Fluorescence In Situ Hybridization Testing Research Articles

Loss of Chromosome 3q Is a Prognostic Marker in Fusion-Negative Rhabdomyosarcoma.

Soft tissue sarcomas (STS) are rare mesenchymal neoplasms that frequently show complex chromosomal aberrations such as amplifications or deletions of DNA sequences or even whole chromosomes. We recently found that gain of chromosome (chr) 8 is associated with worse overall survival (OS) in STS as a group. We therefore aimed to investigate the overall copy number profile of rhabdomyosarcoma (RMS) to evaluate for prognostic signatures. Fluorescence in situ hybridization (FISH) testing was performed on a cohort of STS to assess for chr8 gain. Copy number variation (CNV) data from the National Cancer Institute were analyzed to assess for prognostically significant CNV aberrations in FOXO1 fusion-negative (FN)- versus fusion-positive (FP)-RMS. FISH testing was performed on a cohort of FN-RMS to assess for chr3q loss and correlate with outcomes. Chr8 gain is a highly prevalent CNV in embryonal RMS and shows slightly improved prognosis. Meanwhile, loss of chr3q was associated with worse outcome in FN-RMS compared with FP-RMS. The pathogenesis of STS including FN-RMS remains poorly understood, emphasizing the need for new therapeutic advances and adequate risk stratification. Our data demonstrate that loss of chr3q is associated with poor OS in FN-RMS, supporting it as an important tool for risk stratification.

Evaluation of the diagnostic efficiency of voided urine fluorescence in situ hybridization for predicting the pathology of preoperative "low-risk" upper tract urothelial carcinoma.

To evaluate the clinical utility of voided urine fluorescence in situ hybridization (FISH) for predicting the pathology of preoperative "low-risk" upper tract urothelial carcinoma (UTUC). Information of patients preoperatively diagnosed with "low-risk" UTUC receiving radical nephroureterectomy (RNU) between May 2014 and October 2019 were retrospectively collected. All of the patients accepted the FISH test and then were divided into two groups according to the results of FISH. The diagnostic value of FISH was assessed through the receiver operating characteristics (ROC) curve and area under the curve. Logistic regression analysis was applied to examine FISH as a predictive factor of tumor final stage and grade of preoperative "low-risk" UTUC. In total, 129 patients were included. Of them, 70 (54.2%) were marked with positive FISH result. The difference at final pathology in tumor stage and tumor grade between these two groups of FISH (-) and FISH (+) had significantly statistical significance (p<0.001). Regarding to the tumor stage at final pathology, the sensitivity, specificity, positive predictive value and negative predictive value of FISH were 70.7 (58.9-80.3)68.5 (54.3-80.1)75.7 (63.7-84.8) and 62.7 (49.1-74.7), respectively. Regarding to the tumor grade at final pathology, the sensitivity, specificity, positive predictive value and negative predictive value of FISH were 64.7 (53.5-74.6), 65.9 (50.0-79.1), 78.6 (66.8-87.1) and 49.1 (36.5-62.3), respectively. The results of logistic regression analysis indicated that FISH could predict the pathologic characteristics of preoperative "low-risk" UTUC independently. FISH was qualified with relatively high diagnostic estimates for predicting tumor stage and grade of preoperative "low-risk" UTUC, and could be an independent predictive factor in clinical practice. For preoperative "low-risk" UTUC patients but with positive FISH result, choosing nephron-sparing surgery may require special caution.

HER-2 overexpression in female genital tract clear cell carcinomas: Evaluation of different scoring guidelines, clinicopathological features and prognostic impact

BackgroundClear cell carcinoma (CCC) is a rare high-grade adenocarcinoma associated with poor response to platinum-based chemotherapy agents in the female genital tract. Human epidermal growth factor receptor 2 (HER2) overexpression is routinely used as a biomarker for targeted therapy in breast and gastric carcinomas, but its role in CCC remains unclear. MethodsIn this study, HER2 overexpression was evaluated by immunohistochemistry (IHC) using College of American Pathologists (CAP) HER2 scoring guidelines for breast and endometrial serous carcinoma (ESC) on tissue microarray blocks. In equivocal and positive cases, fluorescence in situ hybridization (FISH) was performed. IHC score 3, and all amplified cases on FISH test were considered positive. ResultsThirty-six cases of ovarian (OCCC), 36 endometrial (ECCC), and 2 cervical CCC were included. According to ESC and breast scoring guidelines, 20 % and 15.1 % of ECCC and 14.7 % and 6 % of OCCC were HER2 positive, respectively. Both cases of cervical CCC were negative. Scoring based on breast carcinoma guideline showed higher concordance (100 %) with gene amplification results, in comparison with ESC guideline (82.7 %). On multivariate survival analysis, HER2 positive ECCC and OCCC (based on ESC scoring methods) had significantly lower overall and disease-free survivals (OS, DFS) (P < 0.05). ConclusionHER2 immunoscoring based on ESC guideline can yield a higher sensitivity with relevant clinical and prognostic features in OCCC and ECCC. HER2 can be considered a potential biomarker for targeted therapy and future clinical trials.

Paediatric Spitzoid Neoplasms: 10-Year Retrospective Study Characterizing Histological, Clinical, Dermoscopic Presentation and FISH Test Results.

Spitzoid lesions are a wide tumour class comprising Spitz nevus (SN), atypical Spitz tumour (AST) and Spitz melanoma (SM). We conducted a single-centre-based retrospective survey on all histologically diagnosed spitzoid lesions of paediatric patients (1-18 years) of the last 10 years (2012-2022). Histopathological reports and electronic records of patients were used to retrieve relevant data regarding patients' features, clinical and dermatoscopical aspects of lesions when recorded, and FISH tests when present. Of 255 lesions, 82% were histologically benign, 17% atypical, 1% malignant. Clinically, 100% of SM were large (≥6 mm) and raised; AST were mainly large (63%), raised (98%), pink (95%). Small (≤5 mm), pigmented, flat lesions correlated with benign histology (respectively 90%, 97%, 98% SN) (p < 0.0001). Dermatoscopical patterns were analysed in 100 patients: starburst pattern correlated with benign histology (26% SN (p = 0.004)), while multicomponent pattern correlated with atypical/malignant lesions (56% AST, 50% SM (p = 0.0052)). Eighty-five lesions were subjected to fluorescence in situ hybridization (FISH): 34 (71% AST; 29% SN) were FISH-positive; 51 (63% SN; 37% AST) were FISH-negative (p = 0.0038). This study confirmed predominant benign histology (82%) of paediatric spitzoid lesions, thus detecting 17% AST and 1% SM, highlighting the need for caution in handling spitzoid lesions. Until AST are considered potentially malignant proliferations and no reliable criteria are identified to distinguish them, the authors suggest a prudent approach, especially in children.

Round-robin testing for LMO2 and MYC as immunohistochemical markers to screen MYC rearrangements in aggressive large B-cell lymphoma

Aggressive large B-cell lymphomas (aLBCL) include a heterogeneous group of lymphomas with diverse biological features. One of the approaches to the diagnosis of aLBCL is based on the identification of MYC rearrangements (MYC-R), in addition to BCL2 and BCL6 rearrangements by genetic techniques, mainly fluorescent in situ hybridization (FISH). Because of the low incidence of MYC-R, the identification of useful immunohistochemistry markers to select cases for MYC FISH testing may be useful in daily practice. In a previous work, we identified a strong association between the profile CD10 positive/LMO2 negative expression and the presence of MYC-R in aLBCL and obtained good intralaboratory reproducibility. In this study, we wanted to evaluate external reproducibility. To evaluate whether LMO2 can be a reproducible marker between observers 50 aLBCL cases were circulated among 7 hematopathologists of 5 hospitals. Fleiss’ kappa index for LMO2 and MYC were 0.87 and 0.70, respectively, indicating high agreement between observers. In addition, during 2021–2022, the enrolled centers included LMO2 in their diagnostic panels to evaluate prospectively the utility of the marker, and 213 cases were analyzed. Comparing LMO2 with MYC, the group of CD10 positive cases showed higher specificity (86% vs 79%), positive predictive value (66% vs 58%), likelihood positive value (5.47 vs 3.78), and accuracy (83% vs 79%), whereas the negative predictive values remained similar (90% vs 91%). These findings place LMO2 as a useful and reproducible marker to screen MYC-R in aLBCL.

HER2 Status Assessment in Endometrial Serous Carcinoma: Comparative Analysis of Two Proposed Testing and Interpretation Algorithms.

HER2 status is now routinely assessed in endometrial serous carcinoma (ESC) due to the reported predictive value of HER2 protein overexpression and/or gene amplification. Herein the authors compare 2 proposed testing and interpretation guidelines for HER2 in ESC. Forty-three consecutive cases of ESC that had been dually tested by both HER2 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) were interpreted using 2 sets of guidelines. Guideline set 1 (GS1) is the 2018 American Society of Clinical Oncology/College of American Pathologists guidelines for breast cancer. Guideline set 2 (GS2) is a recent proposal that is a slight modification of the enrollment criteria for the clinical trial (NCT01367002) that demonstrated a survival benefit for anti-HER2 therapy in ESC. By IHC, GS1 and GS2, respectively classified 39.5% (17/43) and 28% (12/43) of ESC as HER2-negative, 37.2% (16/43) and 53.4% (23/43) as HER2 equivocal, and 23.2% (10/43) and 18.6% (8/43) as HER2-positive (P > 0.05 for all). IHC and FISH were highly concordant at the extremes using either set of guidelines, as no cases were found to be IHC3+/FISH-negative or IHC 0-1+/FISH-positive. GS1 and GS2 were comparable regarding the proportion of IHC equivocal cases that were HER2 amplified by FISH (19% vs 23% respectively; [P = 0.71]). GS1 and GS2 displayed 98% (42/43) concordance regarding the final (IHC and/or FISH-based) classification of tumors as being HER2-positive or negative, and the same 13 cases were ultimately classified as HER2 amplified using either GS1 or GS2. One "discordant" case was classified as HER2-positive using GS2 but HER2-negative using GS1 (HER2 IHC score 2+ using both guidelines, HER2:CEP17 signal ratio of 3, HER2 signal number of 3.4). Six (14%) of the 43 cases (FISH Groups: 2, 3, and 4) would require IHC results to interpret the FISH findings using GS1. Because GS1 requires that the HER2 IHC staining be observed within a homogeneous and contiguous invasive cell population, and this is not a requirement in GS2, GS2 may be better suited for ESC given its frequently heterogeneous staining pattern. Additional studies may be required on the optimal interpretation of problematic dual-probe FISH scenarios in GS2 and the necessity for IHC correlation in such scenarios. Using either set of guidelines, our findings support a reflex testing strategy of restricting FISH testing to cases that are IHC equivocal.

NTRK Gene Fusions in Non-Small-Cell Lung Cancer: Real-World Screening Data of 1068 Unselected Patients.

(1) Background: The main objectives of our study are (i) to determine the prevalence of NTRK (neurotrophic tyrosine kinase) fusions in a routine diagnostic setting in NSCLC (non-small cell lung cancer) and (ii) to investigate the feasibility of screening approaches including immunohistochemistry (IHC) as a first-line test accompanied by fluorescence in situ hybridization (FISH) and RNA-(ribonucleic acid-)based next-generation sequencing (RNA-NGS). (2) Methods: A total of 1068 unselected consecutive patients with NSCLC were screened in two scenarios, either with initial IHC followed by RNA-NGS (n = 973) or direct FISH testing (n = 95). (3) Results: One hundred and thirty-three patients (14.8%) were IHC positive; consecutive RNA-NGS testing revealed two patients (0.2%) with NTRK fusions (NTRK1-EPS15 (epidermal growth factor receptor pathway substrate 15) and NTRK1-SQSTM1 (sequestosome 1)). Positive RNA-NGS was confirmed by FISH, and NTRK-positive patients benefited from targeted treatment. All patients with direct FISH testing were negative. RNA-NGS- or FISH-positive results were mutually exclusive with alterations in EGFR (epidermal growth factor receptor), ALK (anaplastic lymphoma kinase), ROS1 (ROS proto-oncogene 1), BRAF (proto-oncogene B-Raf), RET (rearranged during transfection) or KRAS (kirsten rat sarcoma viral oncogene). Excluding patients with one of these alterations raised the prevalence of NTRK-fusion positivity among panTrk-(tropomyosin receptor kinase-) IHC positive samples to 30.5%. (4) Conclusions: NTRK fusion-positive lung cancers are exceedingly rare and account for less than 1% of patients in unselected all-comer populations. Both RNA-NGS and FISH are suitable to determine clinically relevant NTRK fusions in a real-world setting. We suggest including panTrk-IHC in a diagnostic workflow followed by RNA-NGS. Excluding patients with concurrent molecular alterations to EGFR/ALK/ROS1/BRAF/RET or KRAS might narrow the target population.

Philadelphia-Like Genetic Rearrangements in Adults With B-Cell ALL: Refractoriness to Chemotherapy and Response to Tyrosine Kinase Inhibitor in ABL Class Rearrangements.

Philadelphia-like (Ph-like) B-cell ALL is a high-risk subtype of B-cell ALL that shares a gene expression profile with Ph-positive ALL, but without a BCR::ABL1 fusion. A subgroup of these patients have fusions or rearrangements involving genes such as ABL1, ABL2, PDGFRβ, JAK2, and EPOR, some of which are potentially sensitive to tyrosine kinase inhibitors (TKIs). Prompt identification of these genetic aberrations are important for prognostication and treatment decisions. We performed a retrospective review of patients with B-cell ALL treated at MD Anderson Cancer Center to identify recurrent genetic fusions commonly seen in Ph-like ALL and focus on patients treated with TKI. We identified 23 patients with recurrent genetic fusions commonly seen in Ph-like ALL; 14 had ABL class fusions (eight ABL1, one ABL2, and five PDGFRβ) and nine had JAK2 class fusions (five JAK2 and four EPOR). Notably, several of these fusions were cryptic by conventional cytogenetics and fluorescent in situ hybridization (FISH) assays and identified only by multiplex fusion assay. Thirteen of these 23 patients received a TKI as part of their treatment; this included ABL1 fusion (n = 8), PDGFRβ fusion (n = 4), and EPOR fusion (n = 1). All four patients with ABL1 fusions who received TKI with induction chemotherapy are alive in first remission. Understanding the genomics of B-cell ALL is important for disease prognostication and for precise treatment planning. Besides conventional cytogenetics and directed FISH testing, multiplex fusion assays can help identify recurrent chromosomal translocations that are seen in patients with Ph-like ALL. Early initiation of TKI appears beneficial; larger studies are required to fully understand the benefit of TKI and to design rational combination therapies for these patients.

Comprehensive FISH testing using FFPE tissue microarray of primary lymph node tissue identifies secondary cytogenetic abnormalities in Mantle Cell Lymphoma

IntroductionMantle Cell Lymphoma (MCL), is characterised by the reciprocal translocation t(11;14) resulting in CCND1-IGH gene fusion and subsequent upregulation of the CCND1 gene. Rearrangements of MYC and losses of CDKN2A and TP53 have been identified as biomarkers informing prognostic and potentially therapeutic information however these are not routinely assessed in MCL investigation. We aimed to identify additional cytogenetic changes using fluorescence in situ hybridisation (FISH) on formalin fixed paraffin embedded (FFPE) primary lymph node tissue microarrays in a cohort of 28 patients diagnosed with MCL between 2004 and 2019. FISH results were compared with corresponding immunohistochemistry (IHC) biomarkers to determine if IHC was a reliable screening tool to direct FISH testing. MethodFFPE lymph node tissue samples were constructed into tissue microarrays (TMA) which were stained with 7 immunohistochemical biomarkers: Cyclin D1, c-Myc, p16, ATM, p53, Bcl-6 and Bcl-2. The same TMAs were hybridised with FISH probes for the corresponding genes; CCND1-IGH, MYC, CDKN2A, ATM, TP53, BCL6 and BCL2. FISH and the corresponding IHC biomarkers were analysed to determine if secondary cytogenetic changes could be identified and if IHC could be used as a reliable, inexpensive predictor of FISH abnormalities to potentially direct FISH testing. ResultsCCND1-IGH fusion was detected in 27/28 (96%) of samples. Additional cytogenetic changes were identified by FISH in 15/28 (54%) of samples. Two additional abnormalities were detected in 2/28 (7%) samples. Cyclin D1 IHC overexpression was an excellent predictor of CCND1-IGH fusion. MYC and ATM IHC were useful screening tests to direct FISH testing and identified cases with poor prognostic features including blastoid change. IHC did not show clear concordance with FISH for other biomarkers. ConclusionFISH using FFPE primary lymph node tissue can detect secondary cytogenetic abnormalities in patients with MCL which are associated with an inferior prognosis. An expanded FISH panel including MYC, CDKN2A, TP53 and ATM should be considered in cases where anomalous IHC expression or is seen for these markers or if the patient appears to have the blastoid variant of the disease.

Abstract 2133: Next-generation sequencing-based MET focal amplification can predict treatment efficacy of MET inhibitors in lung cancer

Abstract Background: MET amplification (METamp) occurs in 1-5% of treatment-naïve or 5-20% of epidermal growth factor receptor tyrosine kinase inhibitors-treated lung cancers (LC). It is a promising therapeutic target in LC. Although fluorescence in situ hybridization (FISH), next-generation sequencing (NGS), and immunohistochemical staining (IHC) are available for METamp detection, but the most appropriate detection method and criteria for defining METamp are uncertain. Here, we explored the concordance of these three methods in informing METamp status and identified patients likely to benefit from MET inhibitors. Methods: Tissue samples from LC patients who underwent MET detection by FISH, NGS, and IHC tests at Shanghai Chest Hospital were retrospectively collected. MET focal amplification and polysomy by FISH were determined as MET/CEP7 ratio ≥ 2, and &amp;lt; 2 with the average MET signals per cell ≥ 5, respectively. NGS-based MET focal amplification and polysomy were determined with in-house scripts (Burning Rock Biotech). Focal amplification and polysomy were defined as METamp-positive. IHC-based MET positive was determined with H-score ≥ 200. FISH was used as a reference. Results: A total of 231 patients with a median age of 65 years were enrolled. With FISH as reference testing, NGS detection for METamp showed 66.9% (87/130) sensitivity and 95.1% sensitivity (96/101), and IHC had 71.5% (93/130) sensitivity and 91.1% (92/101) specificity. Furthermore, NGS detection for MET focal amplification achieved 87.2% (75/86) sensitivity and 96.6% (140/145) specificity, while MET polysomy detection showed 20.5% (9/44) sensitivity and 98.4% (184/187) specificity. Of 153 treatment-naïve patients, patients with focal amplification (FISH: 16.7%; NGS: 16.3%) had a significantly lower frequency of classic LC oncogene alterations than those with polysomy (FISH: 51.6%, p = 0.001; NGS: 58.3%, p = 0.006) and METamp-negative patients (METneg; FISH: 72.1%, p &amp;lt; 0.001; NGS: 64.1%, p &amp;lt; 0.001). A total of 27 patients had follow-up data. The disease control rate (DCR) to MET inhibitors was 73.1% (19/26) for overall METamp, 81.0% (17/21) for focal amplification, and 40.0% (2/5) for polysomy using FISH results. In contrast, corresponding DCRs using NGS results were 84.2% (16/19), 88.9% (16/18), and 0% (0/1), respectively. Moreover, patients with NGS-based focal amplification had a significantly longer progression-free survival (PFS) than those with polysomy or METneg. Of note, 1 patient with METneg by FISH was determined to harbor focal amplification by NGS and achieved partial response to crizotinib with a PFS of 314 days. Conclusion: Our results suggest that MET focal amplification leads to oncogenic MET addiction and is associated with promising efficacy of MET inhibitors. MET focal amplification by NGS tests might be a feasible and powerful biomarker to identify LC patients who benefit from MET inhibitors. Citation Format: Chan Xiang, Lianying Guo, Ruiying Zhao, Haohua Teng, Zhou Zhang, Ting Kuang, Xinze Lv, Ting Hou, Chenglin Liu, Wenjie Sun, Haiwei Du, Yuchen Han. Next-generation sequencing-based MET focal amplification can predict treatment efficacy of MET inhibitors in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2133.

Abstract 4294: Bridging the gap between targeted NGS and FISH gene-level CNV detection capabilities in hematologic malignancies

Abstract Background: Copy Number Variations (CNVs) are prominent features of cancer cells. From a clinical standpoint, their accurate detection at a low cost is a priority. With regular increases in the number of markers to be tested, the cost effectiveness and practicality of gold standard techniques like Fluorescence In Situ Hybridization (FISH) are slowly decreasing. Cost-efficient Next Generation Sequencing (NGS) targeted gene panels can be scaled up but accurately detecting CNVs from the resulting data remains challenging. We demonstrate large amounts of data and machine learning can help bridge the gap between the two techniques. Methods: We collected the sequencing data of 6,277 patients tested using a custom amplicon based NGS assay designed to detect somatic alterations in 297 hematological cancer relevant genes such that at least one concurrent FISH test was also performed. FISH results were used to infer the gain, loss, or normality information for each corresponding gene. The annotated genes were then used to curate a training set by extracting 20 features per gene from the alignment results. A 3-class random forest classifier was trained using this dataset. The selected model was evaluated on a distinct set of 2,738 patients. Results: Evaluation results are provided in Table 1 for 8 genes for which the FISH probe used to infer the gain, loss, or normality information directly spanned the gene region. The predicted CNVs are almost a perfect match with FISH for 6 of these genes with a limit of detection at 20% abnormal cells. In most cases, the model reduces discordant calls by over 50% compared to using existing CNV detection software only. Conclusion: We show the CNV detection capabilities of a targeted NGS assay can closely match the gold-standard FISH technique by analytically correcting the biases introduced by the targeting procedures. The model presented here is used to detect CNVs in ALL patients after a successful formal validation in our laboratory. Table 1. Evaluation results. Gene FISH Positive Cases (Gain/Loss) FISH Negative Cases (Normal) All FISH Cases Total Concordant Sensitivity Total Concordant Specificity Total Concordant Accuracy ATM 72 72 100.00% 641 629 98.13% 713 701 98.32% CBFB 23 22 95.65% 517 506 97.87% 540 528 97.78% EGR1 171 169 98.83% 1,541 1,538 99.81% 1,712 1,707 99.71% KMT2A 27 25 92.59% 474 472 99.58% 501 497 99.20% MET 113 113 100.00% 1,593 1,582 99.31% 1,706 1,695 99.36% NF1 15 15 100.00% 908 908 100.00% 923 923 100.00% TERT 10 10 100.00% 1,723 1,709 99.19% 1,733 1,719 99.19% TP53 76 73 96.05% 1,567 1,556 99.30% 1,643 1,629 99.15% Citation Format: Christophe N. Magnan, Hyunjun Nam, Shashikant Kulkarni, Segun C. Jung. Bridging the gap between targeted NGS and FISH gene-level CNV detection capabilities in hematologic malignancies. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4294.

Fluorescence in situ hybridization for ETV6 gene rearrangements on destained cytological smears: Role in diagnosis of secretory carcinoma of salivary gland.

Fine-needle aspiration cytology (FNAC) is the first-line diagnostic procedure for salivary gland masses. Secretory carcinoma (SC) is characterized by ETV6 and RET rearrangements detected by fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction optimized for paraffin-embedded and fresh-frozen tissue, respectively. The authors performed FISH on cytological material to assess its role in the diagnosis of SC. FNACs with SC as a diagnostic consideration and cases diagnosed as SC on histology with a corresponding FNAC with any diagnosis were evaluated for ETV6 rearrangement by FISH. If acinic cell carcinoma (ACC) was a differential diagnosis and ETV6 rearrangement was absent, NR4A3 FISH was performed. FISH results were compared with those on histological specimens, where available. Fifteen cases were included. FISH initially performed on three cell blocks did not yield good results, was then performed on direct smears, and was interpretable in 14 cases (93.3%). An ETV6 rearrangement was identified in seven cases (50%), and an NR4A3 rearrangement was identified in three cases (21.4%), providing a confirmatory diagnosis in 10 of 15 cases (66.7%). The Milan System for Reporting Salivary Gland Cytopathology category was altered in two cases (6.7%). Complete correlation (100%) was seen with FISH on corresponding histological specimens. With minor modifications, the FISH procedure can be optimized for FNAC smears with results comparable to those on histological specimens. ETV6 FISH testing on cytological smears in cases suspected as SC improves the diagnostic accuracy of FNAC and can help lower the proportion of the Milan categories salivary gland neoplasm of uncertain malignant potential and suspicious for malignancy, maximizing diagnostic information from less invasive samples and aiding in patient management.

Application of fluorescence in situ hybridization technique to verify the clonalities of non-clonal cytogenetic abnormalities identified in Myelodysplastic syndrome

To assess the value of fluorescence in situ hybridization (FISH) technique for the verification of the clonalities of non-clonal cytogenetic abnormalities (n-CCA) identified by conventional chromosome banding analysis (CBA) in patients with Myelodysplastic syndrome (MDS). Clinical data and results of karyotyping and FISH assays for 91 patients of MDS with n-CCA identified by CBA were retrospectively analyzed. In total 94 non-clonal +8, 5q-, -7/7q- or 20q- were detected by CBA, among which 43 (45.7%) were verified to be clonal abnormalities by FISH. The detection rates for +8, 5q-, -7/7q- and 20q- by FISH were 47.6% (30/63), 25% (2/8), 41.7% (5/12), 40% (2/5) and 66.7% (4/6), respectively, with the positive cells accounting for 4% to 90% of all counted cells, with a median value of 7%. The 91 patients were divided into three groups including ≥ 20, 10 ~< 20 and < 10 based on the numbers of metaphase cells in CBA, and the detection rates by FISH for the three groups were 43.7% (31/71), 33.3% (3/9) and 63.6% (7/11), respectively, which showed no statistically difference (P > 0.05). Continuous CBA and FISH surveys were conducted for 26 patients who received supportive treatment, and the results revealed that 91.7% (11/12) of FISH-verified positive abnormalities had persisted, whereas 92.9% (13/14) of the n-CCA verified as negative by FISH was transient. Nearly half of the CBA identified n-CCA have been verified as clonal aberrations by FISH, and the FISH detection rate showed no correlation with the number of metaphase cells. FISH test is strongly recommended for verifying the clonalities of n-CCA detected by CBA, and continuous cytogenetic survey of the patients with MDS is necessary.

Integrated Genomic DNA/RNA Profiling vs Fluorescence in Situ Hybridization in the Detection of MYC and BCL2 (and BCL6) Rearrangements in Large B-Cell Lymphomas: Updates Amid the New WHO Classification of Lymphoid Neoplasms.

Large B-cell lymphomas (LBCLs) are a heterogeneous group of lymphoid neoplasms whose molecular and cytogenetic profile has predictive and prognostic implications. The concept of double-hit lymphomas (DHLs) was recently updated in the fifth edition of the World Health Organization classification, with the exclusion of MYC and BCL6 rearranged tumors from the group. Now, DHLs are referred to as diffuse large B-cell lymphoma/high-grade B-cell lymphoma with MYC and BCL2 rearrangements. Fluorescence in situ hybridization (FISH) is the current gold standard for detecting rearrangements in LBCLs, but comprehensive genomic profiling (CGP) has recently been suggested to be at least as accurate as FISH in classifying these neoplasms and providing additional genetic information. We analyzed a cohort of 131 patients in whom FISH and CGP studies were performed as part of our normal clinical workflow and compared the effectiveness of FISH and CGP in detecting these clinically relevant rearrangements. Our findings are in agreement with our previously published study, which analyzed a cohort of 69 patients, supporting our hypothesis that the best approach to maximize detection of DHLs while limiting waste seems to be a combination of CGP and MYC break-apart FISH testing, the latter to capture the presence of non-IGH::MYC events. Our study supports the combined use of FISH and GCP rather than either method alone to better detect MYC and BCL2 (and BCL6) gene rearrangements.

Abstract HER2-14: HER2-14 HER-2 low status in early stage invasive lobular carcinoma of the breast: associated factors and outcomes in an institutional series

Abstract Objectives: The concept of human epidermal growth factor receptor 2 (HER2)-low status has been proposed as a potential treatment target for breast cancers previously considered to be HER2-negative. Defined by an immunohistochemistry (IHC) score of 1+ or 2+ and negative fluorescent in situ hybridization (FISH) for HER2, HER2-low status predicts significant clinical benefit from novel therapeutic compounds in recent clinical trials. The prevalence and clinical implications of HER2-low status in patients with early stage invasive lobular carcinoma (ILC) has not been described. We aimed to describe the clinicopathologic features and prevalence of HER2-low status in ILC, and identify any potential differences in clinical outcome. Methods: We evaluated stage I-III ILC tumors from a prospectively maintained institutional database of patients where both IHC and FISH testing for HER2 status was performed as standard clinical care. Tumors were classified as HER2 negative (IHC=0), HER2-low (IHC=1+ or 2+ and negative FISH), or HER2 positive (IHC=3+ or FISH ratio ⇒2). Data were analyzed in Stata 16.1 using chi-squared tests, t-tests, and Cox proportional hazards models for disease free survival (DFS). Results: 666 ILC tumors with available HER2 status were available for analysis. The mean age at diagnosis was 59.8 years (range 21-91). The majority of patients had stage I disease (63.1%) with an average follow up time of 6.7 years (standard deviation [5.4]). Overall, 184 (27.6%) tumors were HER2 negative, 434 (65.1%) were HER2-low, and 48 (7.2%) were HER2 positive. There were no associations between HER2 status and age, menopausal status, body mass index, tumor stage, grade, presence of lymphovascular invasion, or molecular assay results. Hormone receptor status was significantly associated with HER2 status, with HER2 positive tumors significantly less likely to be estrogen receptor (ER) positive than both HER2 negative and HER2-low tumors (89.6% versus 97.3% and 96.8% respectively, p=0.03). HER2-low tumors were also significantly more likely to have progesterone receptor (PR) positivity (86.6% compared to 79.9% of HER2 negative and 72.9% of HER2 positive tumors, p = 0.01). This difference remained significant when comparing just HER2-low to HER2 negative cases (p=0.034). While there were no differences in use of neoadjuvant or adjuvant chemotherapy by HER2 status, HER2-low patients were significantly more likely to undergo mastectomy versus lumpectomy when compared to HER2 negative and HER2 positive patients (53.7% versus 38.0% and 43.8% respectively, p= 0.001). In a multivariable Cox proportional hazards model adjusting for tumor size, number of positive nodes, ER/PR status, and local therapy received, patients with HER2-low status had worse DFS than those with HER2 negative tumors (hazard ratio 2.0, 95% confidence interval 1.0 - 4.1, p=0.05). Conclusions: In this analysis of 666 early stage ILC cases, we found that most tumors were HER2-low, and that those with HER2-low disease were significantly more likely to have PR positive tumors and to undergo mastectomy. When adjusting for these variables, we identified a difference in DFS between HER2 negative and HER2-low early stage ILC. These findings support the contention that HER2-low and HER2 negative disease represent two different clinical entities. Further investigation of the potential benefit of HER2 targeted therapy in ILC, which predominately lacks HER2-amplified disease, is needed to ensure optimal outcomes in this understudied tumor type. Citation Format: Harriet T. Rothschild, Elle Clelland, Anne Patterson, Julissa Molina-Vega, Mandeep Kaur, Mary Kathryn Abel, W. Fraser Symmans, Christopher J. Schwartz, Rita Mukhtar. HER2-14 HER-2 low status in early stage invasive lobular carcinoma of the breast: associated factors and outcomes in an institutional series [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr HER2-14.

Improvement of diagnosis in children with Burkitt lymphoma in Kenya: feasibility study for the implementation of fluorescence in situ hybridisation testing for MYC and the MYC/IGH translocation.

Indiana University (IU) initiated fluorescence in situ hybridisation (FISH) methodology for Burkitt Lymphoma (BL) to advance the accuracy and speed of diagnosis in the AMPATH Reference Laboratory at Moi Teaching and Referral Hospital (MTRH) in Eldoret, Kenya. Standard diagnostic testing for BL at MTRH includes morphology of the biopsy specimen or aspirate and limited immunohistochemistry panels. Tumour specimens from 19 children enrolled from 2016 to 2018 in a prospective study to improve the diagnosis and staging of children with suspected BL were evaluated. Touch preps from biopsy specimens or smears from fine needle aspiration were collected, stained with Giemsa and/or H&E and reviewed by pathologists to render a provisional diagnosis. Unstained slides were stored and later processed for FISH. Duplicate slides were split between two laboratories for analysis. Flow cytometry results were available for all specimens. Results from the newly established FISH laboratory in Eldoret, Kenya were cross-validated in Indianapolis, Indiana. Concordance studies found 18 of 19 (95%) of specimens studied yielded analysable FISH results for one or both probe sets (MYC and MYC/IGH) in both locations. There was 94% (17/18) concordance of results between the two FISH laboratories. FISH results were 100% concordant for the 16 specimens with a histopathological diagnosis of BL and two of three non-BL cases (one case no result in IU FISH lab). FISH was similarly concordant with flow cytometry for specimens with positive flow results with the exception of a nasopharyngeal tumour with positive flow results for CD10 and CD20 but was negative by FISH. The modal turn-around time for FISH testing on retrospective study specimens performed in Kenya ranged between 24 and 72 hours. FISH testing was established, and a pilot study performed, to assess the feasibility of FISH as a diagnostic tool for the determination of BL in a Kenyan paediatric population. This study supports FISH in limited resource settings to improve the accuracy and speed of diagnosis of BL in Africa.

Agreement between FGFR2 immunohistochemistry assays and fluorescence in situ hybridization (FISH) in metastatic gastric cancer: A comparison study.

301 Background: FGFR2 status of a patient with metastatic gastric adenocarcinoma could be an important factor in determining optimal treatment strategy with FGFR2 inhibitors and antibodies. The question remains how well different assays agree on the FGFR2 status of the same patient and whether one test can be substituted by another. Methods: Pairwise comparison of 4 tests based on the same patient population was performed: 3 IHC assays [Abcam clone EPR24075-418, R&amp;D clone 98706, Santa Cruz clone C-8] and one FISH test. One hundred and nine formalin-fixed, paraffin embedded samples (including 64 primary tumors and 45 metastases of same patients) were obtained and were stained with FGFR2 IHC assays. Two trained pathologists independently evaluated the percentages of tumor staining and their intensity. FGFR2 FISH was performed as described previously [Su, BJC 2014]. The concordance analysis was performed to assess (1) correlation of FGFR2 expression/amplification between different assays in primary and metastases, (2) the predictive properties of one test of another. Results: After evaluating the expression in the first 19 patients, further study was carried out only using the Abсam assay due to pronounced nuclear staining with other IHC tests. FGFR2 any level expression was detected in 29 (47%) primary tumors and 18 (40%) metastases with concordance of 91%. The prevalence of FGFR2 amplification was 9.4% and intratumoral heterogeneity was observed in 33% of FGFR2 amplified cases. Pearson Correlation Coefficients (PCC) were: 0.89, 0.38 and 0.35 between IHC3+/FISH, IHC≥1% stained cells/FISH and IHC≥10%/FISH, respectively. The table represents how well one assay can predict the same outcome (positivity or negativity) of another assay. Conclusions: Among patients who were negative by FISH, 86%-93% of the patients were negative by IHC assay (Abcam). Among patients who were positive by FISH, 75-80% of them were positive by IHC. FISH should not be recommended as a substitute for a FGFR2 IHC assay due to high probability of false negative prediction as a result of intratumoral heterogeneity and low PCC. [Table: see text]

Correlation between Expression Patterns of CD117/CD200 in Plasma Cells and Molecular Genetic Prognostic Parameters in Multiple Myeloma

To investigate the correlation between the expression of CD117 and CD200 in plasma cells and molecular genetic abnormalities in patients with multiple myeloma (MM). 100 newly diagnosed MM patients were selected, and fresh bone marrow fluid was collected from the patients. The immunophenotypes and chromosomal structural variations of plasma cells were detected by flow cytometry (FCM) and fluorescence in situ hybridization (FISH). The positive expression frequencies of CD117 and CD200 in abnormal plasma cells of all MM patients were 44.0% and 44.0%, respectively. At least one molecular genetic abnormality was detected in 53 of the 75 patients who underwent FISH testing, and the overall detection rate was 70.7% (53/75). The detection rates of 1q21 (CKS1B ) duplication, 1p32 (CDKN2C ) deletion, p53 deletion and IgH rearrangement were 48.6% (36/74), 10.6% (7/66), 11.1% (8/72) and 32.9% (24/73), respectively. The incidence of IgH rearrangement in CD117+ patients was significantly lower than that in CD117- patients (P<0.05), and the proportion of 1p32 (CDKN2C ) deletion in CD200- patients was significantly lower than that in CD200+ patients (P<0.05). According to the expressions of CD117 and CD200, the patients were divided into 4 groups: CD117+CD200+, CD117+CD200-, CD117-CD200+ and CD117-CD200-. Further analysis showed that the incidence of IgH rearrangement in the CD117+CD200- group was significantly lower than that in the CD117-CD200+ group (P<0.05), and the deletion rate of 1p32 (CDKN2C ) gene in CD117+CD200- group was significantly lower than that in CD117+CD200+ group and CD117-CD200+ group (P<0.05). The difference in the expression patterns of CD117 combined with CD200 shows important value in judging the prognosis of MM patients, and the MM patients with CD117-CD200+ expression patterns in abnormal plasma cells have a worse prognosis.

First proficiency testing for NGS-based and combined NGS- and FISH-based detection of FGFR2 fusions in intrahepatic cholangiocarcinoma.

Intrahepatic cholangiocarcinoma harbours druggable genetic lesions including FGFR2 gene fusions. Reliable and accurate detection of these fusions is becoming a critical component of the molecular work-up, but real-world data on the performance of fluorescence in situ hybridisation (FISH) and targeted RNA-based next-generation sequencing (NGS) are very limited. Bridging this gap, we report results of the first round robin test for FGFR2 fusions in cholangiocarcinoma and contextualise test data with genomic architecture. A cohort of 10 cholangiocarcinoma (4 fusion positive and 6 fusion negative) was tested by the Institute of Pathology, University Hospital Heidelberg, Germany. Data were validated by four academic pathology departments in Germany. Fusion-positive cases comprised FGFR2::BICC1, FGFR2::DBP, FGFR2::TRIM8, and FGFR2::ATE1 fusions. In a second step, a round robin test involving 21 academic and non-academic centres testing with RNA-based NGS approaches was carried out; five participants performed FISH testing in addition. Thirteen of 16 (81%) centres successfully passed the NGS only and 3 of 5 (60%) centres passed the combined NGS + FISH round robin test. Identified obstacles were bioinformatic pipelines not optimised for the detection of FGFR2 fusions and assays not capable of detecting unknown fusion partners. This study shows the benefit of targeted RNA-NGS for the detection of FGFR2 gene fusions. Due to the marked heterogeneity of the genomic architecture of these fusions, fusion partner agnostic (i.e. open) methodological approaches that are capable of identifying yet unknown fusion partners are superior. Furthermore, we highlight pitfalls in subsequent bioinformatic analysis and limitations of FISH-based tests.

Fluorescence in situ hybridization test for detection of endometrial carcinoma cells by non-invasive vaginal swab.

Endometrial cancer (EC) is the most common gynaecological malignancy with increasing incidence in developed countries. As gold standard, hysteroscopy confirms only 30% of suspected ECs. The detection of EC cells in the vagina by fluorescence in situ hybridization (FISH) after a smear test could reduce invasive procedures in the future. Using array-based comparative genome hybridization (aCGH) on 65 endometrial carcinomas, most frequently imbalanced regions of the tumour genome were identified. Bacterial artificial chromosomes were used to generate FISH-probes homologue to these human regions. The FISH test was hybridized on swabs specimens collected from the vaginal cavity. Samples from six patients without EC were selected as a negative control and on 13 patients with known EC as a positive control. To distinguish between benign and EC cases, the cut-off value has been defined. A first validation of this EC-FISH Test was performed with swabs from 41 patients with suspected EC. The most common genomic imbalances in EC are around the CTNNB1, FBXW7 and APC genes. The cut-off is defined at 32% of analysed cells without diploid signal pattern. This differs significantly between the positive and negative controls (p < 0.001). In a first validation cohort of 41 patients with suspected EC, the EC-FISH Test distinguishes patients with and without EC with a sensitivity of 91% and a specificity of 83%. The negative predictive value is 96%. This is the first report of a non-invasive EC-FISH Test to predict EC in women with suspected EC.