Fluorescence In Situ Hybridization Positive Cases Research Articles

MLH1/PMS2 Expression Could Tell Classical NTRK Fusion in Fluorescence In Situ Hybridization Positive Colorectal Carcinomas.

To gain insight into the clinicopathologic profile of colorectal carcinomas harboring oncogenic NTRK fusions based on eastern populations as well as make the best testing algorithm for the screen, we use pan-Trk immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) respectively to screen NTRK fusions in a large, unselected cohort of 819 colon cancers; either IHC or FISH positive cases were further detected by next-generation sequencing (NGS). IHC staining was observed in ten (1.22%) cases. FISH positive was observed in 13 (1.59%) cases, and finally, a total of 18 cases were under both a DNA-based and an RNA-based NGS assay. RNA-based NGS was positive in 13 of 18 cases, whereas DNA-based NGS was only positive in three of 18 cases. In total 13 RNA-based NGS NTRK fusion-positive cases, only six cases were pan-TRK IHC positive versus 12 were FISH positive. More important, in 13 RNA-based NGS cases only five cases contain the full length of NTRK tyrosine kinase (TK) domain and form the classical fusion chimeras, other six cases only maintain parts of the TK domain and form the sub-classical fusion chimeras, two cases totally miss the TK domain and form the non-classical fusions. For clinicopathologic characteristics, besides the MMR (mismatch repair) status (p = 0.001), there is no difference between the NTRK fusion-positive and negative cases. Nevertheless, classical fusion cases prefer low differentiation (p = 0.001) and different patterns of growth (p < 0.001). Besides, we found all five classical NTRK fusion cases, and only one sub-classical case was harboring MLH1/PMS2 deficiency. When combining FISH and MMR (Mismatch Repair) status, besides one sub-classical case, all five classical fusions were detected, which means MLH1/PMS2 expression could further narrow the classical fusions in FISH NTRK fusion positive cases. Given the low sensitivity and specificity of the pan-Trk antibody, it would be useless to use IHC to screen NTRK fusion-positive CRCs. Combining FISH and MLH1/PMS2 IHC would be a good testing algorithm for the screen effective NTRK fusions. Finally, if patients are going to undergo TRK-based targeted therapy, only RNA-based NGS for detection of the specific fusion could tell the precise rearrangement information.

A Validation Study of Human Epidermal Growth Factor Receptor 2 Immunohistochemistry Digital Imaging Analysis and its Correlation with Human Epidermal Growth Factor Receptor 2 Fluorescence In situ Hybridization Results in Breast Carcinoma

Background: The Visiopharm human epidermal growth factor receptor 2 (HER2) digital imaging analysis (DIA) algorithm assesses digitized HER2 immunohistochemistry (IHC) by measuring cell membrane connectivity. We aimed to validate this algorithm for clinical use by comparing with pathologists’ scoring and correlating with HER2 fluorescence in situ hybridization (FISH) results. Materials and Methods: The study cohort consisted of 612 consecutive invasive breast carcinoma specimens including 395 biopsies and 217 resections. HER2 IHC slides were scanned using Philips IntelliSite Scanners, and the digital images were analyzed using Visiopharm HER2-CONNECT App to obtain the connectivity values (0–1) and scores (0, 1+, 2+, and 3+). HER2 DIA scores were compared with Pathologists’ manual scores, and HER2 connectivity values were correlated with HER2 FISH results. Results: The concordance between HER2 DIA scores and pathologists’ scores was 87.3% (534/612). All discordant cases (n = 78) were only one-step discordant (negative to equivocal, equivocal to positive, or vice versa). Five cases (0.8%) showed discordant HER2 IHC DIA and HER2 FISH results, but all these cases had relatively low HER2 copy numbers (between 4 and 6). HER2 IHC connectivity showed significantly better correlation with HER2 copy number than HER2/CEP17 ratio. Conclusions: HER2 IHC DIA demonstrates excellent concordance with pathologists’ scores and accurately discriminates between HER2 FISH positive and negative cases. HER2 IHC connectivity has better correlation with HER2 copy number than HER2/CEP17 ratio, suggesting HER2 copy number may be more important in predicting HER2 protein expression, and response to anti-HER2-targeted therapy.

Utility of Flow Cytometry and Fluorescence in Situ Hybridization in Follow-up Monitoring of Multiple Myeloma

Introduction Diagnosis and follow-up monitoring of Multiple Myeloma (MM) requires documentation of (clonal) plasma cells using morphological bone marrow assessment and other ancillary studies including CD138 immunohistochemistry (IHC), flow cytometry (FC), and myeloma-specific fluorescence in situ hybridization (FISH). While IHC and FC have traditionally been shown to be the more sensitive methods for the assessment of residual disease, the detection rates of FISH have markedly increased with the recent use of magnetic cell sorting for CD138 cell enrichment. We, therefore, aimed to revisit the clinical utility of these ancillary studies in the diagnosis and follow-up of MM. Methods We retrospectively reviewed the reports of bone marrow biopsy specimens received for the initial diagnosis or follow-up assessment of MM from October 2015 to January 2019. All cases that had both FC and FISH performed were included in the analysis. Patient demographics, treatment history and the results of bone marrow evaluation were recorded. Results During the study period, we evaluated a total of 1,712 biopsy specimens from 464 MM patients (mean±SD age: 64.0±9.4 years; females 41.4%). Of these, 87 cases were submitted for initial diagnosis and 1,625 cases had already established MM and were being evaluated for post-treatment residual disease. For both initial diagnosis and follow-up cases, CD138+ IHC demonstrated highest plasma cell burden (mean: 49.1% and 4.6%, respectively) followed by morphological aspirate count (mean: 29.6% and 2.3%, respectively) and FC (mean: 10.9% and 1.8%, respectively). Both FC and FISH had comparable detection rates at the time of initial diagnosis (95.4% versus 97.7%, respectively) and for follow-up cases (28.6% versus 28.2%, respectively). The FC and FISH results were concordant in 97.7% of the initial diagnosis cases and 89.7% of follow-up cases. Discordant cases with positive FISH results and negative FC results included 2 (2.3%) initial diagnosis cases and 81 (5.0%) follow-up cases whereas those with negative FISH and positive FC results included 87 (5.3%) follow-up cases. In comparison with all concordant cases, the FISH positive, FC negative discordant cases were older in age, more likely to have received treatment with Daratumumab, and less likely to have received stem cell transplantation (p &lt;0.05) (Table 1). When compared to the FC and FISH positive concordant cases; both discordant groups had significantly lower plasma cell counts detected by the aspirate smear and CD138+ IHC (Figure 1). Among all FC positive cases, the discordant cases had lower FC detected plasma cell counts and were less likely to have aberrant CD56 expression as compared to the concordant cases (p &lt;0.05) (Table 2). Finally, among all FISH positive cases, the discordant cases were less likely to have 13q lesion and aneuploidy of chromosomes 5, 9, and 15 (p &lt;0.05) as compared to the concordant cases. Also, between these groups, the percentage of plasma cells with individual FISH aberrations was significantly lower among the discordant cases (Table 3). Conclusion Overall, FISH (with magnetic cell sorting) and FC have comparable detection rates at the initial diagnosis and follow-up assessment. Approximately 10% of the follow-up cases have discordant FISH and FC results where residual disease is detected by only one of these modalities. Also, the discordant cases have significantly lower plasma cell counts as compared to the FC and FISH positive concordant cases. Therefore, this study suggests that both FC and FISH are useful for the follow-up monitoring of MM, especially in the cases with low plasma cell burden. Finally, the higher frequency of Daratumumab treatment in FISH positive, FC negative discordant cases might suggest Daratumumab's potential interference with the residual disease detection by FC. Disclosures No relevant conflicts of interest to declare.

Impact of the 2018 American Society of Clinical Oncology/College of American Pathologists HER2 Guideline Updates on HER2 Assessment in Breast Cancer With Equivocal HER2 Immunohistochemistry Results With Focus on Cases With HER2/CEP17 Ratio

The American Society of Clinical Oncology/College of American Pathologists HER2 testing guideline in breast cancer was updated in 2018 to address issues on interpretation of uncommon results using dual-probe in situ hybridization according to the 2013 guideline. To assess impact of the 2018 guideline on breast cancer with equivocal HER2 immunohistochemistry results. We retrospectively reviewed HER2 fluorescence in situ hybridization (FISH) data (HER2/CEP17 ratio and average HER2 copy number per cell) of HER2 immunohistochemistry-equivocal (2+ or 1+ to 2+) breast cancers at our center between January 2014 and May 2018 and compared HER2 FISH results according to 2013 and 2018 guidelines. A total of 1666 HER2 FISH results from 1421 patients with equivocal HER2 immunohistochemistry were reviewed. Based on the 2013 guideline, HER2 FISH results were amplified in 346 cases (20.8%), equivocal in 242 (14.5%), and nonamplified in 1078 (64.7%). Using the 2018 guideline, 258 cases (16%) were reclassified, including 242 previously equivocal test results (15%) and 16 previously positive results (1%) reclassified as negative. The subset of 2013 HER2-equivocal and 2018 HER2-nonamplified cases with HER2/CEP17 ratio lower than 2.0 and average HER2 copy number 4.0 or higher and lower than 6.0 showed higher incidence of micropapillary morphology compared with HER2-amplified cases. Despite most patients in this group not receiving HER2-targeted treatment, 96% had no evidence of disease at follow-up. The 2018 guideline eliminated HER2 FISH-equivocal cases by reclassifying HER2-equivocal cases and cases with nonclassical amplification without HER2 overexpression as HER2 negative. As a consequence, we observed a considerable increase in HER2 FISH-negative cases and a slight decrease in HER2 FISH-positive cases.

Immunohistochemical Expression (IHC) and Fluorescence In Situ Hybridization (FISH) of EGFR in Colorectal Carcinoma

Adenocarcinoma of the colon is the most common malignancy of the gastrointestinal tract and is a major cause of morbidity and mortality worldwide. Epidermal growth factor receptor (EGFR) is also known as HER-1 or erb-B1. The beginning of EGF to EGFR produces a biological signal to the cell that initiates several functions that promote tumor growth, including cell invasion and metastasis, repair and new blood vessel formation. Thus, EGFR is recognized as an important player in colorectal cancer (CRC) initiation and progression. In this study, total 61 cases of colorectal carcinoma were included and histological grading, immuno-histochemical (IHC) expression and fluorescence in situ hybridization of EGFR were conducted. For the grading, 11/61(18%) cases were well differentiated, 38/61(62%) cases were moderately differentiated and 12/61(20%) were poorly differentiated colorectal carcinoma. EGFR IHC immune expression was positive in 50/61(82%) cases and negative in 11/61(18%) cases. All 11 cases of well differentiated cases gave EGFR IHC positive immunoreaction. Among the 38 cases of moderately differentiated adenocarcinoma, 30 cases showed EGFR IHC positivity and 8 cases gave no reaction. Nine out of 12 cases of poorly differentiated adenocarcinoma showed EGFR IHC positive and 3 cases gave no reaction. Half (10/20, 50%) of the EGFR IHC highly positive cases showed FISH positive and other half cases give FISH negative reaction. Detection of EGFR is mainly for anti-EGFR targeted therapy. Therefore, this study aids in selection of patients for anti-EGFR targeted therapy and helpful in treatment options and disease management. Moreover, EGFR FISH can be tested together with KRAS mutation and can predict the treatment response and the disease outcome.

Abstract 3127: Multicenter study evaluating the ROS1 status in lung adenocarcinoma using the novel SP384 immunohistochemistry clone. Towards a new algorithm for ROS1 status assessment in routine

Abstract Background: The detection of a ROS1 rearrangement in advanced or metastatic lung adenocarcinoma (LUAD) lead to a targeted treatment with tyrosine kinase inhibitors with improved progression free survival (PFS) and overall survival (OS) of the patients. Thus, it is mandatory to screen systematically for the ROS1rearrangement in this patient population. ROS1 rearrangements can be detected using fluorescence in situ hybridization (FISH), however ROS1 immunohistochemistry (IHC) can be used as a screening test since is largely available, easy, rapid to perform, and cost-effective. However, some false positive and negative IHC results are observed when using the D4D6 clone leading to confirmatory ROS1 FISH in IHC positive samples. Patients and methods: We evaluated the sensitivity and specificity of anti-ROS1 SP384 (Ventana, Tucson, AZ) and D4D6 (Cell Signaling, Danvers, MA) antibodies in a multicenter population of 336 LUAD cases enriched for ROS1 FISH positive cases (n=51) provided from 6 French molecular pathology platforms. Three senior lung pathologists independently scored the SP384 slides as positive or negative around a cutoff of staining in &amp;gt;30% tumor cells at a ≥2+ intensity level, and for the D4D6 clone around a cutoff of ≥2+ intensity level in any tumor cells. Inter-reader precision between pathologists was assessed. Results were correlated to the PFS and the OS of patients treated with crizotinib. Results: Sensitivity and specificity rates were 100% (95%CI 93.2-100%) and 99.31% (95%CI 97.51-99.92%) for the SP384 clone, and 90.6% (95%CI 79.34-96.87%) and 99.65% (95%CI 98.05-99.99%) for the D4D6 clone, respectively. Inter-reader agreement was 97.5% (95%CI 94.8-99.7) for the SP384 clone and 86.3% (95%CI 91.3-95.6) for the D4D6 clone. Overall, when compared to ROS1 FISH analysis, the SP384 clone had an accuracy of 99.4%, while D4D6 clone of 98.2%. Using log-rank test, we observed that LUAD with positive ROS1 SP384 status had a longer PFS than those characterized by the D4D6 clone (P=0.021). Conclusions: Interpretation above a cutoff of &amp;gt;30% tumor cells with staining at a ≥2+ intensity level, the ROS1 SP384 clone demonstrates superior sensitivity to D4D6 clone, while preserving similar specificity rate for the detection of ROS1 rearrangements. The presented data provide evidence that the SP384 clone may be used for effective stratification prior to confirmation with orthogonal methods. Citation Format: Véronique Hofman, Isabelle Rouquette, Sandra Lassalle, Simon Heeke, Jean-Christophe Sabourin, Nicolas Piton, Julien Mazières, Jean-Michel Vignaud, Clémence Yguel, Anne Laure Lepage, Frédéric Bibeau, Elodie Long-Mira, Katia Zahaf, Hugues Begueret, Jonathan Benzaquen, Michel Poudenx, Charles-Hugo Marquette, Marius Ilie, Paul Hofman. Multicenter study evaluating the ROS1 status in lung adenocarcinoma using the novel SP384 immunohistochemistry clone. Towards a new algorithm for ROS1 status assessment in routine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3127.

Impact of 2013 American Society of Clinical Oncology/College of American Pathologists Guidelines on HER2 Fluorescent In Situ Hybridization Testing in Breast Cancers : Experience From a National Reference Laboratory.

We compared the impact of 2013 American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guidelines on human epidermal growth factor receptor 2 (HER2) fluorescence in situ hybridization (FISH) testing results on breast cancers. HER2 FISH testing performed between May 2015 and April 2016 following 2013 ASCO/CAP guidelines was included. HER2 to control probe ratios, mean HER2, and control probe copy numbers were used to reassign HER2 status using 2007 ASCO/CAP and US Food and Drug Administration (FDA) guidelines. HER2 FISH results were available in 2,017 cases. A total of 342 (17.0%) cases were amplified, 301 (14.9%) were equivocal, and 1,374 (68.1%) were nonamplified. After additional testing with the alternate probe, amplified cases increased to 21.6%. HER2 positivity rates following the 2013 ASCO/CAP guidelines were significantly higher compared with the 2007 ASCO/CAP and FDA guidelines. The 2013 ASCO/CAP guidelines lead to a higher number of HER2 FISH positive and equivocal cases. In a reference laboratory setting where an alternative control probe was used to resolve equivocal FISH cases, 31.2% of patients with initial equivocal results became HER2 positive.

Efficacy of crizotinib in ALK mutant non-small cell lung cancers that are positive by IHC but negative by FISH compared to FISH positive cases.

A small proportion of Non-Small Cell Lung Cancers (NSCLC) are detected with Anaplastic Lymphoma Kinase (ALK) mutation by immunohistochemistry (IHC) but are negative by Fluorescence in situ Hybridization (FISH). Data on responses and outcome of this subset of patients when treated with crizotinib is limited. We analyzed the outcomes of such patients who received crizotinib. Demographics, treatment details, response to treatment, date of progression and date of death were collected for patients who were IHC positive and FISH negative for ALK mutation from a prospectively maintained database. Depending upon feasibility, patients received either platinum based doublet chemotherapy or the ALK inhibitor crizotinib as first line therapy. Outcomes were compared to our previously published historical cohort of FISH positive patients who were treated with crizotinib. Thirteen patients were detected to be IHC+/FISH- and out of these seven received crizotinib. Objective response rate for crizotinib was 57.15% with an estimated mean PFS of 9.6 months (95% CI 3.8 -15.5 months). The difference in ORR of ALK IHC+/FISH- when compared to our historical cohort of ALK FISH positive treated with crizotinib was not statistically significant (57.15% vs 69.8%; P = 0.265). Estimated mean and median PFS was similar between the two cohorts (median PFS 6.0 months vs 14 months; mean PFS 9.6 months versus 14.7 months; P = 0.467). NSCLCs positive for ALK mutation by IHC but not detected by FISH show good response to crizotinib and merit treatment with the same.

A sensitive and high throughput TaqMan-based reverse transcription quantitative polymerase chain reaction assay efficiently discriminates ALK rearrangement from overexpression for lung cancer FFPE specimens

ObjectivesALK fusion gene is an oncogenic driver in lung cancer with low prevalence, which can be ameliorated by crizotinib. Currently, ALK fusion gene can be diagnosed by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), but inconstistnt results between the two methods are encountered regularly. To make the ALK fusion gene screening more efficient and to provide a simple solution to clarify the discrepancy between FISH and IHC results, a sensitive TaqMan-based reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay was established. Materials and methodsThe 3-plex TaqMan-based RT-qPCR assay was established and performed on 102 archived formalin-fixed, paraffin-embedded (FFPE) NSCLC samples to detect ALK rearrangement and overexpression. Break-apart FISH and automatic immunohistochemistry based ALK assays were performed side by side using tissue microarray. ResultsThe RT-qPCR was performed successfully for 80 samples and 10 of them showed positive signals. Three out of the 10 qPCR positive cases were further confirmed by FISH and IHC test. Two others were IHC positive and FISH negative, and expressed full-length ALK transcript. The rest were neither FISH nor IHC positive and their ALK expression level was significantly lower than those FISH or IHC positive cases. ConclusionOur RT-qPCR assay demonstrates that the capability and reliability of ALK detection is comparable to FISH and IHC, but it is more effective at discriminating ALK rearrangement from overexpression. The RT-qPCR assay easily clarifies the discrepancy between FISH and IHC, and can be incorporated into routine ALK screening for lung cancer.

Assessment of cytology based molecular analysis to guide targeted therapy in advanced non-small-cell lung cancer.

To investigate the use of molecular testing on cytological specimens in selecting advanced non-small cell lung cancer (NSCLC) patients who are adequate for targeted treatment, a total of 137 NSCLC cases were analyzed by fluorescence in situ hybridization (FISH) for anaplastic lymphoma kinase (ALK) rearrangements, and Epidermal growth factor receptor (EGFR), kirsten rat sarcoma viral oncogene homolog (KRAS) mutations were evaluated by quantitative real-time PCR (qRT-PCR) platform combining amplification refractory mutation system (ARMS) primers and TaqMan probes. Cytological specimens included 91 fine-needle aspirates, 5 fibreoptic bronchoscopic derived samples and 41 pleural effusions. Among 137 NSCLCs analyzed for ALK FISH, 16 (11.7%, of 137) were detected to harbor ALK rearrangement. FISH positive cases were all defined as adenocarcinoma (ADC) histologic subtype and the FNA samples showed the highest ALK positive rate (13.2%, 12/91). Of the 9 ALK FISH positive patients who received crizotinib treatment, 8 (88.9%) patients exhibited tumor regression. In addition, 60 (44.8%, of 134) cases were found to harbor EGFR mutations and 22 patients with EGFR sensitive mutations who received gefitinib or erlotinib treatment showed a median PFS of 16.0 months. Mutations of KRAS occurred in 8 (6.0%, of 134) cases and this was mutually exclusive from EGFR mutation. Our results demonstrated that ALK FISH and EGFR, KRAS mutational analysis on cytological specimens are sensitive methods for screening advanced stage NSCLC patients who are adequate for targeted treatment.

Potentially actionable kinase fusions in inflammatory myofibroblastic tumors.

10513 Background: Inflammatory myofibroblastic tumor (IMT) is a rare mesenchymal neoplasm that harbors anaplastic lymphoma kinase (ALK) gene rearrangements in approximately 50% of cases. ALK inhibitors have been validated as an effective therapeutic approach in this subset of IMTs. The goal of this study was to characterize a series of IMTs using both immunohistochemistry (IHC) and next generation sequencing (NGS). Methods: 30 formalin-fixed, paraffin-embedded IMT specimens from 28 patients were evaluated by IHC for ALK expression using standard techniques. DNA was extracted and sequenced using a targeted capture-based NGS assay for 3769 exons of 236 cancer-related genes and 47 introns of 19 commonly rearranged genes, including 8 tyrosine kinases in a CLIA laboratory (Foundation Medicine). Selected specimens were also evaluated for ALK fusions by fluorescence in-situ hybridization (FISH). Results: 20 samples were ALK positive and 10 samples were ALK negative by IHC. Targeted NGS was successfully performed in 16/20 ALK positive and 10/10 ALK negative cases. Among the 16 ALK positive cases analyzed by NGS, 12 harbored ALK fusions with various 5’ gene fusion partners, including LMNA, TPM3, TPM4, SEC31A, TFG, RANBP2, and CLTC. The remaining 4 were also negative by FISH suggesting a different mechanism of ALK overexpression. Among the 10 ALK negative cases, 2 harbored ALK fusions (EML4-ALK, TPM3-ALK). In the other 8 ALK negative samples, 2 contained distinct ROS1 fusions (YWHAE-ROS1, TFG-ROS1) and 1 contained a PDGFRβ fusion (NAB2-PDGFRβ), none of which have been described in IMT samples to date. Overall, kinase gene fusions were identified in 18/26 (69%) evaluable samples. Conclusions: This study represents the most comprehensive NGS analysis of IMTs. 12/12(100%) ALK IHC and FISH positive cases contained ALK fusions, while 5/8 (63%) of distinct ALK IHC negative cases harbored kinase fusions, involving ALK, ROS1, or PDGFRβ. Since these fusions are all targetable with existing kinase inhibitors (i.e. crizotinib, dasatinib), this study suggests that IMTs should be routinely profiled for kinase fusions and not just by ALK IHC. Efforts are ongoing to identify “driver mutations” in the fusion-negative specimens.

P1-049 - Coexistence of Positive MET Fish Status with EGFR Mutations Signifies Poor Prognosis in Primary Lung Adenocarcinoma

ABSTRACT Overexpression of MET has been reported in various malignancies and is associated with cell proliferation, inhibition of apoptosis and metastasis. MET amplification has been reported to contribute to acquired resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKI) in non-small-cell lung cancer (NSCLC), being observed among 5–10% of those patients. Therefore, MET gene alterations could be both prognostic and predictive, and evaluation of that is indispensable in practice. However, the frequency of positive cases varies due to a lack of standardized criteria of fluorescence in situ hybridization (FISH). The purpose of this study is to find which criteria could be useful in terms of the association with clinical characteristics. We evaluated the MET gene copy number of FISH using two different criteria in lung adenocarcinoma: the Cappuzzo scoring system and PathVysion and its association with clinicopathological characteristics. MET positive cases according to the Cappuzzo scoring system evidenced both aneuploidy and true amplification, whereas PathVysion revealed only amplification. One hundred and thirty-eight lung adenocarcinoma tissue samples were evaluated, and the proportion of MET FISH positive cases was 15 and 4% determined by the Cappuzzo system and PathVysion, respectively. PathVysion demonstrated higher frequencies of MET FISH positives among men and smokers and evidenced no MET FISH positives in patients with bronchioloalveolar carcinoma. Prognosis was significantly associated with MET FISH positive only as defined by the PathVysion system (gene amplification), not by the Cappuzzo system. However, the progression-free survival time of patients with both EGFR mutations and MET FISH positive defined by the Cappuzzo scoring system was significantly shorter than with EGFR mutations alone. These results suggest that MET FISH is a potential prognostic factor and co-existence of MET FISH with EGFR mutations signifies worse prognosis.

Abstract 1737: Co-existence of positive MET FISH status with EGFR mutations signifies poor prognosis in lung adenocarcinoma

Abstract MET, which is located in 7q31, is a receptor tyrosine kinase for hepatocyte growth factor. Overexpression of MET has been reported in various malignancies and is associated with cell proliferation, inhibition of apoptosis, and metastasis. MET amplification has been reported to contribute to acquired resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKI) in non-small cell lung cancer(NSCLC), being observed among 5-10% of those patients. Therefore, MET gene alterations could be both prognostic and predictive. To evaluate MET gene copy number, fluorescence in situ hybridization (FISH), real-time PCR, and comparative genomic hybridization (CGH) have been used. The results of real-time PCR do not directly reflect cancer cells. CGH is not suitable for the evaluation of a large number of specimens due to cost. Therefore, FISH is the most practical method for evaluation of MET gene copy number. However, the frequency of positive cases varies due to a lack of standardized criteria. We evaluated MET gene copy number in lung adenocarcinoma and its association with clinicopathological characteristics. FISH was applied to evaluate high MET gene copy number and true amplification in 138 lung adenocarcinoma patients using two criteria: the Cappuzzo scoring system and PathVysion. MET positive cases according to the Cappuzzo scoring system evidenced both aneuploidy and true amplification, whereas PathVysion revealed only amplification. Proportion of MET FISH positive cases was 15% and 4% determined by the Cappuzzo system and PathVysion, respectively. PathVysion demonstrated higher frequencies of MET FISH positives among men and smokers and evidenced no MET FISH positives in patients with bronchioloalveolar carcinoma, which is recognized as pure lepidic growth without invasion of stroma, blood vessels, or pleura. Prognosis was significantly associated with MET FISH positive only as defined by the PathVysion system (gene amplification), not by the Cappuzzo system. However, progression-free survival time of patients with both EGFR mutations and MET FISH positive defined by the Cappuzzo scoring system was significantly shorter than with EGFR mutations alone. These results suggest that MET FISH is a potential prognostic factor and co-existence of EGFR mutation and MET FISH positive status evidences poorer prognosis compared to EGFR mutation alone, which is consistent with the results of in vitro experiments. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1737. doi:1538-7445.AM2012-1737

P3-01-11: Increased Gene Copy Number of c-KIT and VEGFR2 at 4q12 in Primary Breast Cancer Is Related to an Aggressive Phenotype and Impaired Prognosis.

Abstract Introduction: Triple-negative breast cancer (TNBC) accounts for approximately 15% of all female breast cancer and is associated with aggressive clinical behaviour. No targeted treatments are available for TNBC. Drugs inhibiting tyrosine kinases, such as vascular endothelial growth factor receptor 2 (VEGFR2) and c-KIT, have however shown some promising results for patients with TNBC. The aim of the present study was to investigate whether gains and/or amplifications of VEGFR2 and c-KIT occur in TNBC. These genes may constitute novel candidate biomarkers for selecting TNBC patients for treatment with tyrosine kinase inhibitors. Material &amp; Methods: Fluorescence in situ hybridization (FISH) was used to quantify gene copy numbers of VEGFR2 and c-KIT in 83 primary human breast cancers, of which 31 were classified as TNBC. Gains were defined as ≥4 gene copies in more than 40% of the cancer cells, while amplification was defined as gene copy/CEP ratio &amp;gt;2 in more than 10% of the cancer cells. A tumour was considered FISH positive for c-KIT and/or VEGFR2 if it displayed copy number gain and/or amplification. Immunohistochemical (IHC) staining was performed for assessment of c-KIT protein expression. Results: Ten (32%) of the TNBCs were VEGFR2 FISH positive and nine (29%) were c-KIT FISH positive, whereas non-TNBCs were FISH positive for VEGFR2 and c-KIT in nine (18%) cases for both genes. No significant difference in frequency between TNBCs and non-TNBCs was found. There was a correlation between FISH positivity for VEGFR2 and c-KIT (c2 test, P&amp;lt;0.001), and VEGFR2 and c-KIT FISH positivity correlated to ER/PgR negativity and high Nottingham histological grade (NHG). A significantly worse breast cancer specific survival (BCSS) was seen for FISH positive cases in the whole cohort as well as among untreated patients and non-TNBCs, but not among TNBC cases. Discussion: The high correlation between VEGFR2 and c-KIT FISH positivity suggests that the genes are co-amplified. Increased copy number of both genes was related to aggressive disease and a worse prognosis, and thus has the potential of functioning as a novel predictive biomarker for selected targeted therapy particularly in the difficult-to-treat TNBC patient category. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-01-11.

Increased gene copy number of KIT and VEGFR2 at 4q12 in primary breast cancer is related to an aggressive phenotype and impaired prognosis

Triple-negative breast cancer (TNBC) is associated with poor prognosis and no targeted treatments are available for TNBC. Drugs inhibiting tyrosine kinases, such as vascular endothelial growth factor receptor 2 (VEGFR2) and KIT, have shown some promising results for patients with TNBC. The aim of the study was to investigate whether gains and/or amplifications of VEGFR2 and KIT, located at 4q12, occur in TNBC. Fluorescence in situ hybridization (FISH) was used to quantify gene copy numbers of VEGFR2 and KIT in 83 primary human breast cancers including 31 TNBCs. Gains were defined as ≥ 4 gene copies in >40% of the cancer cells, whereas amplification was defined as CEP >2 in more than 10% of the cancer cells. A tumor was considered FISH positive for KIT and/or VEGFR2 if it displayed copy number gain and/or amplification. Ten (32%) of the TNBCs were VEGFR2 FISH positive and nine (29%) were KIT FISH positive, whereas non-TNBCs were FISH positive for VEGFR2 and KIT in nine (18%) cases for both genes, but no significant difference between TNBCs and non-TNBCs was found. FISH positivity for VEGFR2 and KIT was significantly correlated (χ(2) test, P < 0.001), and significantly related to ER negativity and high Nottingham histological grade (NHG). A significantly worse 5-year breast cancer specific survival (BCSS) was seen for FISH positive cases. Increased copy number of VEGFR2 and KIT thus has the potential of functioning as a novel predictive biomarker for selected targeted therapy particularly in the difficult-to-treat TNBC patient category.

Evaluation of Genetic Status of HER-2/neu and Aneusomy 17 by Fluorescence In Situ Hybridization and Comparison with Immunohistochemistry Assay from Indian Breast Cancer Patients

The HER-2/neu proto-oncogene is amplified in 15%-25% of breast cancers. In the current study, we evaluated HER-2/neu status of 396 cases of breast cancer by fluorescence in situ hybridization (FISH), and the results were correlated with immunohistochemistry (IHC) for HER-2/neu protein expression. Overall, HER-2/neu amplification was observed in 38.4% of cases. Concordance between IHC and FISH was 90.4% considering only IHC score 0, 1 (negative), and 3 (positive). However, only 37.3% of the IHC score 2 (equivocal) cases showed HER-2/neu gene amplification. A majority of the discordant cases within the IHC negative (score 0 and 1) and IHC positive (score 3) were high-grade tumors. Polysomy 17 and monosomy 17 was seen in 7.3% of the total cases of each. Furthermore, a majority of FISH positive cases were noted in Intraductal Carcinoma grade III and cases with regional lymph nodal metastasis. Polysomy 17 was seen in 7.9% of the FISH positive cases and in 6.3% of the FISH negative cases. Monosomy 17, however was more preponderant in FISH negative cases. We believe that the FISH test should be considered as the gold standard in the estimation of the HER-2/neu status due to its increased sensitivity and better appreciation of aneusomy 17.

Co-existence of positive MET FISH status with EGFR mutations signifies poor prognosis in lung adenocarcinoma patients

MET, a receptor tyrosine kinase for hepatocyte growth factor, is associated with tumor progression and acquired resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKI). Therefore, MET gene alterations could be both prognostic and predictive. Fluorescence in situ hybridization (FISH) is one method for assessing gene alteration, but the frequency of positive cases varies due to a lack of standardized criteria. We evaluated MET gene copy number in lung adenocarcinoma and its association with clinicopathological characteristics. FISH was applied to evaluate high MET gene copy number and true amplification in 138 lung adenocarcinoma patients using two criteria: the Cappuzzo scoring system and PathVysion. MET positive cases according to the Cappuzzo scoring system evidenced both aneuploidy and true amplification, whereas PathVysion revealed only amplification. Proportion of MET FISH positive cases was 15% and 4% determined by the Cappuzzo system and PathVysion, respectively. PathVysion demonstrated higher frequencies of MET FISH positives among men and smokers and evidenced no MET FISH positives in patients with bronchioloalveolar carcinoma. Prognosis was significantly associated with MET FISH positive only as defined by the PathVysion system (gene amplification), not by the Cappuzzo system. However, progression-free survival time of patients with both EGFR mutations and MET FISH positive defined by the Cappuzzo scoring system was significantly shorter than with EGFR mutations alone. These results suggest that MET FISH is a potential prognostic factor and coexistence of MET FISH with EGFR mutations signifies worse prognosis.

Evaluation of 7q31 region improves the accuracy of EGFR FISH assay in non small cell lung cancer

BackgroundIncrease of EGFR gene copy number consequent to gene amplification and/or polysomy of chromosome 7 has been significantly associated with better clinical outcome in Non Small Cell Lung Cancer (NSCLC) patients treated with Tyrosin-Kinase Inhibitors (TKIs).The primary method to detect EGFR copy number is FISH (Fluorescence in Situ Hybridization), that in lung cancer requires a precise standardization due to the presence of intratumor heterogeneity and high frequency of chromosome 7 polysomy.Recommendations and interpretative guidelines to discriminate NSCLC patients into FISH positive (gene amplification and high chromosome 7 polysomy) and FISH negative have been proposed by the University of Colorado Cancer Center (UCCC). However, in a subset of cases the distinction between EGFR amplification and chromosome 7 polysomy can be controversial because of a complex pattern of multiple EGFR and centromere signals.MethodsIn order to distinguish more accurately these two genetic events, 20 NSCLC FISH positive patients, showing a controversial pattern of EGFR and centromere specific signals, were further evaluated for the status of 7q31 distal region.ResultsA discrepancy between FISH results obtained with UCCC scoring system and 7q31 control was evidenced in 2 patients (10%).ConclusionOur data strengthen the usefulness of 7q31 region evaluation to discriminate EGFR amplification from chromosome 7 polysomy in controversial EGFR FISH positive cases. Since it has been reported a possible different contribution of amplification and polysomy to TKIs susceptibility in NSCLC, the clear distinction between these two genetic events may be important to identify a subset of patients more responsive to the therapy.

Detection of HER2 Amplification in Breast Carcinomas: Comparison of Multiplex Ligation-Dependent Probe Amplification (MLPA) and Fluorescence In Situ Hybridization (FISH) combined with Automated Spot Counting

In this study the detection of HER2 gene amplification was evaluated using Fluorescence In Situ Hybridization (FISH; PathVysion) in comparison with Multiplex Ligation-dependent Probe Amplification (MLPA), a PCR based technique. These two methods were evaluated on a series of 46 formalin fixed paraffin embedded breast carcinomas, previously tested for protein overexpression by HercepTest (grouped into Hercep 1+, 2+ and 3+). HER2 gene amplification (ratio ≥ 2.0) by FISH was found in 9/10, 10/30 and 0/6 in IHC 3+, 2+ and 1+/0 cases, respectively. Digitalized automated spot counting performed with recently developed CW4000 CytoFISH software was 100% concordant with manual FISH scoring. Using MLPA 18/46 samples showed a clear HER2 amplification. Comparing MLPA and IHC showed the same results as for FISH and IHC. All but one FISH positive cases (18/19) were confirmed by MLPA for the presence of the gene amplification. The overall concordance of detection of Her2 gene amplification by FISH and MLPA was 98% (45/46). Furthermore, both the level of amplification and equivocal results correlated well between both methods. In conclusion, MLPA is a reliable and reproducible technique and can be used as an either alternative or additional test to determine HER2 status in breast carcinomas.