivity for mutation detection down to 3% was demonstrated. NGS results showed 100% concordance with the results from single molecular pathology tests Assay in 30 cases with 24 known positive mutations and 14 known negative mutations, and another NGS panel of the Oncomine focus in seven cases.The CHV2 NGS test for solid tumours using Ion chef system and S5 XL system in clinical molecular pathology laboratories for analysis of solid tumours could be routinely used and could replace some single molecular pathology tests after a stringent and thorough validation process.     

Molecular diagnostic testing as an adjunct to morphologic evaluation of pancreatic ductal system brushings: potential augmentation for diagnostic sensitivity

Malignancies arising from the pancreatic and biliary ductal systems present the gastroenterologist and pathologist with diagnostic challenges. Tumors of the pancreatic and/or biliary ductal system may present as either duct strictures or mass lesions. When lesions present as strictures without associated demonstrable masses, brushing cytology may represent the only reasonable diagnostic technique aside from open biopsy. Diagnostic sensitivities for brushing cytology have ranged from 18 to 90%. Positive diagnoses of malignancy are of great clinical value but a negative result is of relatively little clinical aid when the radiographic or clinical findings are suspicious for a malignancy.A variety of techniques have been used in an attempt to improve diagnostic sensitivity for brushing cytology. These have included immunohistochemistry and various molecular diagnostic techniques. Using the high resolution melting curve technique, we performed mutational analysis on 20 bile duct brushing specimens for mutations in p53, K-ras, BRAF, and EGFR genes. Eleven specimens had corresponding surgical specimens, which were similarly analyzed. Our series included twelve adenocarcinomas, one islet cell tumor, one case of dysplasia, and six benign cases. K-ras mutations were found in cytology specimens of 3 out of 12 malignancies. No EGFR or B-raf mutations were detected and only a single p53 mutation in an adenocarcinoma was detected in the corresponding cytology specimen. No mutations were detected in benign lesions or in the dysplasia. Only 8% of specimens from adenocarcinomas had p53 mutations and only 33% of cases had K-ras mutations. Mutational analysis did not appear to improve the cytologic detection of adenocarcinoma by bile duct brushings.