Optimizing the DNA yield for molecular analysis from cytologic preparations

Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples

BACKGROUND

Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels.

METHODS

A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina).

RESULTS

Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden.

CONCLUSIONS

Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks.

"SMART" cytology: The next generation cytology for precision diagnosis

Cytology plays an important role in diagnosing and managing human diseases, especially cancer, as it is often a simple, low cost yet effective, and non-invasive or minimally invasive diagnostic tool. However, traditional morphology-based cytology practice has limitations, especially in the era of precision diagnosis. Recently there have been tremendous efforts devoted to apply computational tools and to perform molecular analysis on cytological samples for a variety of clinical purposes. Now is probably the appropriate juncture to integrate morphology, machine learning, and molecular analysis together and transform cytology from a morphology-driven practice to the next level - "SMART" Cytology. In this article we will provide a rather brief review of the relevant works for computational analysis on cytology samples, focusing on single-cell-based multiplex quantitative analysis of biomarkers, and introduce the conceptual framework of "SMART (Single cell, Multiplex, AI-driven, and Real Time)" Cytology.

Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing

INTRODUCTION

RNA sequencing (RNAseq) analysis is emerging as a clinical research or diagnostic approach for cytologic samples, but there is need for formal comparison of different sample preparation methods in the cytology laboratory to identify which pre-analytic methods could provide alternatives to formalin-fixed paraffin-embedded (FFPE) sections.

MATERIALS AND METHODS

We prepared 13 malignant effusions (metastatic estrogen receptor-positive breast cancer) in the cytology laboratory using 6 routine cytologic methods: FFPE cell block, Carnoy's solution, 95% ethanol (EtOH), air-dried and Diff-Quik, ThinPrep, and SurePath preparations. Measurements of RNA quality, expression of 2 multigene expression signatures, molecular subtype, and 4 common activating mutation sites in each preparation were compared with fresh frozen (FF) cell pellet in RNA preservative using distribution of fragment length and concordance correlation coefficient (CCC).

RESULTS

The fraction of RNA fragments measuring 200 bases or more (DV200) were 24% higher from cytospins fixed in Carnoy's solution or 95% EtOH than DV200 from FFPE cell blocks. SurePath samples failed RNAseq quality control. There was high concordance of gene expression measurements with FF samples using cytospins fixed in Carnoy's solution, 95% EtOH, Diff-Quik (CCC = 0.829, 0.812, 0.760, respectively), or ThinPrep (CCC = 0.736), but lower using FFPE cell block (CCC = 0.564). The proportion of mutant transcripts was concordant between FF and any cytologic preparation methods.

CONCLUSIONS

Cytospin preparations fixed with Carnoy's or 95% ETOH then Papanicolaou stained produced RNAseq results that were equivalent to FF samples and superior to FFPE cell block sections.

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.

Prospective Optimization of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Lymph Node Assessment for Lung Cancer: Three Needle Agitations Are Noninferior to 10 Agitations for Adequate Tumor Cell and DNA Yield

Introduction

Methods

Results

Conclusions

Molecular diagnosis in non-small-cell lung cancer: expert opinion on ALK and ROS1 testing

The effectiveness of targeted therapies with tyrosine kinase inhibitors in non-small-cell lung cancer (NSCLC) depends on the accurate determination of the genomic status of the tumour. For this reason, molecular analyses to detect genetic rearrangements in some genes (ie, ALK, ROS1, RET and NTRK) have become standard in patients with advanced disease. Since immunohistochemistry is easier to implement and interpret, it is normally used as the screening procedure, while fluorescence in situ hybridisation (FISH) is used to confirm the rearrangement and decide on ambiguous immunostainings. Although FISH is considered the most sensitive method for the detection of ALK and ROS1 rearrangements, the interpretation of results requires detailed guidelines. In this review, we discuss the various technologies available to evaluate ALK and ROS1 genomic rearrangements using these techniques. Other techniques such as real-time PCR and next-generation sequencing have been developed recently to evaluate ALK and ROS1 gene rearrangements, but some limitations prevent their full implementation in the clinical setting. Similarly, liquid biopsies have the potential to change the treatment of patients with advanced lung cancer, but further research is required before this technology can be applied in routine clinical practice. We discuss the technical requirements of laboratories in the light of quality assurance programmes. Finally, we review the recent updates made to the guidelines for the determination of molecular biomarkers in patients with NSCLC.

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.

Artificial intelligence-augmented histopathologic review using image analysis to optimize DNA yield from formalin-fixed paraffin-embedded slides

To achieve minimum DNA input requirements for next-generation sequencing (NGS), pathologists visually estimate macrodissection and slide count decisions. Unfortunately, misestimation may cause tissue waste and increased laboratory costs. We developed an artificial intelligence (AI)-augmented smart pathology review system (SmartPath) to empower pathologists with quantitative metrics for accurately determining tissue extraction parameters. SmartPath uses two deep learning architectures, a U-Net based network for cell segmentation and a multi-field-of-view convolutional network for tumor area segmentation, to extract features from digitized H&E-stained formalin-fixed paraffin-embedded slides. From the segmented tumor area, SmartPath suggests a macrodissection area. To predict DNA yield per slide, the extracted features from within the macrodissection area are correlated with known DNA yields to fit a regularized linear model (R = 0.85). Then, a pathologist-defined target yield divided by the predicted DNA yield per slide gives the number of slides to scrape. Following model development, an internal validation trial was conducted within the Tempus Labs molecular sequencing laboratory. We evaluated our system on 501 clinical colorectal cancer slides, where half received SmartPath-augmented review and half traditional pathologist review. The SmartPath cohort had 25% more DNA yields within a desired target range of 100-2000 ng. The number of extraction attempts was statistically unchanged between cohorts. The SmartPath system recommended fewer slides to scrape for large tissue sections, saving tissue in these cases. Conversely, SmartPath recommended more slides to scrape for samples with scant tissue sections, especially those with degraded DNA, helping prevent costly re-extraction due to insufficient extraction yield. A statistical analysis was performed to measure the impact of covariates on the results, offering insights on how to improve future applications of SmartPath. With these improvements, AI-augmented histopathologic review has the potential to decrease tissue waste, sequencing time, and laboratory costs by optimizing DNA yields, especially for samples with scant tissue and/or degraded DNA.

Molecular testing on serous effusion: An update

Cytological examination of the effusion fluid provides valuable information regarding the presence of malignancy. At times, it is challenging to diagnose malignant cells in serous effusion. The various ancillary techniques are available to solve the problem including immunocytochemistry, DNA ploidy, and multicolored flow cytometry. At present, the molecular tests on the effusion sample are of growing interest. The effusion sample is rich in cells and cell-free fluid that contains free DNA, cytokines, and extracellular vesicles. Molecular tests in effusion sample not only provide a diagnosis of malignancy but can also give valuable information that may be essential for the individualized therapy, management, and prognostic assessment. In this paper, we reviewed the application of the different molecular tests in the effusion sample.

Technical aspects of the use of cytopathological specimens for diagnosis and predictive testing in malignant epithelial neoplasms of the lung

Lung cancer is a leading cause of cancer mortality worldwide but recent years have seen a rapidly rising proportion of cases of advanced non-small cell carcinoma amenable to increasingly targeted therapy, initially based on the differential response to systemic treatment of tumours of squamous or glandular differentiation. In two-thirds of the cases, where patients present with advanced disease, both primary pathological diagnosis and biomarker testing is based on small biopsies and cytopathological specimens. The framework of this article is an overview of the technical aspect of each stage of the specimen pathway with emphasis on maximising potential for success when using small cytology samples. It brings together the current literature addressing pre-analytical and analytical aspects of specimen acquisition, performing rapid onsite evaluation, and undertaking diagnostic and predictive testing using immunocytochemistry and molecular platforms. The advantages and drawbacks of performing analysis on cell block and non-cell block specimen preparations is discussed.

Next generation sequencing in cytology

The application of next generation sequencing (NGS) technology to cytological samples has significantly modified molecular cytopathology practice. Cytological samples represent a valid source of high-quality DNA for NGS analysis, especially for predicting patients' response to targeted treatments and for refining the risk of malignancy in indeterminate cytological diagnoses. However, several pre-analytical factors may influence the reliability of NGS clinical analysis. Here, we briefly review the challenges of NGS in cytology practice, focusing on those pre-analytical factors that may negatively affect NGS success rates and routine diagnostic applications. Finally, we address the future directions of the field.

Robust assessment of tumor mutational burden in cytological specimens from lung cancer patients

OBJECTIVES

Tumor mutational burden (TMB) has emerged as a promising predictive biomarker for immune checkpoint inhibitor therapy. While the feasibility of TMB analysis on formalin-fixed paraffin-embedded (FFPE) samples has been thoroughly evaluated, only limited analyses have been performed on cytological samples, and no dedicated study has investigated concordance of TMB between different sample types. Here, we assessed TMB on matched histological and cytological samples from lung cancer patients and evaluated the accuracy of TMB estimation in these sample types.

MATERIALS AND METHODS

We analyzed mutations and resulting TMB in FFPE samples and matched ethanol-fixed cytological smears (n = 12 matched pairs) by using a targeted next-generation sequencing assay (Oncomine™ Tumor Mutational Load). Two different variant allele frequency (VAF) thresholds were used to estimate TMB (VAF = 5% or 10%).

RESULTS

At 5% VAF threshold, 73% (107/147) of mutations were concordantly detected in matched histological and cytological samples. Discordant variants were mainly unique to FFPE samples (34/40 discordant variants) and mostly C:G > T:A transitions with low allelic frequency, likely indicating formalin fixation artifacts. Increasing the VAF threshold to 10% clearly increased the number of concordantly detected mutations in matched histological and cytological samples to 96% (100/106 mutations), and drastically reduced the number of FFPE-only mutations (from 34 to 4 mutations). In contrast, cytological samples showed consistent mutation count and TMB values at both VAF thresholds. Using FFPE samples, 2 out of 12 patients were classified as TMB-high at VAF cutoff of 5% but TMB-low at 10%, whereas cytological specimens allowed consistent patient classification independently from VAF cutoff.

CONCLUSION

Our results show that cytological smears provide more consistent TMB values due to high DNA quality and lack of formalin-fixation induced artifacts. Therefore, cytological samples should be the preferred sample type for robust TMB estimation.

A rapid and simple bead-bashing-based method for genomic DNA extraction from mammalian tissue

Conventional genomic DNA (gDNA) extraction methods can take hours to complete, may require fume hoods and represent the most time-consuming step in many gDNA-based molecular assays. We systematically optimized a bead bashing-based (BBB) approach for rapid gDNA extraction without the need for a fume hood. Human tissue specimens (n = 34) subjected to the 12-min BBB method yielded 0.40 ± 0.17 (mean ± SD) μg of gDNA per milligram of tissue, sufficient for many downstream applications, and 3- and 6-min extensions resulted in an additional 0.43 ± 0.23 μg and 0.48 ± 0.43 μg per milligram of tissue, respectively. The BBB method provides a simple and rapid method for gDNA extraction from mammalian tissue that is applicable to time-sensitive clinical applications.

Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations

Background

Gene expression profiling has consistently identified three molecular subtypes of lung adenocarcinoma that have prognostic implications. To facilitate stratification of patients with this disease into similar molecular subtypes, we developed and validated a simple, mutually exclusive classification.

Methods

Mutational status of EGFR, KRAS, and TP53 was used to define seven mutually exclusive molecular subtypes. A development cohort of 283 cytology specimens of lung adenocarcinoma was used to evaluate the associations between the proposed classification and clinicopathologic variables including demographic characteristics, smoking history, fluorescence in situ hybridization and molecular results. For validation and prognostic assessment, 63 of the 283 cytology specimens with available survival data were combined with a separate cohort of 428 surgical pathology specimens of lung adenocarcinoma.

Results

The proposed classification yielded significant associations between these molecular subtypes and clinical and prognostic features. We found better overall survival in patients who underwent surgery and had tumors enriched for EGFR mutations. Worse overall survival was associated with older age, stage IV disease, and tumors with co-mutations in KRAS and TP53. Interestingly, neither chemotherapy nor radiation therapy showed benefit to overall survival.

Conclusions

The mutational status of EGFR, KRAS, and TP53 can be used to easily classify lung adenocarcinoma patients into seven subtypes that show a relationship with prognosis, especially in patients who underwent surgery, and these subtypes are similar to classifications based on more complex genomic methods reported previously.

Invited review-next-generation sequencing: a modern tool in cytopathology

In recent years, cytopathology has established itself as an independent diagnostic modality to guide clinical management in many different settings. The application of molecular techniques to cytological samples to identify prognostic and predictive biomarkers has played a crucial role in achieving this goal. While earlier studies have demonstrated that single biomarker testing is feasible on cytological samples, currently, this provides only limited and increasingly insufficient information in an era where an increasing number of biomarkers are required to guide patient care. More recently, multigene mutational assays, such as next-generation sequencing (NGS), have gained popularity because of their ability to provide genomic information on multiple genes. The cytopathologist plays a key role in ensuring success of NGS in cytological samples by influencing the pre-analytical steps, optimizing preparation types and adequacy requirement in terms of cellularity and tumor fraction, and ensuring optimal nucleic acid extraction for DNA input requirements. General principles of the role and potential of NGS in molecular cytopathology in the universal healthcare (UHC) European environment and examples of principal clinical applications were discussed in the workshop that took place at the 30th European Congress of Pathology in Bilbao, European Society of Pathology, whose content is here comprehensively described.

Overview of Molecular Testing of Cytology Specimens

OBJECTIVE

Utilizing cytology specimens for molecular testing has attracted increasing attention in the era of personalized medicine. Cytology specimens are clinically easier to access. The samples can be quickly and completely fixed in a very short time of fixation before tissue degradation occurs, compared to hours or days of fixation in surgical pathology specimens. In addition, cytology specimens can be fixed without formalin, which can significantly damage DNA and RNA. All these factors contribute to the superb quality of DNA and RNA in cytology specimens for molecular tests.

STUDY DESIGN

We summarize the most pertinent information in the literature regarding molecular testing in the field of cytopathology.

RESULTS

The first part focuses on the types of cytological specimens that can be used for molecular testing, including the advantages and limitations. The second section describes the common molecular tests and their clinical application.

CONCLUSION

Various types of cytology specimens are suitable for many molecular tests, which may require additional clinical laboratory validation.

Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration for Diagnosis and Staging of Lung Cancer

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) is fundamental to the diagnosis of lung cancer, as many patients present with more advanced stages of lung cancer, with enlarged hilar and mediastinal lymph nodes. It also represents a way to sample pulmonary masses directly to make the diagnosis, whereby no other accessible tissue is present and the mass sits adjacent to a large central airway. Very importantly also, EBUS TBNA is the widely accepted first procedure in lung cancer staging. A combined procedure of EUS TBNA can be performed to improve diagnostic accuracy.

Cytology Smears in the Era of Molecular Biomarkers in Non-Small Cell Lung Cancer: Doing More With Less

CONTEXT

- The rapid advances in targeted therapies in non-small cell lung cancer (NSCLC) make the optimization and implementation of cytology specimens for molecular testing a priority. Up to 70% of patients with NSCLC are diagnosed at advanced stages and tissue biopsies often cannot be taken. Although cytology samples provide high-quality material for molecular testing, molecular cytopathology is not yet well known or widely used.

OBJECTIVE

- To report the many advances in molecular cytopathology and the suitability and utility of cytology samples in molecular and genetic testing of NSCLC.

DATA SOURCES

- Data sources comprised published peer-reviewed literature and personal experience of the authors.

CONCLUSIONS

- Molecular testing can be performed on cytologic specimens, especially on direct smears. Rapid on-site evaluation by cytopathologists has improved the adequacy and the management of cytology samples for molecular testing. Mutational profiling of NSCLC using next-generation sequencing can be performed on cytology samples from very small amounts of DNA. Fluorescence in situ hybridization assays on cytology specimens, including stained direct smear, offer some distinct advantages over their histologic counterpart, and are used to detect ALK and ROS1 rearrangements in NSCLC. Cytology specimens allow assessment of the entire tumor cell nucleus, avoiding signal loss from truncation artifacts. The use of cytology samples for assessing programmed death ligand-1 protein expression is currently being developed. Protocols for bisulfite conversion and DNA droplet digital polymerase chain reaction assays have been optimized for cytology smear to investigate aberrant DNA methylation of several NSCLC-related genes.

Implementing TMB measurement in clinical practice: considerations on assay requirements

Clinical evidence demonstrates that treatment with immune checkpoint inhibitor immunotherapy agents can have considerable benefit across multiple tumours. However, there is a need for the development of predictive biomarkers that identify patients who are most likely to respond to immunotherapy. Comprehensive characterisation of tumours using genomic, transcriptomic, and proteomic approaches continues to lead the way in advancing precision medicine. Genetic correlates of response to therapy have been known for some time, but recent clinical evidence has strengthened the significance of high tumour mutational burden (TMB) as a biomarker of response and hence a rational target for immunotherapy. Concordantly, immune checkpoint inhibitors have changed clinical practice for lung cancer and melanoma, which are tumour types with some of the highest mutational burdens. TMB is an implementable approach for molecular biology and/or pathology laboratories that provides a quantitative measure of the total number of mutations in tumour tissue of patients and can be assessed by whole genome, whole exome, or large targeted gene panel sequencing of biopsied material. Currently, TMB assessment is not standardised across research and clinical studies. As a biomarker that affects treatment decisions, it is essential to unify TMB assessment approaches to allow for reliable, comparable results across studies. When implementing TMB measurement assays, it is important to consider factors that may impact the method workflow, the results of the assay, and the interpretation of the data. Such factors include biopsy sample type, sample quality and quantity, genome coverage, sequencing platform, bioinformatic pipeline, and the definitions of the final threshold that determines high TMB. This review outlines the factors for adoption of TMB measurement into clinical practice, providing an understanding of TMB assay considerations throughout the sample journey, and suggests principles to effectively implement TMB assays in a clinical setting to aid and optimise treatment decisions.

Cytological preparations for molecular analysis: A review of technical procedures, advantages and limitations for referring samples for testing

Minimally invasive procedures such as endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) must yield not only good quality and quantity of material for morphological assessment, but also an adequate sample for analysis of molecular markers to guide patients to appropriate targeted therapies. In this context, cytopathologists worldwide should be familiar with minimum requirements for refereeing cytological samples for testing. The present manuscript is a review with comprehensive description of the content of the workshop entitled Cytological preparations for molecular analysis: pre-analytical issues for EBUS TBNA, presented at the 40th European Congress of Cytopathology in Liverpool, UK. The present review emphasises the advantages and limitations of different types of cytology substrates used for molecular analysis such as archival smears, liquid-based preparations, archival cytospin preparations and FTA (Flinders Technology Associates) cards, as well as their technical requirements/features. These various types of cytological specimens can be successfully used for an extensive array of molecular studies, but the quality and quantity of extracted nucleic acids rely directly on adequate pre-analytical assessment of those samples. In this setting, cytopathologists must not only be familiar with the different types of specimens and associated technical procedures, but also correctly handle the material provided by minimally invasive procedures, ensuring that there is sufficient amount of material for a precise diagnosis and correct management of the patient through personalised care.

Tumor mutational burden in non-small cell lung cancer-the pathologist's point of view

In non-small cell lung cancer (NSCLC), the pathologist has contributed to the development of personalized medicine from the determination of the right histological type to EGFR and ALK/ROS1 molecular screening for targeted therapies. With the development of immunotherapies, pathologists intervene forefront with programmed death-ligand 1 (PD-L1) immunohistochemical testing, companion test for pembrolizumab monotherapy, first line and complementary test to the other programmed cell death-1 (PD-1) PD-L1 inhibitors. Recently, tumor mutational burden has emerged as a promising tool to evaluate sensitivity to immunotherapy (IO). The pathologist has a crucial role in the setting of tumor mutational burden (TMB) testing for the selection and the preparation of the sample for high throughput molecular analysis, and in the first steps of the next-generation sequencing (NGS) workflow.

Committee II: Guidelines for cytologic sampling techniques of lung and mediastinal lymph nodes

The Papanicolaou Society of Cytopathology has developed a set of guidelines for pulmonary cytology including indications for bronchial brushings, washings, and endobronchial ultrasound guided transbronchial fine-needle aspiration (EBUS-TBNA), technical recommendations for cytological sampling, recommended terminology and classification schemes, recommendations for ancillary testing and recommendations for post-cytological management and follow-up. All recommendations are based on the expertise of the authors, an extensive literature review and feedback from presentations at national and international conferences. This document selectively presents the results of these discussions. The present document summarizes recommendations regarding techniques used to obtain cytological and small histologic specimens from the lung and mediastinal lymph nodes including rapid on-site evaluation (ROSE), and the triage of specimens for immunocytochemical and molecular studies.

Updates in Effusion Cytology

Effusion cytology plays multiple roles in the management of benign and malignant disease, from primary diagnosis to tissue allocation for ancillary diagnostic studies and biomarker testing of therapeutic targets. This article summarizes recent advances in pleural effusion cytology, with a focus on the practical application of immunohistochemical markers, cytogenetic techniques, flow cytometry, and molecular techniques for the diagnosis and management of primary and secondary neoplasms of the pleura.

Advances in Molecular Testing Techniques in Cytologic Specimens

There has been a paradigm shift in the practice of cytopathology with the advent of highly sensitive molecular tests using small amounts of tissue that can provide diagnostic, prognostic, and predictive information for clinical management. The cytopathologist plays a key role in providing a timely and accurate diagnosis as well as ensuring appropriate processing and handling of the specimen and judicious triaging of the tissue for molecular testing that guide therapeutic decisions. As the era of "precision medicine" continues to evolve and expand, cytopathology remains a dynamic field with advances in the practice of molecular cytopathology providing new paradigms in clinical care.

Evaluation of the diagnostic utility of cytologic examination of renal fine-needle aspirates from dogs and the use of ultrasonographic features to inform cytologic diagnosis

OBJECTIVE To describe cytologic characteristics of renal fine-needle aspirate (FNA) samples from dogs, evaluate proportions of cytologic specimens deemed adequate for interpretation (diagnostic yield), assess diagnostic utility of cytologic examination for neoplastic and nonneoplastic diseases, and characterize ultrasonographic features of evaluated kidneys to determine whether the imaging characteristics could be used to inform cytologic interpretations. DESIGN Retrospective, observational study. SAMPLE 102 cytologic specimens and 97 ultrasonographic studies from 100 dogs. PROCEDURES Medical records were reviewed to identify dogs that underwent ultrasound-guided renal FNA. Slides were categorized as adequate or inadequate for interpretation; adequate slides were used for retrospective cytologic diagnosis. Sensitivity, specificity, and predictive values of cytologic examination for detection of neoplastic and nonneoplastic conditions were calculated by comparison with histologic or lymphoid cell clonality assay results. Ultrasonographic characteristics of neoplastic and nonneoplastic renal lesions were described. RESULTS 74 of 102 (72%) specimens had slides adequate for interpretation; 26 were included in the diagnostic accuracy analysis. Sensitivity of cytologic examination was 78% and 50% for detection of neoplastic and nonneoplastic conditions, respectively, with specificities of 50% and 77%, respectively; sensitivity for detection of lymphoma was 100%. Ultrasonographic appearance of kidneys with confirmed neoplasia varied; masses were most commonly found in kidneys with carcinoma (5/5), lymphoma (5/7), or other neoplasia (3/4) and absent in kidneys with nonneoplastic conditions (n = 5). CONCLUSIONS AND CLINICAL RELEVANCE Renal FNA specimens were adequate for interpretation at rates comparable with those reported for other organs and were considered clinically useful for diagnosis of neoplasia. Imaging characteristics may potentially aid differentiation between neoplastic and nonneoplastic lesions; however, further investigation is needed.

Molecular Pathology of Lung Cancer Cytology Specimens: A Concise Review

CONTEXT

- There has been a paradigm shift in the understanding of molecular pathogenesis of lung cancer. A number of oncogenic drivers have been identified in non-small cell lung carcinoma, such as the epidermal growth factor receptor ( EGFR) mutation and anaplastic lymphoma kinase ( ALK) gene rearrangement. Because of the clinical presentation at an advanced stage of disease in non-small cell lung carcinoma patients, the use of minimally invasive techniques is preferred to obtain a tumor sample for diagnosis. These techniques include image-guided biopsies and fine-needle aspirations, and frequently the cytology specimen may be the only tissue sample available for the diagnosis and molecular testing for these patients.

OBJECTIVE

- To review the current literature and evaluate the role of cytology specimens in lung cancer mutation testing. We reviewed the types of specimens received in the laboratory, specimen processing, the effect of preanalytic factors on downstream molecular studies, and the commonly used molecular techniques for biomarker testing in lung cancer.

DATA SOURCES

- PubMed and Google search engines were used to review the published literature on the topic.

CONCLUSIONS

- Mutation testing is feasible on a variety of cytologic specimen types and preparations. However, a thorough understanding of the cytology workflow for the processing of samples and appropriate background knowledge of the molecular tests are necessary for triaging, and optimum use of these specimens is necessary to guide patient management.

Molecular testing on endobronchial ultrasound (EBUS) fine needle aspirates (FNA): Impact of triage

BACKGROUND

Endobronchial ultrasound (EBUS)-guided fine needle aspiration (FNA) is performed to diagnose and stage lung cancer. Multiple studies have described the value of Rapid On-Site Evaluation (ROSE), but often the emphasis is upon diagnosis than adequacy for molecular testing (MT). The aim was to identify variable(s), especially cytology-related, that can improve MT.

METHODS

A search for EBUS-FNAs with ROSE was conducted for lung adenocarcinomas or when this diagnosis could not be excluded. All such cases underwent reflex MT on cell blocks. The impact of cytology-related variables [i.e., number of pass(es), dedicated pass(es) directly into media, cytotechnologist (CT), laboratory technician (LT) and triage with 1 or >1 cytologist] was evaluated. The latter category was divided into Group A [ROSE, triage and slide preparation by cytopathologist (CP) and CT at start of the procedure] and Group B (ROSE only by CT or by CT/CP after start of procedure; triage and slide preparation by CT or clinical staff). The impact of all these variables on MT was assessed.

RESULTS

A total of 100 cases were identified, and 79 had sufficient tissue for MT. Of all variables evaluated, MT was positively affected by performing a direct dedicated pass (P = 0.013) and ROSE by Group A (P = 0.033).

CONCLUSIONS

ROSE with appropriate triage, including performing a dedicated pass and proper slide preparation, improves MT, and this is enhanced by having >1 cytologist at the start of the procedure. In the era of personalized medicine, "adequate" should denote sufficient tissue for diagnosis and MT.

Initial Diagnostic Workup of Acute Leukemia: Guideline From the College of American Pathologists and the American Society of Hematology

CONTEXT

- A complete diagnosis of acute leukemia requires knowledge of clinical information combined with morphologic evaluation, immunophenotyping and karyotype analysis, and often, molecular genetic testing. Although many aspects of the workup for acute leukemia are well accepted, few guidelines have addressed the different aspects of the diagnostic evaluation of samples from patients suspected to have acute leukemia.

OBJECTIVE

- To develop a guideline for treating physicians and pathologists involved in the diagnostic and prognostic evaluation of new acute leukemia samples, including acute lymphoblastic leukemia, acute myeloid leukemia, and acute leukemias of ambiguous lineage.

DESIGN

- The College of American Pathologists and the American Society of Hematology convened a panel of experts in hematology and hematopathology to develop recommendations. A systematic evidence review was conducted to address 6 key questions. Recommendations were derived from strength of evidence, feedback received during the public comment period, and expert panel consensus.

RESULTS

- Twenty-seven guideline statements were established, which ranged from recommendations on what clinical and laboratory information should be available as part of the diagnostic and prognostic evaluation of acute leukemia samples to what types of testing should be performed routinely, with recommendations on where such testing should be performed and how the results should be reported.

CONCLUSIONS

- The guideline provides a framework for the multiple steps, including laboratory testing, in the evaluation of acute leukemia samples. Some aspects of the guideline, especially molecular genetic testing in acute leukemia, are rapidly changing with new supportive literature, which will require on-going updates for the guideline to remain relevant.

Preanalytic specimen triage: Smears, cell blocks, cytospin preparations, transport media, and cytobanking

With increasing requests for the evaluation of prognostic and predictive molecular biomarkers, great attention must be paid to the preanalytical issues regarding sample quality and DNA/RNA yield from all different types of cytological preparations. The objectives of this review were: 1) to provide an update regarding the importance of specimen triage as well as specimen handling and collection; 2) to discuss the different cell preparations that can be used for molecular testing, their advantages and limitations; and 3) to highlight the strategies for biobanking cytology samples. Good-quality DNA/RNA can be harvested from fresh cells in cell suspensions, formalin-fixed paraffin-embedded cell blocks, archival stained smears, archival unstained cytospin preparations, liquid-based cytology slides, FTA cards, and cryopreserved cells. In contrast to formalin-fixed paraffin-embedded tissue specimens (small biopsies and surgical resections), the multitude of types of sample preparations as well as the diversity in sample collection and processing procedures make cytology an ideal specimen for most genomic platforms, with less DNA and RNA degradation and a purer sample, usually with a higher concentration of tumor cells. The broad incorporation of cytological specimens into clinical practice. A should increase the number of samples potentially available for molecular tests and avoid repeat invasive procedures for tissue procurement, thereby increasing patient safety. In this context, it is of utmost importance that cytopathologists become familiar with the variables that can affect test results and embrace the goal of excellence in sample quality. Cancer Cytopathol 2017;125(6 suppl):455-64. © 2017 American Cancer Society.

Stage I lung adenocarcinoma: the value of quantitative CT in differentiating pathological subtypes and predicting growth of subsolid nodules

The aim of this study was to investigate feasibility of quantitative computed tomography (CT) measurements in predicting invasiveness and growth of nodular ground glass opacities (nGGOs).A set of 203 patients (group A) with nGGOs that were confirmed stage-I adenocarcinomas and 79 patients (group B) with nGGOs that were completely followed up were included. Lesions diameters, volume (VOL), maximum (MAX), mean (MEN), and standard deviation (STD) of CT attenuation were measured. P53 labeling index (LI) was evaluated through immunohistochemistry in group-A patients. Multivariate linear stepwise regressions were performed based on group-A lesions to calculate P53-LI prediction from CT measurements. The receiver operating characteristic (ROC) curve analyses were performed to assess the performance of P53-LI prediction in predicting invasiveness and growth of nGGOs. The Cox regression analysis was conducted to identify correlation between P53-LI Prediction and volume doubling time (VDT) of lesions in group B.Diameter, VOL, MEN, STD, and the P53 LI showed significant differences between lesions of different pathological invasiveness (P < .01). By multivariate linear regressions, MEN and STD were identified as independent variables indicating P53 LI (P < .001); thus, an equation was established to calculate P53-LI Prediction as: P53LI Prediction = 0.013 ×  MEN + 0.024 × STD + 9.741 (R square = 0.411, P < .001). The P53-LI Prediction showed good performance, similar as the actual one, in differentiating pathological invasiveness of nGGOs. In addition, the P53-LI Prediction demonstrated excellent performance in predicting growth of nGGOs (AUC = 0.833, P < .001) and independently forecasted VDT of nGGOs (β = 1.773, P < .001).The P53-LI Prediction that was calculated from preoperative quantitative CT measurements of nGGOs indicates lesions' invasiveness and allows for predicting growth of nGGOs.

Cell block samples from endobronchial ultrasound transbronchial needle aspiration provide sufficient material for ancillary testing in lung cancer-a quaternary referral centre experience

BACKGROUND

Rapid on site examination (ROSE) is encouraged at endobronchial ultrasound transbronchial needles aspiration (EBUS-TBNA) to improve diagnostic yield. Due to new therapeutic options in lung cancer, it is not sufficient to merely distinguish between non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC). Immunohistochemistry (IHC) distinction is now standard practice, as well as additional molecular testing where clinically indicated. We investigated the diagnostic yield of on-site smears vs. cell block and the provision of cellular material for ancillary testing at our centre.

METHODS

A retrospective audit of all EBUS-TBNA procedures performed until July 2012 was undertaken. Diagnostic yield on smears versus cell block was recorded. Cell blocks were reviewed by an experienced pathologist to determine diagnostic accuracy and whether IHC and molecular testing were possible.

RESULTS

In total, 234 procedures were recorded with 101 (43.2%) malignant cases, 107 (45.7%) benign cases and an initial 26/234 (11.1%) insufficient for diagnosis of which 11/234 (4.7%) were false negatives for malignancy after further follow up. The average number of passes was 4.5. For malignancies, smear diagnosis was possible in 95% (96/101) of cases and cell block diagnosis in 93.5% (87/93) of cases. There was sufficient material for IHC in 97.7% (85/87) of malignant cases. In 79.3% (69/87) of NSCLCs molecular testing for epidermal growth factor receptor (EGFR) mutation analysis was theoretically possible on samples obtained.

CONCLUSIONS

Cell blocks are not inferior to smears for diagnostic accuracy and provide sufficient samples for histology. However, ROSE assists the physician on how best to manage samples for ancillary testing.

Biomarker Testing in Lung Carcinoma Cytology Specimens: A Perspective From Members of the Pulmonary Pathology Society

The advent of targeted therapy in lung cancer has heralded a paradigm shift in the practice of cytopathology with the need for accurately subtyping lung carcinoma, as well as providing adequate material for molecular studies, to help guide clinical and therapeutic decisions. The variety and versatility of cytologic-specimen preparations offer significant advantages to molecular testing; however, they frequently remain underused. Therefore, evaluating the utility and adequacy of cytologic specimens is critical, not only from a lung cancer diagnosis standpoint but also for the myriad ancillary studies that are necessary to provide appropriate clinical management. A large fraction of lung cancers are diagnosed by aspiration or exfoliative cytology specimens, and thus, optimizing strategies to triage and best use the tissue for diagnosis and biomarker studies forms a critical component of lung cancer management. This review focuses on the opportunities and challenges of using cytologic specimens for molecular diagnosis of lung cancer and the role of cytopathology in the molecular era.

Predictive value of mutant p53 expression index obtained from nonenhanced computed tomography measurements for assessing invasiveness of ground-glass opacity nodules

Purpose

To predict p53 expression index (p53-EI) based on measurements from computed tomography (CT) for preoperatively assessing pathologies of nodular ground-glass opacities (nGGOs).

Methods

Information of 176 cases with nGGOs on high-resolution CT that were pathologically confirmed adenocarcinoma was collected. Diameters, total volumes (TVs), maximum (MAX), average (AVG), and standard deviation (STD) of CT attenuations within nGGOs were measured. p53-EI was evaluated through immunohistochemistry with Image-Pro Plus 6.0. A multiple linear stepwise regression model was established to calculate p53-EI prediction from CT measurements. Receiver-operating characteristic curve analysis was performed to compare the diagnostic performance of variables in differentiating preinvasive adenocarcinoma (PIA), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IAC).

Results

Diameters, TVs, MAX, AVG, and STD showed significant differences among PIAs, MIAs, and IACs (all P-values <0.001), with only MAX being incapable to differentiate MIAs from IACs (P=0.106). The mean p53-EIs of PIAs, MIAs, and IACs were 3.4±2.0, 7.2±1.9, and 9.8±2.7, with significant intergroup differences (all P-values <0.001). An equation was established by multiple linear regression as: p53-EI prediction =0.001* TVs +0.012* AVG +0.022* STD +9.345, through which p53-EI predictions were calculated to be 4.4%±1.0%, 6.8%±1.3%, and 8.5%±1.4% for PIAs, MIAs, and IACs (Kruskal–Wallis test P<0.001; Tamhane’s T2 test: PIA vs MIA P<0.001, MIA vs IAC P<0.001), respectively. Although not significant, p53-EI prediction has a little higher area under the curve (AUC) than the actual one both in differentiating MIAs from PIAs (AUC 0.938 vs 0.914, P=0.263) and in distinguishing IACs from MIAs (AUC 0.812 vs 0.786, P=0.718).

Conclusion

p53-EI prediction of nGGOs obtained from CT measurements allows accurately estimating lesions’ pathology and invasiveness preoperatively not only from radiology but also from pathology.