Overview of Molecular Testing of Cytology Specimens

The impact of different fixatives on immunostaining of lung adenocarcinomas in pleural effusion cell blocks

BACKGROUND

Cell blocks (CBs) are widely used for biomarker analyses such as immunostaining. Although immunohistochemistry on formalin-fixed paraffin-embedded tissues is standardized, there are multiple preparation methods and fixatives for cytology. Our objective was to investigate the effect of different common fixatives on the immunoreactivity of pleural effusion CBs with metastatic lung adenocarcinomas.

METHODS

This prospective study included 24 malignant pleural effusions from different patients with lung adenocarcinoma. From each case, four identical CBs were fixed in 10% neutral buffered formalin, PreservCyt, CytoLyt, and CytoRich Red (only 17 of the cases), respectively. Samples containing <100 malignant cells were excluded. All CBs were stained with thyroid transcription factor 1 (TTF-1; clones 8G7G3/1 and SPT24), napsin A, claudin 4, CEA, CK7, and epithelial cell adhesion molecule (EpCAM; clones BS14, Ber-Ep4, and MOC-31). The fraction and intensity of stained cells were evaluated.

RESULTS

Of the investigated markers, a significant difference in staining proportion was seen for TTF-1 clone 8G7G3/1 and EpCAM clone MOC-31, especially with cases being negative in CytoLyt (33.3% and 83.3% positive, respectively) and PreservCyt (62.5% and 83.3%) whereas being positive in CytoRich Red (76.5% and 94.1%) and formalin (both 95.8%). A significantly weaker intensity of staining was seen for all alcohol-based fixatives compared to formalin for TTF-1 clone 8G7G3/1, napsin A, and EpCAM clone MOC-31, whereas EpCAM clone Ber-Ep4 was significantly weaker only in PreservCyt compared with formalin.

CONCLUSIONS

Immunocytochemical expression and concordance with formalin-fixed CBs differ depending on the used fixative as well as the antibody and clone, warranting investigation of the reliability of each biomarker for non-formalin-fixed cytology.

Comprehensive Genomic Studies on the Cell Blocks of Pancreatic Cancer

Pancreatic cancer is one of the deadliest malignancies, characterized by late-stage diagnosis and limited treatment options. Comprehensive genomic profiling plays an important role in understanding the molecular mechanisms underlying the disease and identifying potential therapeutic targets. Cell blocks (CBs), derived from EUS-FNA, have become valuable resources for diagnosis and genomic analysis. We examine the molecular profile of pancreatic ductal adenocarcinoma (PDAC) using specimens obtained from CB EUS-FNA, across a large gene panel, within the framework of next-generation sequencing (NGS). Our findings revealed that over half (55%) of PDAC CB cases provided adequate nucleic acid for next-generation sequencing, with tumor cell percentages averaging above 30%. Despite challenges such as low DNA quantification and degraded DNA, sequencing reads showed satisfactory quality control statistics, demonstrating the detection of genomic alterations. Most cases (84.6%) harbored at least one gene variant, including clinically significant gene mutation variants such as KRAS, TP53, and CDKN2A. Even at minimal concentrations, as long as the extracted DNA is of high quality, performing comprehensive molecular profiling on PDAC samples from cell blocks has remained feasible. This strategy has yielded valuable information about the diagnosis, genetic landscape, and potential therapeutic targets, aligning closely with a precision cytopathology approach.

Telecytology rapid onsite evaluation, with real-time communication between cytopathologist, cytotechnologist, and proceduralist, offers better adequacy rates for lymph node, but not thyroid, fine-needle aspirations

INTRODUCTION

Rapid onsite evaluation (ROSE) decreases rates of inadequate fine-needle aspirations (FNAs). Telecytology allows pathologists to perform ROSE without being physically "on site", thereby saving cytopathologists' travel time and allowing them to perform ROSE for multiple institutions. Little research exists comparing telecytology to non-telecytology ROSE for FNA inadequacy rates.

MATERIALS AND METHODS

Using previously obtained quality metrics, we compared inadequacy rates for lymph node and thyroid FNAs with and without ROSE and with non-telecytology ROSE compared with telecytology ROSE. Use of ROSE was determined by the proceduralist. Type of ROSE was location-based, as only certain locations at our institution have telecytology capabilities. Chi-squared testing was used to compare proportions of populations and P value was set to 0.05.

RESULTS

A total of 1168 lymph node and 1177 thyroid FNAs were included in our adequacy analysis. We found any ROSE decreased our inadequacy rate for both lymph node (20.4% to 12.7%, P = 0.002) and thyroid (34.7% to 4.8%, P = 7.4 × 10-18) FNAs. We found telecytology further decreased our inadequacy rate for lymph node (13.8% to 5.9%, P = 0.016), but not thyroid (3.3% to 5.0%, P = 0.34), FNAs.

CONCLUSIONS

At our institution, when using telecytology, slides are read in real time with the cytotechnologist and the proceduralist looking at slides together near the patient bedside, while the cytopathologist is on the phone looking at slides on the computer screen via Dameware. When non-telecytology ROSE is performed, the cytotechnologist evaluates a slide, brings it to the cytopathologist's office and then the cytopathologist calls the proceduralist to discuss the slide. We believe telecytology offers an opportunity for more inclusive communication thereby improving adequacy rates for more complex cases, like lymph nodes, without affecting adequacy rates for cases where assessment of adequacy is less complex, like thyroid. This research supports use of telecytology especially for complex cases.

Pre-analytical effects on whole transcriptome and targeted RNA sequencing analysis in cytology: The effects of prolonged time in storage of effusion specimens prior to preservation

OBJECTIVES

To investigate the pre-analytics of the molecular testing of cytology specimens, we studied the effects of time in refrigerator storage (4°C) of malignant effusions on RNA sequencing (RNAseq) results.

METHODS

Ten effusion specimens were stored in a refrigerator (4°C) for different durations (day 0, 1, 4, and 7). All specimens were prepared as cytospins fixed in either Carnoy's solution or 95% ethanol (EtOH) and in an RNA preservative for a fresh frozen (FF) high-quality reference. Whole transcriptome (wt) and targeted (t)RNAseq of two multigene expression signatures were performed. We then compared transcript expression levels (including mutant allele fraction) according to pre-analytical variables using a concordance correlation coefficient (CCC) and a mixed effect model.

RESULTS

Sequencing results were mostly stable over increasing time in storage. Cytospins fixed in Carnoy's solution were more concordant with FF samples than cytospins fixed in 95% EtOH at all timepoints. This finding was consistent for both wtRNAseq (averages: day 0 CCC = 0.98 vs 0.91; day 7 CCC = 0.88 vs 0.78) and tRNAseq methods (averages: day 0 CCC = 0.98 vs 0.81; day 7 CCC = 0.98 vs 0.90). Cytospins fixed in Carnoy's solution did not show significant changes in expression over timepoints or between expression signatures, whereas 95% EtOH did.

CONCLUSION

RNAseq can be accurately performed on effusion specimens after prolonged refrigerator storage. RNA extracted from scraped cytospin slides fixed in Carnoy's solution was marginally superior to 95% EtOH fixation, but either method had comparable analytic performance to high-quality FF RNA samples.

Cell block-based RNA next generation sequencing for detection of gene fusions in lung adenocarcinoma: An institutional experience

OBJECTIVE

Targeted therapy is an important part of the treatment of lung adenocarcinoma. Tests for EGFR mutation, ALK, ROS1, RET and NTRK gene fusions are needed to make a treatment decision. These gene fusions are traditionally detected by fluorescence in situ hybridisation (FISH) or immunohistochemistry. In this study, we investigated whether gene fusions in pulmonary adenocarcinoma could be accurately detected by RNA next-generation sequencing (RNA-NGS) and whether cytology cell blocks could be used effectively for this test.

METHODS

Archived cytological specimens of lung adenocarcinoma submitted for RNA sequencing between 2019 and 2022 at Fox Chase Cancer Center were retrospectively retrieved. Hybrid capture-based targeted RNA next generation sequencing was used, which covers 507 fusion genes, including ALK, ROS1, RET and NTRKs, irrespective of their partner genes. DNA NGS, FISH and chromosomal microarray analysis were used to confirm the results of the RNA-NGS.

RESULTS

A total of 129 lung adenocarcinoma cytology specimens were submitted for molecular testing. Eight of 129 (6.2%) cases were excluded from RNA sequencing as their cell blocks contained inadequate numbers of tumour cells. One case (0.8%) failed to yield adequate RNA. The overall success rate was 93% (120/129). Ten of 120 (8.3%) cytology cases were positive for gene fusions, including 7 ALK, 2 ROS1 fusion genes, and 1 RET fusion gene. Twenty-two cell block cases were also tested for ALK fusion genes using FISH. However, 11 of 22 (50%) failed the testing due to inadequate material.

CONCLUSIONS

Cytology cell blocks can be used as the main source of material for molecular testing for lung cancer. Detection of gene fusions by RNA-based NGS on cell blocks is convenient and reliable in daily practice.

The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology

Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.

Combined Use of Cell Block and Smear Improves the Cytological Diagnosis of Malignancy in Non-Palpable Breast Lesions Screened by Imaging

Background

Currently, core needle biopsy is replacing fine needle aspiration biopsy (FNAB) for pathological diagnosis of breast lesions. However, FNAB is extensively used for diagnosing breast lesions, including screened lesions, at our hospital. Furthermore, direct smears as well as cell blocks (CBs) from the FNAB specimens have been used. To prepare the CBs, hematoxylin and eosin (HE) staining as well as immunostaining with a mixture of p63 and cytokeratin 5/6 antibodies are routinely used. Therefore, in the current study, we sought to assess the efficacy of diagnosing breast lesions using conventional smears and CB immunostaining.

Methods

Breast FNAB reports of direct smears and CBs from The Nagoya Medical Center between December 2014 and March 2020, were reviewed. The efficiency of diagnoses made with direct smears and CBs were compared using histology-based diagnoses.

Results

Among the 169 histologically confirmed malignant lesions, 12 lesions that were reported as unsatisfactory, benign, or atypia probably benign, using direct smears were diagnosed as malignant using CB. Histologically, these lesions were diagnosed as carcinomas with mild atypia or papillary structures. Ten (83.3%) of the twelve lesions were non-palpable and only detected upon imaging.

Conclusion

Combined use of CB and conventional smear leads to the detection of more malignant lesions in breast FNAB specimens, particularly in lesions detected by imaging alone. Immunostaining of CB sections using a mixture of p63 and cytokeratin 5/6 antibodies provides more information than HE staining alone. Breast FNAB with CB preparation can be successfully applied for evaluation of breast lesions in developed countries.

Doing more with less: multiple uses of a single slide in veterinary cytology. A practical approach

Veterinary cytology faced a remarkable evolution in the last 15 years, in part due to increase recognition of the advantages of the cytology by veterinary clinicians. Simultaneously, there has been a growing awareness by the owners about the importance of a complete diagnostic workup aimed at defining a proper treatment protocol. With the extended use of cytology, challenging diagnostic cases are more frequent, and more clinically useful answers are requested. In this scenario, the use of cytology specimens to perform ancillary techniques is a valid approach. Rather than being simply archived, cytology slides can be a valuable source and a good platform to carry out cytochemistry, immunocytochemistry, and molecular techniques. Therefore, several diagnostic techniques can be applied in tiny samples, thus following the "doing more with less" principle. The aim of this approach is to refine the cytologic diagnosis and provide additional prognostic and therapeutic information. Herein, we detailed this principle in veterinary cytology and reviewed the use of cytology specimens for ancillary techniques as a single procedure, i.e., using the whole slide, or multiple procedures, i.e., multiple procedures applied in the same slide.

Optimal Preservations of Cytological Materials Using Liquid-Based Cytology Fixatives for Next-Generation Sequencing Analysis

INTRODUCTION

Molecular targeted therapies have been established for various diseases, including cancers, and there is an increasing need for molecular testing on cytology specimens. The aim of this study was to determine the optimal preservation methods of liquid-based cytology (LBC) materials for molecular testing.

METHODS

Cytological samples from 35 surgical resected non-small cell lung carcinoma specimens were obtained between June 2016 and June 2021. The samples were fixed in CytoRich™ red Preservative and stored at 4°C. One week later, three tubes were prepared from each specimen sample and divided into the following groups: the SurePath™ group (continued storage at 4°C), Frozen (Fr) group (stored at -80°C after centrifugation), and LBC-Cell Block (LBC-CB) group (generation of paraffin-embedded CB and storage at 4°C). Samples from 5 patients were used for the time course analysis, and we performed evaluations on these samples at 1, 3, 6, 12, 24, and 36 months. The concentrations and purities of extracted DNA and RNA were measured. The double-stranded DNA (dsDNA) and RNA concentrations were also measured by a fluorometer. The DNA and RNA integrities were quantified by the DNA and RNA integrity number.

RESULTS

Evaluation of samples was performed at baseline and the six timepoints. In the LBC-CB group, DNA and dsDNA concentrations were higher rather than those in the other groups. The RNA concentration of the LBC-CB group was relatively high compared with those of the other groups at the 36-month timepoint. The Fr group maintained higher DNA quality compared with the other groups over 3 years. The LBC-CB group maintained a higher RNA quality than the other groups until 24 months.

CONCLUSION

LBC-CB preparation is an effective method to maintain DNA/RNA quality and quantity in long-duration preservation for eventual molecular testing. Therefore, LBC-CB may have applications on preanalytical stage for molecular genomic testing such as next-generation sequencing.

Molecular Diagnostics of Lung Cancer in Serous Effusion Samples

For molecular diagnostics of lung cancer samples, often only a small amount of material is available. The ever-increasing number of biomarker testing is in contrast to the amount of material obtained. In that case, cytological specimens, such as serous effusion samples, are one possible option. Effusion samples were prepared as sediment smears or cytospins or as a cell block if needed. Suitable tumor cells areas were marked by a cytopathologist and used for molecular diagnostics, including fast track analysis, parallel sequencing, and/or fluorescence in situ hybridization. In 62 cases of malignant effusion with cells of pulmonary adenocarcinoma, molecular diagnostics were carried out. A fast-track result with the high-resolution melting method for hotspot mutation of KRAS Exon 2 and EGFR exon 21 and fragment length analysis of EGFR exon 19 was available for 43 out of 47 samples (92%). Parallel sequencing was successful for 56 out of 60 samples (93.3%). In the same period, 108 FISH analyses were performed for MET amplification, followed by ROS1, RET, and ALK translocation analysis. If only a limited amount of tissue/biopsy is available, a malignant effusion is advisable to perform on the molecular diagnostics with a high success rate.

Role of Pathologist in the Era of Image-Guided and EUS-Guided Aspirations: A 10-Year Study at a Single Tertiary Care Oncology Institute in North India

BACKGROUND

With improved and readily accessible imaging techniques, the shift in fine-needle aspiration cytology (FNAC) from palpation-guided FNA (PGFNA) to image-guided FNA (IGFNA) and endoscopic ultrasound-guided FNA (EUS-FNA) became evident in last few decades. The present study evaluates the impact of IGFNA and EUS-FNA on the practice of cytopathology at our 300-bedded oncology institute.

STUDY DESIGN

A 10-year audit of three aspiration modalities PGFNA, IGFNA, and EUS-FNA was done. The number of aspirates, inadequacy rates, new patient registration numbers, and tissue biopsy numbers were compared.

RESULTS

A total of 29,610 FNAC were evaluated against a total 141,333 new patient registrations over a period of 10 years. The new cancer patient registration over last 10 years showed a 56% increase, with a comparable increase of 60% in diagnostic biopsies; whereas, the number of FNAC increased by only 6%. This reduction in the number of aspirates was mainly due to fall in the number of PGFNA to 18% of all procedures in the year of 2019 from a high of 44% in 2011. Further, PGFNA showed a reduction by 50% over 3 years. The inadequacy rates of PGFNA increased to 9.1% (in 2019) from 1.6% (in 2012). The IGFNA constituted 46%-60% of procedures, with inadequacy varying from 8.5% to 12.1% over years. The EUS-FNAC gradually increased from 3% to 22% from 2013, and the inadequacy rates were variable overtime showing parallelism with the use of rapid on-site adequacy evaluation (ROSE) by the endoscopist. Inadequacy rates ranged from 7.1% (2013) to 2.6% (2016), 7.7% (2017), and 5.4% (2019).

CONCLUSION

The utility of ROSE and diminishing role of pathologist is highlighted in our study. Judicious ROSE improves diagnostic accuracy, decreases the rate of missed diagnosis and the repetition of procedures. The study sheds light on the ever-increasing lacuna in the training of pathologists for blind as well as in image-guided FNAC. Further, it enumerates the factors leading to the underutilization of ROSE, its undisputed advantages, operator variations in procedure, smear preparation, and screening.

Evaluation of Cytologic Sample Preparations for Compatibility With Nucleic Acid Analysis

Objectives

In this study, the influence of several key elements of the cytologic sample workflow on DNA and RNA content was evaluated.

Methods

The A549 cell line, patient-derived organoids, and pleural effusions were used to investigate the effect of (1) several collection media and delayed time to processing; (2) cytology specimens; (3) cytologic staining; and (4) formalin-fixed, paraffin-embedded (FFPE) cell block processing on nucleic acid quality and quantity as determined by fragment analyzer, Qubit analysis (Thermo Fisher Scientific), and quantitative polymerase chain reaction–based analysis on the Idylla platform (Biocartis).

Results

Alcohol-based collection media (CytoRich Red [Thermo Fisher Scientific] and EtOH95%) displayed high DNA and RNA preservation capacity, while phosphate-buffered saline and, to a lesser extent, formalin were associated with high RNA quality. Cytospin and smear cytology specimens were subject to DNA and RNA loss. Cytologic staining had no further impact on sample quality, hence destaining is not necessary. Both H&E-stained and unstained FFPE sections are compatible with nucleic acid analysis, despite a strong decrease in DNA and RNA quality.

Conclusions

Although several key elements of the cytologic sample workflow have an influence on DNA and RNA quality and quantity, the selection of these elements is also dependent on the downstream (ancillary) testing methods.

Tissue Microarray from Cell Block Material (cbTMA)—An Additional Shot for Cytology in the Predictive Pathology Era: The PD-L1 Experience

Generally, predictive biomarker tests are clinically validated on histological formalin-fixed, paraffin-embedded (FFPE) samples. In addition to FFPE samples, cytological samples have also emerged as a useful approach to detect predictive biomarkers. However, as of today, despite the promising results reported in the recent literature, their full implementation in routine clinical practice is still lagging owing to a lack of standardized preparatory protocols, challenging assessments of cyto-histological correlation, and variable inter-observer agreement. The aim of this report was to explore the possibility of implementing a large-scale validation of predictive biomarker testing on cytological material. To this aim, we evaluated the technical feasibility of PD-L1 assessment on a cell block (CB)-derived tissue microarray (cbTMA). Consecutive and unselected CBs prepared from metastatic lymph node fine-needle cytology (FNC) samples were retrospectively collected and used for TMA construction. PD-L1 immunohistochemistry (IHC) was carried out on cbTMA sections with the companion diagnostic kit SP263 assay. TMA contained 33 CB-derived cores. A total of 20 sections were hematoxylin and eosin (H&E) stained. Overall, 29 (88%) samples were visible at least in one H&E-stained slide. Four cases out of five sections stained with the SP263 assay (4/29, 13.8%) showed PD-L1 positivity in neoplastic and/or immune cells; remarkably, no unspecific background was observed. Although our study was based on a limited and non-selected series, our findings do provide proof of concept for the use of cbTMA in predictive biomarker testing on cytological material in large-scale post-clinical trial validation studies, multicenter studies, and quality control programs.

ATR-Spin: an open-source 3D printed device for direct cytocentrifugation onto attenuated total reflectance crystals

Infrared spectroscopy (IR) enables the direct and rapid characterization of cells at the molecular level. Achieving a rapid and consistent cell preparation is critical for the development of point-of-care diagnostics for cell analysis. Here we introduce an open-source, 3D printed device for integrating the isolation, preconcentration, and measurement of attenuated total reflectance IR spectra of cells from biofluids. The tool comprises a disposable card for cytocentrifugation, equipped with magnets, which allows reproducible integration into the pathlength of the IR spectrophotometer. Preliminary results using cell culture media containing A549 cells indicate that this system enables a qualitative and quantitative characterization of cells down to 10 cells μL^-1 by using a single and cost-effective device and within a few minutes.

Factors Influencing Concordance of PD-L1 Expression between Biopsies and Cytological Specimens in Non-Small Cell Lung Cancer

PD-L1 expression assessed by immunohistochemical staining is used for the selection of immunotherapy in non-small cell lung cancer (NSCLC). Appropriate validation of PD-L1 expression in cytology specimens is important as cytology is often the only diagnostic material in NSCLC. In a previous study comprising two different cohorts of paired biopsies and cytological specimens, we found a fairly good cyto-histological correlation of PD-L1 expression in one, whereas only a moderate correlation was found in the other cohort. Therefore, that cohort with additional new cases was now further investigated for the impact of preanalytical factors on PD-L1 concordance in paired biopsies and cytological specimens. A total of 100 formalin-fixed paraffin-embedded cell blocks from 19 pleural effusions (PE), 17 bronchial brushes (BB), and 64 bronchoalveolar lavage (BAL) and concurrent matched biopsies from 80 bronchial biopsies and 20 transthoracic core biopsies from NSCLC patients were stained using the PD-L1 28-8 assay. Using the cutoffs ≥1%, ≥5%, ≥10%, and ≥50% positive tumour cells, the overall agreement between histology and cytology was 77-85% (κ 0.51-0.70) depending on the applied cutoff value. The concordance was better for BALs (κ 0.53-0.81) and BBs (κ 0.55-0.85) than for PEs (κ -0.16-0.48), while no difference was seen for different types of biopsies or histological tumour type. A high number of tumour cells (>500) in biopsies was associated with better concordance at the ≥50% cutoff. In conclusion, the study results suggest that PEs may be less suitable for evaluation of PD-L1 due to limited cyto-histological concordance, while a high amount of tumour cells in biopsies may be favourable when regarding cyto-histological PD-L1 concordance.

Clinical Application of Chromosome Microarray Analysis in the Diagnosis of Lipomatous Tumors

Well-differentiated liposarcoma/atypical lipomatous tumor (WDLS/ALT) and dedifferentiated liposarcoma (DDLS) have characteristic supernumerary ring and giant marker chromosomes involving the chromosomal region 12q13-15 which contains MDM2 (12q15), CDK4 (12q14.1), HMGA2 (12q14.3), YEATS4 (12q15), CPM (12q15), and FRS2 (12q15). Detecting MDM2 amplification by fluorescence in situ hybridization (FISH) is considered to be the gold standard for the diagnosis of WDLS/ALT and DDLS. In this study, formalin fixed paraffin embedded clinical specimens (16 liposarcomas and 19 benign lipomatous tumors) were used to detect MDM2 amplification and other chromosomal alterations in WDLS/ALT and DDLS by single nucleotide polymorphism-based chromosome microarray (CMA). All 16 liposarcomas showed MDM2 amplification with a MDM2/cep12 ratio from 2.4 to 8.4 by CMA. Ten (62.5%) of these cases had CDK4/cep12 ratio ≥2.0. All the cases without CDK4 amplification were from the thigh. The MDM2/cep12 ratio of all the benign lipomatous tumors (19/19) was within the normal limits. Twenty-one of the 35 benign lipomatous tumors and liposarcomas were also tested for MDM2 amplification by FISH. All the FISH results were consistent with the CMA results (100%). Along with MDM2 amplification, all 16 liposarcomas (100%) also showed amplification of YEATS4, CPM and FRS2. Only 11 of 16 (69%) cases showed HMGA2 amplification. In conclusion, this study demonstrated that CMA on routine formalin fixed paraffin embedded tissue is a sensitive and specific clinical test for detection of MDM2 gene amplification. Moreover, CMA allows simultaneous detection of genomic changes of interest including CDK4 and others, which provides enriched information for diagnosing lipomatous tumors.

EGFR analysis on scrapings from cytology smears in lung carcinoma, an effective alternative to testing on trucut biopsies

BACKGROUND

Lung carcinomas are a leading cause of cancer morbidity and mortality. Many cases present at an advanced stage of disease where definitive treatment by surgical resection is not feasible. Molecular testing using materials derived from minimally invasive procedures aid in targeted therapy with least iatrogenic burden to the patient.

METHODS

Cases diagnosed as non-small cell lung carcinoma (NSCLC) on cytology were included in the study. Scrapings from the smears with adequate tumor cell load were submitted for molecular testing. The DNA was extracted and quantified. Mutations in exons 18, 19, 20, and 21 of the EGFR gene were detected using Sanger sequencing. DNA quantity and EGFR mutation status on equal number of consecutive trucut biopsy specimens were also analyzed.

RESULTS

Seventy cases of NSCLC tested for EGFR mutation had a median DNA concentration of 40.2 ng/μl and 31% cases showed mutation. Majority of mutations (14/21, 66.66%) were identified in exon 19. Among 70 trucut biopsy samples, DNA concentration was 41.42 ng/μl and 30% cases showed mutation. No significant difference was seen in DNA quantity and EGFR mutation between cytology smears and trucut biopsies.

CONCLUSION

EGFR testing on cytology smears provides adequate DNA yield with minimal invasiveness and is equally effective as biopsies. Testing on samples like pleural effusion allows for concomitant diagnosis, staging, and molecular testing in one procedure. Tests done on the smears rather than on cell block or trucut biopsies ensures superior quality DNA from the tumor cells as they are unexposed to cross linking formalin fixative.

Molecular cytology of the respiratory tract and pleura

There is growing evidence that molecular testing is feasible on all types of cytological preparation, which is fortunate as more diagnostic markers and biomarkers for targeted therapies are discovered for use in pulmonary and pleural malignancies. In this article we will discuss the pre-analytic, analytic, and post-analytic (interpretive) considerations for successful implementation of molecular tests for diagnostic and predictive markers in respiratory and pleural cytology. The vast majority of laboratories are familiar with, and have validated their molecular protocols for, formalin-fixed paraffin-embedded surgical specimens, which are not directly applicable to cytology specimens. Thus, rigorous validation must be performed for each type of fixative and cytology preparation before it is implemented in the clinical setting.

BOC-PLAG1, a new fusion gene of pleomorphic adenoma: Identified in a fine-needle aspirate by RNA next-generation sequencing

Pleomorphic adenoma (PA) is the most common benign salivary gland tumor. Fine-needle aspiration (FNA) of PA exhibits variable combinations of bland ductal epithelial cells, myoepithelial cells, and characteristic magenta fibrillary stroma on Diff-Quik/Romanowsky stain. However, a cellular PA with scant chondromyxoid stroma can be a diagnostic challenge on FNA. Around 70% of PAs have a translocation involving PLAG1 or HMGA2. The presence of either PLAG1 or HMGA2 fusion gene can be used to diagnose PA since they have not been reported in other salivary gland tumors except for carcinoma ex PA. In this case report, we describe a case of cellular PA initially diagnosed on FNA as a "low grade salivary gland neoplasm, favor PA." RNA next-generation sequencing performed on the cell block showed a BOC-PLAG1 fusion gene. The presence of PLAG1 fusion gene in conjunction with cytomorphology supported a diagnosis of PA. The mass was surgically removed and proved to be a cellular PA with scattered foci of chondromyxoid and collagenous stroma. To our knowledge, this is the first reported PA bearing BOC-PLAG1. RNA next-generation sequencing performed on cytology specimens can be helpful in achieving a more specific diagnosis of salivary gland tumors.

Molecular Profiling of Malignant Pleural Effusions with Next Generation Sequencing (NGS): Evidence that Supports Its Role in Cancer Management

Malignant pleural effusions (MPEs) often develop in advanced cancer patients and confer significant morbidity and mortality. In this review, we evaluated whether molecular profiling of MPEs with next generation sequencing (NGS) could have a role in cancer management, focusing on lung cancer. We reviewed and compared the diagnostic performance of pleural fluid liquid biopsy with other types of samples. When applied in MPEs, NGS may have comparable performance with corresponding tissue biopsies, yield higher DNA amount, and detect more genetic aberrations than blood-derived liquid biopsies. NGS in MPEs may also be preferable to plasma liquid biopsy in advanced cancer patients with a MPE and a paucicellular or it could be difficult to obtain tissue/fine-needle aspiration biopsy. Of interest, post-centrifuge supernatant NGS may exhibit superior results compared to cell pellet, cell block or other materials. NGS in MPEs can also guide clinicians in tailoring established therapies and identifying therapy resistance. Evidence is still premature regarding the role of NGS in MPEs from patients with cancers other than lung. We concluded that MPE processing could provide useful prognostic and theranostic information, besides its diagnostic role.

Results from the 2019 American Society of Cytopathology survey on rapid onsite evaluation (ROSE)-part 2: subjective views among the cytopathology community

INTRODUCTION

This study aims to improve understanding of the cytopathology community's perspective regarding the value of rapid onsite evaluation (ROSE) in clinical practice.

MATERIALS AND METHODS

The American Society of Cytopathology membership was surveyed in 2019 to obtain subjective data on the cytopathology community's perceptions regarding ROSE. Comments were categorized by major themes and attitudes and analyzed by respondent's role in laboratory, practice size, and practice setting (Fisher's exact and χ² tests).

RESULTS

A total of 541 responses were received from 255 cytopathologists/pathologists, 261 cytotechnologists, 19 trainees, and 6 others (as previously reported). Reasons for which cytopathology personnel provide this service aligned with their perceptions of why clinicians request ROSE. A minority of respondents, disproportionally from high volume centers, felt ROSE is unnecessary. Overall attitude regarding ROSE was generally positive. There were no significant differences in attitude regarding ROSE according to role in laboratory or practice size, but respondents from academic centers provided a significantly higher percentage of positive comments than those in private or community practice. Although survey respondents generally felt that ROSE is valuable to patient care, they also highlighted several challenges, including staffing, time commitment, and inadequate reimbursement. Implementation of telecytology was felt to potentially alleviate some of these challenges.

CONCLUSIONS

Survey results show that the cytology community views ROSE favorably, practices vary considerably, and there is a perceived need for improved reimbursement. Data from this study may be used to identify areas that warrant additional research to clarify the clinical value of ROSE.

Diagnostic accuracy of molecular testing with three molecular markers on thyroid fine-needle aspiration cytology with abnormal category

BACKGROUND

Cases with abnormal category, determined by thyroid fine-needle aspiration (FNA), frequently undergo surgical resection, despite the majority of cases being identified as benign after resection. Additional diagnostic markers are needed to guide the management of patients with abnormal thyroid nodules.

MATERIALS AND METHODS

The retrospective study enrolled 150 cases diagnosed abnormal by FNA cytology that had undergone molecular testing with three markers (BRAF V600E, NRAS, and KRAS) on the cell block. Seventy-one cases had a surgical follow-up.

RESULTS

When NIFTP is not considered as malignant, positive predictive values (PPVs) of cytology and combined cytology and molecular testing (CC-MT) were 67.6% (95% CI: 0.555-0.782) and 89.2% (95% CI: 0.746-0.970) (P = .004), respectively. The sensitivity of the CC-MT was 68.8%, specificity was 82.5%, and the false-positive rate was 17.4%. When NIFTP is considered as malignant, PPVs of cytology and CC-MT were 83.1% (95% CI: 0.743-0.918) and 94.6% (95% CI: 0.873-1.018) (P = .047), respectively. The sensitivity of the CC-MT was 59.3%, specificity was 83.3%, and the false-positive rate was 16.7%.

CONCLUSION

The addition of molecular testing with a small panel to FNA cytology may increase the PPV of cytology in abnormal categories. Small panel (BRAF V600E, KRAS, and NRAS) with high specificity and high PPVs may be used particularly for the detection of thyroid malignancy. Cell blocks can be an especially useful and straightforward method for molecular diagnostic studies.