Fluorescence In Situ Hybridization Slides Research Articles

Efficient Convolution Network to Assist Breast Cancer Diagnosis and Target Therapy.

Breast cancer is the leading cause of cancer-related deaths among women worldwide, and early detection and treatment has been shown to significantly reduce fatality rates from severe illness. Moreover, determination of the human epidermal growth factor receptor-2 (HER2) gene amplification by Fluorescence in situ hybridization (FISH) and Dual in situ hybridization (DISH) is critical for the selection of appropriate breast cancer patients for HER2-targeted therapy. However, visual examination of microscopy is time-consuming, subjective and poorly reproducible due to high inter-observer variability among pathologists and cytopathologists. The lack of consistency in identifying carcinoma-like nuclei has led to divergences in the calculation of sensitivity and specificity. This manuscript introduces a highly efficient deep learning method with low computing cost. The experimental results demonstrate that the proposed framework achieves high precision and recall on three essential clinical applications, including breast cancer diagnosis and human epidermal receptor factor 2 (HER2) amplification detection on FISH and DISH slides for HER2 target therapy. Furthermore, the proposed method outperforms the majority of the benchmark methods in terms of IoU by a significant margin (p<0.001) on three essential clinical applications. Importantly, run time analysis shows that the proposed method obtains excellent segmentation results with notably reduced time for Artificial intelligence (AI) training (16.93%), AI inference (17.25%) and memory usage (18.52%), making the proposed framework feasible for practical clinical usage.

Digital imaging correlation of immunohistochemistry and fluorescence in situ hybridization in breast carcinoma cases with HER2 genetic heterogeneity

Genetic heterogeneity (GH) is a rare but important event in the evaluation of HER2 amplification status. We investigated whether HER2 fluorescence in situ hybridization (FISH) GHcorrelated with increased protein expression by immunohistochemistry (IHC) and/or morphologic features using image analyses. Retrospective search of HER2 FISH GH cases 2016-2020 was performed. Cases with both FISH and IHC slides available were considered eligible and were digitally imaged. Additional demographic, histological, and treatment information was compiled from pathology and medical records when available. Overall, 11 of 15cases (73.3%) had HER2 FISH GH that matched to areas of HER2 overexpression or focally different morphology. Nine cases with areas of gene amplification overlapped with <10% of intense circumferential protein expression ("Mini 3+"), and 1 case with focal micropapillary features. Clinical information was available on 6patients (40%), all were alive with no evidence of disease (mean follow-up 30.5 months; range, 12-65 months). One patient with GH and a lymph node metastasis showed nonamplified population in the nodal tumor. GH, when defined as discrete clusters of amplified cells following 2013 ASCO/CAP guidelines, even when less than 10% of the tumor cells, frequently has morphologic correlates such as focal intense protein overexpression or micropapillary morphology. Clinical significance of these focal gene amplification and protein overexpression needs to be further investigated.

HER2 fluorescent in situ hybridization signal degradation: a 10-year retrospective study.

Fluorescence in situ hybridization (FISH) analysis is recommended for invasive breast carcinomas with equivocal (2+) immunohistochemical expression of human epidermal growth factor receptor 2 (HER2). However, existing guidelines for the retention and storage requirements for HER2 FISH slides vary widely among countries and laboratories. To determine the degradation rateof HER2 FISH signals, and the optimal retention time and storage conditions for HER2 FISH slides. Dual-probe HER2 FISH slides from March 2009 to June 2019 were retrieved from the archive to assess the presence, intensity and quantity of the green chromosome enumeration probe 17 (CEP 17) and orange HER2 signals. Per the institutional policy, FISH slides are placed in slide boxes and stored in -80°C freezers for up to 4years, whereas older slides are stored at room temperature. After excluding HER2 FISH slides that were deemed uninterpretable due to technical issues, a total of 6255 slides were assessed. Slides from 2009 to 2014 were stored at room temperature, while slides from 2015 to 2019 were stored in -80°C freezers. Slides stored in freezers showed retention of both the green and the orange signals. Slide stored at room temperature demonstrated significant decrease in the signal retention rate and the loss of signal did not progress in a linear fashion. The CEP17 signal was quenched much faster than the HER2 signal. Our study is the first to demonstrate HER2 FISH signal degradation with time and slide storage conditions. Storing HER2 FISH slides in a -80°C freezer allows for retention of both HER2 and CEP17 signals. At room temperature, the signals start to degrade with CEP17 signals lost at a faster rate. The results of the study may be used in official guidelines for storage conditions and retention time for HER2 FISH slides.

Reassignment of HER2 status for subgroups of breast cancer according to the 2018 updated American Society of Clinical Oncology and College of American Pathologists guidelines: The impact of combined immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) reflex testing in a large national reference laboratory.

3144 Background: Updated ASCO/CAP Guidelines for HER2 testing in breast cancer have been most impactful on the resolution of certain challenging groups of FISH results. We review the change in assignment of HER2 status in a large series of breast cancers referred to a large national reference laboratory for FISH testing since the introduction of the 2018 updated guidelines. Methods: Patient samples submitted to the Mayo Clinic Cytogenetics Laboratory (N = 2208) were analyzed by FISH. Samples with Group 2, Group 3, or Group 4 FISH results were reflexed to immunohistochemistry (IHC) in our central laboratory; FISH slides for those cases with equivocal 2+ IHC results were re-scored in the regions of invasive cancer showing more intense membranous staining. A subset of 202 samples with Group 4 FISH results were also reflexed to the previously employed reflex FISH assay (HER2/D17S122), and these were also re-analyzed according to the new reflex IHC/FISH process. Results: 382 of 2208 breast cancer samples tested (17.3%) had FISH results categorized as Group 2 (N = 17, 0.8%), Group 3 (N = 34, 1.5%), or Group 4 (N = 331, 15%) and required reflex IHC testing, and of those, 75% were 2+ equivocal and required targeted re-analysis of the FISH slide according to the 2018 updated guidelines. Re-analysis of the FISH slide resulted in switching between Groups 1-5 in 19.4% of cases, but HER2 status was changed by FISH re-scoring in only 7.7% of cases re-scored (1.0% of all samples), generally due to only minor shifts in HER2 copy number and HER2/control ratios between the initial and IHC-guided reflex FISH scores. In the subset of 202 cases tested by both reflex methods, the previously employed HER2/D17S122 reflex probe set was positive in 123 cases (60.9%), whereas reflex IHC/FISH was positive in only 10 cases (7.9%). Including positive reflex IHC (0.4%) and positive reflex FISH results (2.1%), the overall assignment of positive HER2 status on our series of 2208 cases was 11.5%. Conclusions: Overall rates of HER2 positive FISH results have declined under the most recent ASCO/CAP guideline update as a consequence of new recommendations for reflex testing for Groups 2-4. This change is largely due to reassignment of Group 2 and Group 4 results as negative in the absence of positive IHC.

Chromogenic Tissue-Based Methods for Detection of Gene Amplifications (or Rearrangements) Combined with Protein Overexpression in Clinical Samples.

Immunohistochemistry (IHC) is a well-established, tissue-based assay for the visualization of target proteins. For analysis of DNA targets, chromogenic in situ hybridization (CISH) applications have significant advantages over traditional fluorescence in situ hybridization (FISH). CISH slides can be analyzed using a regular light microscope, while FISH slides require the use of a specialized fluorescence microscope in a dark room. CISH slides allow observers to correlate the gene status (gene amplifications, gene rearrangements, and gene deletions) in the context of tissue morphology better than FISH slides. Recently, a combination of IHC and CISH assays (gene-protein assay, GPA) was developed to study the relationship between gene status and protein expression on the same tissue section. CISH and GPA applications can be optimized using an automated tissue slide processing system to generate reproducible results for a long and complex assay protocol. GPA applications are an ideal approach for tumor status and heterogeneity analyses for research and clinical investigations.

Evaluation of a confocal WSI scanner for FISH slide imaging and image analysis

Background: Technological advances contribute to the maturation of digital pathology in clinical and research applications. However, there are only few reports on fluorescence scanning especially on confocal fluorescence imaging technology in digital pathology, which has superior depth resolution compared to wide-field fluorescence imaging. Here, we explored the features of a confocal WSI scanner for typical diagnostic and research imaging applications of fluorescence in situ hybridization (FISH) assay.Methods: Multi-layer stacking (Z-stack) which stores all image information from each layer, and extended focus which stores the optimal image information from all scanned layers, featured in the Pannoramic Confocal scanner (3DHISTECH Ltd., Budapest, Hungary) were employed in digitizing 14 FISH slides (ALK, EGFR, and multi-gene). The slides were scanned with a 40× water immersion objective producing a final image with pixel resolution of 0.1625 µm/pixel. Z-stack and extended focus were used for N=6, 13, and 26 multiple layers scanning at 1, 0.4, and 0.2 µm depth intervals respectively. Single-layer scanning was also done for comparison. Scanning time and resultant file size were recorded. The CaseViewer from 3DHISTECH was used to visualize images and export the annotated regions, and the exported images were further analyzed in Imaris (Bitplane, Zurich, Switzerland) for 3-dimensional reconstruction, nuclear segmentation, and the quantification and co-localization analysis of dots inside nuclei. Quantification data from Imaris were imported into Excel for statistic analysis.Results: Confocal fluorescence scanning of FISH slides enabled sharper image than wide-field scanning, although it required longer scanning time and larger file storage. More intra-nuclear dots were quantified from multi-layer Z-stack images than single-layer images, and the Z-stack increased scanning time and image file size. Furthermore, there were a reduced in the number of dots and an increased in the number of co-localized dots in extended-focus images compared to Z-stack. Dots in multiple channels were quantified and analyzed automatically, which supports clinical diagnosis of gene amplification, deletion, and translocation. Three-dimensional reconstruction of Z-stack produced precise measurement of spatial distance, which supports molecular research.Conclusion: Confocal provides sharper image than wide-field for FISH slide scanning. Extended focus reduces file size and storage, but could cause inaccurate analysis due to misinterpretation of overlapping information. Z-stack scanning provides high volume image information for spatial analysis. We foresee confocal multi-layer scanning as a digital pathology application tool for FISH imaging in both clinical and research in future.

Fluorescence in situ hybridization testing of chromosomes 6, 8, 9 and 11 in melanocytic tumors is difficult to automate and reveals tumor heterogeneity in melanomas

Malignant melanomas may be difficult to differentiate from benign nevi on the basis of histology. Contrary to nevi, the majority of melanomas harbor chromosomal imbalances. Comparative genomic hybridization-based and fluorescence in situ hybridization (FISH) tests can help differentiating malignant from benign tumors. In the present study, eight-bacterial artificial chromosome (BAC) probes targeting chromosomes 6, 8, 9 and 11 were tested by FISH, and compared with a commercial four-color FISH probe set targeting chromosomes 6 and 11 in a first set of 62 tissue microarray-included melanocytic tumors (47 melanomas and 15 nevi). A second set of 108 tumors (70 melanomas and 38 nevi) was analyzed with the eight-probes kit, and manual counting was compared with the newly developed automated FISH signals counting and with semi-quantitative visual detection of chromosomal imbalances. Intra-tumor heterogeneity was also evaluated in 12 melanomas and 10 patients with paired melanoma samples. Testing the tumors from the first set with the commercial kit and the eight-probes test permitted to correctly identify 45/47 and 47/47 melanomas, respectively. In the second tumor set, 65/70 malignant tumors presented at least one chromosomal imbalance, whereas none was detected in the nevi. The agreement between manual and automated signals counting was better in good-quality FISH slides compared with poor-quality slides. Semi-quantitative visual appreciation of chromosomal imbalances also reached strong agreement with exact manual counting. In addition, a frequent cytogenetic heterogeneity within melanomas and between paired tumors was noticed in patients with metastatic melanomas. To conclude, FISH testing targeting chromosomes 6, 8, 9 and 11 enabled to differentiate the majority of melanomas from nevi but was difficult to automate. Tumor cytogenetic heterogeneity was frequent and could impair FISH testing.

Validation of break-apart and fusion MYC probes using a digital fluorescence in situhybridization capture and imaging system

Introduction: Detection of MYC translocations using fluorescence in situ hybridization (FISH) is important in the evaluation of lymphomas, in particular, Burkitt lymphoma and diffuse large B-cell lymphoma. Our aim was to validate a digital FISH capture and imaging system for the detection of MYC 8q24 translocations using LSI-MYC (a break-apart probe) and MYC 8;14 translocation using IGH-MYC (a fusion probe). Materials and Methods: LSI-MYC probe was evaluated using tissue sections from 35 patients. IGH-MYC probe was evaluated using tissue sections from forty patients. Sections were processed for FISH and analyzed using traditional methods. FISH slides were then analyzed using the GenASIs capture and analysis system. Results: Results for LSI-MYC had a high degree of correlation between traditional method of FISH analysis and digital FISH analysis. Results for IGH-MYC had a 100% concordance between traditional method of FISH analysis and digital FISH analysis. Conclusion: Annotated whole slide images of H and E and FISH sections can be digitally aligned, so that areas of tumor within a section can be matched and evaluated with a greater degree of accuracy. Images can be archived permanently, providing a means for examining the results retrospectively. Digital FISH imaging of the MYC translocations provides a better diagnostic tool compared to traditional methods for evaluating lymphomas.

Diagnostic accuracy of bronchial brush cytology and the added value of immunohistochemistry and fluorescence in situ hybridization of pulmonary neuroendocrine tumors.

Background:Bronchial brush (BB) cytology carries low sensitivity for detecting neuroendocrine carcinomas (NECs), including typical carcinoid (TC) tumors of the lung. We aimed to investigate the detection of neuroendocrine tumors including TC through BB routine cytology cell block (CB), immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH).Materials and Methods:A SNOMED search showed 187 lung biopsy or resection specimens from 2008 through 2011 containing neuroendocrine or carcinoid in the diagnosis. Residual BB specimens retained in PreservCyt were used to prepare a ThinPrep slide for FISH analysis. CBs were stained with H and E and IHC for chromogranin and synaptophysin.Results:Of the 187 cases, 16 had residual BB material available within 1 year of diagnosis and were used in CB preparation for IHC and FISH slides. Cytologic evaluation determined 1 case positive for malignancy (small cell lung carcinoma [SCLC]), 1 suspicious for adenocarcinoma, and 14 negative for malignancy. On the basis of histologic diagnosis, FISH was performed. SCLC showed polysomy (86% abnormal cells); 2 TC tumors showed a gain of 7p12 (15% abnormal cells) and a gain of 5q15 (72% abnormal cells), respectively. Two cases had CBs with positive immunoreactivity for chromogranin and synaptophysin. The sensitivity for detection of NEC was 18.8%, 15.4%, and 25% for cytologic evaluation, CB, and FISH, respectively.Conclusion:Neuroendocrine tumors, including TC are difficult to detect with BB cytologic evaluation, most likely because tumor cells lack in the specimen. Assessment of further studies is needed to explore the role of cytology and ancillary methods for detection of these tumors.

FISHing for pancreatobiliary tract malignancy in endoscopic brushings enhances the sensitivity of routine cytology.

Pancreatobiliary tract carcinoma is a lethal disease with low survival rates and limited treatment options. Diagnosis is complicated by benign conditions that can mimic malignancy on radiological studies (e.g. primary sclerosing cholangitis or PSC) and the suboptimal sensitivity of endoscopic biopsy/brushings obtained by endoscopic retrograde cholangiopancreatography (ERCP). The detection of multiple chromosomal gains by fluorescence insitu hybridization (FISH), referred to as polysomy, has demonstrated improved sensitivity over routine cytological evaluation. The evaluation of brushings by both routine cytology and FISH in our cytopathology laboratory has been in clinical practice since 2003. Strong morphological and screening skills enable cytotechnologists to become proficient in the assessment of FISH slides, which translates into cost and time savings. Multiple reports from various institutions have demonstrated the utility of FISH for patients with and without PSC. The incorporation of routine cytology and FISH results into the management algorithm for patients under suspicion for pancreatobiliary malignancy is a testament to the clinical success of these cytological assays.

Automated processing of fluorescence in-situ hybridization slides for HER2 testing in breast and gastro-esophageal carcinomas

BackgroundHER2 fluorescence in-situ hybridization (FISH) is used in breast and gastro-esophageal carcinoma for determining HER2 gene amplification and patients' eligibility for HER2 targeted therapeutics. Traditional manual processing of the FISH slides is labor intensive because of multiple steps that require hands on manipulation of the slides and specifically timed intervals between steps. This highly manual processing also introduces inter-run and inter-operator variability that may affect the quality of the FISH result. Therefore, we sought to incorporate an automated processing instrument into our FISH workflow. MethodsTwenty-six cases including breast (20) and gastro-esophageal (6) cancer comprising 23 biopsies and three excision specimens were tested for HER2 FISH (Pathvysion, Abbott) using the Thermobrite Elite (TBE) system (Leica). Up to 12 slides can be run simultaneously. All cases were previously tested by the Pathvysion HER2 FISH assay with manual preparation. Twenty cells were counted by two observers for each case; five cases were tested on three separate runs by different operators to evaluate the precision and inter-operator variability. ResultsThere was 100% concordance in the scoring between the manual and TBE methods as well as among the five cases that were tested on three runs. Only one case failed due to poor probe hybridization. In total, seven cases were positive for HER2 amplification (HER2:CEP17 ratio >2.2) and the remaining 19 were negative (HER2:CEP17 ratio <1.8) utilizing the 2007 ASCO/CAP scoring criteria. Due to the automated denaturation and hybridization, for each run, there was a reduction in labor of 3.5h which could then be dedicated to other lab functions. ConclusionThe TBE is a walk away pre- and post-hybridization system that automates FISH slide processing, improves work flow and consistency and saves approximately 3.5h of technologist time. The instrument has a small footprint thus occupying minimal counter space. TBE processed slides performed exceptionally well in comparison to the manual technique with no disagreement in HER2 amplification status.

Recycling and Long-Term Storage of Fluorescence In Situ Hybridization Slides

Although fluorescence in situ hybridization (FISH) technology is adequate, demand exists for additional recycling and long-term storage of FISH slides. Formalin-fixed paraffin-embedded slides derived from breast cancer cases were used for this study. Each slide was probed, and then procedures for removing probes were performed, such as removing the fluorescent probe and diamidino-2-phenylindole signals. Formamide was used for removing probes, and then slides were stored dry at room temperature (22°C), 4°C, -20°C, or -80°C for 101 days. Following storage, each slide was probed in a similar manner to the initial probing. Evaluation was performed using automatic signal count software. Tiles and spots were counted immediately after the initial probing. Reprobed spots for each slide were then compared with the initial probing. Slides stored at -20°C and -80°C for 101 days showed the best recovery of probing. Our approach for probe removal and recycling allows repeated examination of even a limited number of slides.

Negative for Intraepithelial Lesion/Malignancy (NILM) Pap Slides from Women ≥ 30 Years of Age with Positive High-Risk HPV DNA: Focused Rescreening Prior to Report Issuance, an Enhanced Quality Control Measure

Introduction: Fluorescence in situ hybridization (FISH) testing has a published sensitivity and specificity of 35% and 91%, respectively for the detection of biliary tract malignancy. In 2012, our institution experienced a false negative rate of 44% (70/160). The goal of this study was to identify the root causes of false negative FISH results in patients with biliary tract malignancy. Materials and Methods: Biliary brushings were collected and analyzed utilizing the UroVysion(TM) (Abbott Molecular, Des Plaines, IL) probe set. Cases with non-polysomy FISH result and clinicopathologic evidence of malignancy were identified. Malignancy was defined as a mass on imaging, positive biopsy or routine cytology result. A retrospective review of the FISH slide was performed by an experienced FISH technologist. FISH slides were evaluated for cellularity, hybridization quality, presence of obscuring material, and presence of polysomic cells (cells with gains of 2 more probes). Results: There were 70 false negative biliary brushings in 2012 from 49 unique patients. Cellularity and hybridization quality were suboptimal in 17% and 27% of specimens, respectively (Table 1). Fifty-seven percent contained obscuring material. One to four polysomic cells (cut-off for polysomy at our institution is 5 cells) were identified in 40% of specimens. None of the specimens fit the criteria for a positive FISH test on retrospective review. Twentysix percent of specimens had multiple limiting factors identified. Conclusions: Poor specimen quality and inadequate sampling, not test interpretation, were the root causes of false negative FISH results in patients with biliary tract malignancy at our institution, using the UroVysion(TM) probe set. Polysomy, due to chromosome abnormality not recognized by the UroVysion(TM) probe set, may also contribute to false negative cases, but was not assessed in this study.

Primary sclerosing cholangitis with equivocal cytology: Fluorescence in situ hybridization and serum CA 19‐9 predict risk of malignancy

Patients diagnosed with primary sclerosing cholangitis (PSC) and dominant strictures often undergo endoscopic retrograde cholangiopancreatography with brush cytology to exclude or confirm the development of malignancy. Equivocal (atypical or suspicious) routine cytologic results may confound patient management decisions, especially in the absence of a mass on imaging. The objective of the current study was to identify independent predictors of malignancy in patients with PSC with an equivocal cytology diagnosis. Patients with PSC underwent brush cytology for routine cytology and fluorescence in situ hybridization (FISH) during endoscopy as per standard care. FISH slides were classified as polysomy if at least 5 cells displayed a gain of ≥ 2 probes. A retrospective search identified 102 patients without a mass lesion noted on initial imaging studies, an equivocal routine cytology, and ≥ 2 years of follow-up. Of 102 patients, 30 (29%) with an equivocal cytology result developed cancer within 2 years. Serum carbohydrate antigen 19-9 (CA 19-9) levels ≥ 129 U/mL (hazard ratio [HR] 3.19; P = .001) and polysomy (HR 8.70; P < .001) were each found to be predictive of cancer. Of 10 patients who had elevated CA 19-9 levels and polysomy, all went on to develop cancer (9 within 2 years). Although only 10 patients were included in this subset, the combination of elevated CA 19-9 and polysomy was found to be predictive of cancer (HR 10.92; P < .001). Polysomy by FISH identified those patients most likely to have or develop malignancy in the challenging clinical scenario of PSC with no mass at baseline and equivocal cytology. The combination of an elevated serum CA 19-9 level with polysomy is highly suspicious for the presence of malignancy.

Hybridization for human epidermal growth factor receptor 2 testing in gastric carcinoma: a comparison of fluorescence in-situ hybridization with a novel fully automated dual-colour silver in-situ hybridization method

Aims:Amplification of the human epidermal growth factor receptor 2 (HER2) gene has been reported in gastric carcinoma (GC). Accordingly, trastuzumab plus chemotherapy has recently become the new standard treatment for HER2-positive advanced GCs. The aim was to compare the alleged gold standard for hybridization [fluorescence in-situ hybridization (FISH)] with a novel, fully automated brightfield dual-colour silver-enhanced in-situ hybridization (SISH) method.Methods and results:The studies series was comprised of 166 GC samples. Additionally, tumours with discordant results obtained by FISH and SISH were analysed by real-time quantitative polymerase chain reaction (PCR) with the LightMix kit HER-2/neu. Of the samples, 17.5% and 21% were amplified by FISH and SISH, respectively. Heterogeneity was identified in up to 52% of cases. In 96.4% of cases, FISH showed the same results as SISH. All six discordant cases were positive by SISH and negative by FISH. On review of the FISH slides, all contradictory cases were polysomic and were confirmed to be negative for amplification by real-time PCR. Interestingly, all ratios in this latter group were between 2.06 and 2.50, so setting the cut-off for amplification at ≥3 resulted in perfect concordance.Conclusions:Dual-colour SISH represents a novel method for the determination of HER2 status in GC.

Automated detection of residual cells after sex-mismatched stem-cell transplantation – evidence for presence of disease-marker negative residual cells

BackgroundA new chimerism analysis based on automated interphase fluorescence in situ hybridization (FISH) evaluation was established to detect residual cells after allogene sex-mismatched bone marrow or blood stem-cell transplantation.Cells of 58 patients were characterized as disease-associated due to presence of a bcr/abl-gene-fusion or a trisomy 8 and/or a simultaneous hybridization of gonosome-specific centromeric probes. The automatic slide scanning platform Metafer with its module MetaCyte was used to analyse 3,000 cells per sample.ResultsOverall 454 assays of 58 patients were analyzed. 13 of 58 patients showed residual recipient cells at one stage of more than 4% and 12 of 58 showed residual recipient cells less than 4%, respectively. As to be expected, patients of the latter group were associated with a higher survival rate (48 vs. 34 month). In only two of seven patients with disease-marker positive residual cells between 0.1–1.3% a relapse was observed. Besides, disease-marker negative residual cells were found in two patients without relapse at a rate of 2.8% and 3.3%, respectively.ConclusionThe definite origin and meaning of disease-marker negative residual cells is still unclear. Overall, with the presented automatic chimerism analysis of interphase FISH slides, a sensitive method for detection of disease-marker positive residual cells is on hand.

Comparison of fluorescence in situ hybridization and dual color chromogenic in situ hybridization for the assessment of HER2 status on core-needle breast cancer biopsies.

Abstract Abstract #3015 Background: Core-needle biopsies have been shown to be extremely useful for evaluation of prognostic and predictive markers. In breast cancer patients, this is particularly important in the setting of neoadjuvant chemotherapy. However, it is well known that immunohistochemistry can give conflictive results on small biopsies or core-needle biopsies. This study evaluates the concordance between HER2 gene amplification determined by fluorescence in situ hybridization (FISH) and a new dual color cromogenic in situ hybridization (CISH) in a series of core-needle breast biopsies.&amp;#x2028; Material and Methods: A total of 37 invasive breast carcinomas diagnosed on core-nedle breast biopsies were selected from our files. Dual color FISH (Dako, Glostrup) and dual color CISH (Dako, Glostrup) were performed in each case. Scoring of the FISH and CISH slides was identical, counting HER2 and CEN-17 signals from 60 tumour nuclei per case. Finally, the gene to CEN-17 ratio was calculated using the cut-off value of HER2/CEN-17 ratio &amp;gt;2 as amplified.&amp;#x2028; Results: All 37 specimens were analyzed successfully by CISH and FISH. A high concordance was found between FISH and CISH in the assessment of HER2 status. 12 cases were amplified and counted easily with both techniques, showing similar ratios. Polysomy was also detected with both techniques in 5 cases with no amplification.&amp;#x2028; Discussion: Given the presumed heterogeneous expression of HER2 immunohistochemistry on core-needle biopsies, dual color CISH might be an alternative to FISH in this setting. Moreover, CISH allows for a better concurrent analysis of morphology, which is particularly important when studying small samples. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 3015.

Development of automated brightfield double In Situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) for breast carcinomas and an assay performance comparison to manual dual color HER2 fluorescence In Situ hybridization (FISH)

BackgroundHuman epidermal growth factor receptor 2 (HER2) fluorescence in situ hybridization (FISH) is a quantitative assay for selecting breast cancer patients for trastuzumab therapy. However, current HER2 FISH procedures are labor intensive, manual methods that require skilled technologists and specialized fluorescence microscopy. Furthermore, FISH slides cannot be archived for long term storage and review. Our objective was to develop an automated brightfield double in situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) and test the assay performance with dual color HER2 FISH evaluated breast carcinomas.MethodsThe BDISH assay was developed with the nick translated dinitrophenyl (DNP)-labeled HER2 DNA probe and DNP-labeled CEN 17 oligoprobe on the Ventana BenchMark® XT slide processing system. Detection of HER2 and CEN 17 signals was accomplished with the silver acetate, hydroquinone, and H2O2 reaction with horseradish peroxidase (HRP) and the fast red and naphthol phosphate reaction with alkaline phosphatise (AP), respectively. The BDISH specificity was optimized with formalin-fixed, paraffin-embedded xenograft tumors, MCF7 (non-amplified HER2 gene) and BT-474 (amplified HER2 gene). Then, the BDISH performance was evaluated with 94 routinely processed breast cancer tissues. Interpretation of HER2 and CEN 17 BDISH slides was conducted by 4 observers using a conventional brightfield microscope without oil immersion objectives.ResultsSequential hybridization and signal detection for HER2 and CEN 17 ISH demonstrated both DNA targets in the same cells. HER2 signals were visualized as discrete black metallic silver dots while CEN 17 signals were detected as slightly larger red dots. Our study demonstrated a high consensus concordance between HER2 FISH and BDISH results of clinical breast carcinoma cases based on the historical scoring method (98.9%, Simple Kappa = 0.9736, 95% CI = 0.9222 – 1.0000) and the ASCO/CAP scoring method with the FISH equivocal cases (95.7%, Simple Kappa = 0.8993%, 95% CI = 0.8068 – 0.9919) and without the FISH equivocal cases (100%, Simple Kappa = 1.0000%, 95% CI = 1.0000 – 1.0000).ConclusionAutomated BDISH applications for HER2 and CEN 17 targets were successfully developed and it might be able to replace manual two-color HER2 FISH methods. The application also has the potential to be used for other gene targets. The use of BDISH technology allows the simultaneous analyses of two DNA targets within the context of tissue morphological observation.

Comparison of two techniques for transcervical cell sampling performed in the same study population

The aim of this study was to evaluate and compare the presence of fetal cells in transcervical cell (TCC) samples collected in the first trimester of pregnancy by two different procedures [mucus collection and intrauterine lavage (IUL)], performed consecutively in the same subjects scheduled for elective termination of pregnancy (TOP). A total of 126 mucus/IUL sample pairs were retrieved from pregnant women immediately before TOP at a gestational age ranging from 7 to 12 weeks; at termination, samples of placental tissue were collected in all cases. All mucus samples were analysed by a polymerase chain reaction (PCR) assay and, in a subset of experiments involving 56 specimens, also by fluorescence in situ hybridization (FISH) procedure. IULs were divided in two aliquots, one for PCR analysis and one for the preparation of FISH slides. All placental tissue samples obtained at termination were analysed by FISH for fetal sexing. The PCR assay for fetal sex determination was performed by using, in a multiplex reaction, primers for SRY (Y chromosome sex-determining region, 738 bp) and HUMARA (human androgen receptor on the X chromosome, 280 bp) genes. The FISH analysis was carried out using direct-labelled commercial probes for X chromosome alpha-satellite (DXZ1, Xp11.1-q11.1, spectrum green) and Y chromosome alpha-satellite (DYZ3, Yp11.1-q11.1, spectrum orange) regions. In samples from known male pregnancies (n = 67), full concordance between IUL and mucus results could be found in 11 cases (16.4%); in 41 cases, Y chromosome material was detected by FISH (n = 2), by PCR (n = 5) or both (n = 34) in IUL samples, but not in the corresponding mucus samples. Y chromosome material was not documented in 10 mucus/IUL sample pairs. In 5 cases, the FISH (n = 2), the PCR (n = 1) or both (n = 2) failed to detect Y chromosome material in IULs, which was detected, however, by PCR in the corresponding mucus samples. Overall, correct sex prediction was achieved in 55/67 IULs (82%) and in 16/67 (23.9%) mucus samples from male pregnancies. In samples from known female pregnancies (n = 56), full concordance between results of IUL/mucus pairs and those on placental samples could be found in 53 cases (94.6%); in 3 cases, Y chromosome material was documented by PCR in mucus samples, but not in the corresponding IULs. Correct sex prediction was therefore achieved in 56/56 IULs (100%) and in 53/56 (94.6%) mucus samples from female pregnancies. This study provides evidence that, among TCC sampling techniques, IUL, but not mucus collection, can yield fetal cells in a constant and reliable fashion, which is a basic prerequisite for possible clinical usage. This suggestion had already emerged from some previous investigations but, owing to the study design, differences in study populations can no longer be used to explain the very different and sometimes-conflicting results reported in earlier studies.

The Development of a Multitarget, Multicolor Fluorescence in Situ Hybridization Assay for the Detection of Urothelial Carcinoma in Urine

The purpose of this study was to develop a multitarget, multicolor fluorescence in situ hybridization (FISH) assay for the detection of urothelial carcinoma (UC) in urine specimens. Urinary cells obtained from voided urine specimens of 21 patients with UC and 9 normal donors were analyzed with nine different centromere enumeration probes and a single locus-specific indicator probe to determine an optimal set of FISH probes for UC detection. The four probes with the greatest sensitivity for UC detection were then labeled with a unique fluorophore and combined into a single probe set. The probes with the greatest combined sensitivity for UC detection were CEP3, CEP7, CEP17, and the 9p21 (P16) LSI. This probe set was used to evaluate urine specimens acquired from 179 patients for prospective testing (46 with biopsy-proven UC). FISH slides were evaluated by scanning the slide for cells with nuclear features suggestive of malignancy and assessing the FISH signal pattern of these cells for polysomy (ie, gains of two or more different chromosomes). A receiver operator characteristic curve revealed that a cutoff of 5 cells with polysomy as the positive criterion for cancer resulted in an overall sensitivity of 84.2% for patients with biopsy-proven UC and a specificity of 91.8% among patients with genitourinary disorders but no evidence of UC. This study demonstrates that a multitarget, multicolor FISH assay containing centromeric probes to chromosomes 3, 7, and 17 and a locus-specific probe to band 9p21 has high sensitivity and specificity for the detection of UC in voided urine specimens.