Molecular testing in solid tumors: an overview

Molecular testing in anatomic pathology is going to become more and more important during the next decade as we develop assays that can aid in diagnosis, prognosis, and predicting response to therapy. The anatomic pathologist needs to be familiar with the different assays available but also needs to be able to discern which are going to become standard of care and which will not. Three different types of tumors are reviewed: thyroid cancer, oligodendroglioma, and lung carcinoma. Molecular assays that are currently in use or on the near horizon, including translocation analyses for RET-PTC and PPARgamma-PAX8, point mutation analysis for BRAF and epidermal growth factor receptor, and genetic loss for 1p and 19q, are discussed.     

Urinary bladder pathology 2004: an update

The field of urinary bladder pathology is advancing at a rapid rate, with generation of significant new knowledge on molecular pathogenesis and cell and tissue-based diagnosis. The aim of this presentation is to survey selected, recent advances in this broad field, with specific focus on histologic typing, grading, staging, molecular classification, and reporting on neoplasia of the urinary bladder.     

Molecular pathology of solid tumours: some practical suggestions for translating research into clinical practice.

"Molecular pathology" can be broadly defined as the use of genetic data, in addition to the standard pathological parameters, to optimise diagnosis and to indicate treatment and prognosis. The benefit to be gained from the exploitation of molecular techniques to provide additional information to aid patient management is potentially vast. Currently, molecular pathology is rarely used in clinical practice, although it is anticipated that it will eventually become a part of routine practice. However, incorporating molecular techniques into routine practice will not be straightforward because there are several issues to be resolved. Following on from a symposium held at the Royal College of Pathologists to discuss some of these issues, the establishment of a committee of molecular pathology is proposed to plan and coordinate the introduction of molecular pathology into routine clinical practice.     

Investigative pathology: leading the post-genomic revolution

The completion of the Human Genome Project and the development of genome-based technologies over the past decade have set the stage for a new era of personalized medicine. By all rights, molecularly trained investigative pathologists should be leading this revolution. Singularly well suited for this work, molecular pathologists have the rare ability to wed genomic tools with unique diagnostic skills and tissue-based pathology techniques for integrated diagnosis of human disease. However, the number of pathologists with expertise in genome-based research has remained relatively low due to outdated training methods and a reluctance among some traditional pathologists to embrace new technologies. Moreover, because budding pathologists may not appreciate the vast selection of jobs available to them, they often end up choosing jobs that focus almost entirely on routine diagnosis rather than new frontiers in molecular pathology. This review calls for changes aimed at rectifying these troubling trends to ensure that pathology continues to guide patient care in a post-genomic era.     

Integrated expert systems and videodisc in surgical pathology: an overview

We present an overview of our 6-year experience in the design of expert systems for anatomic pathology. Our practical goal is to help practicing pathologists with learning, teaching, and the task of diagnosis by providing them with dynamic expert knowledge by means of a personal computer. This project could only be undertaken by first addressing a scientific goal: to characterize the problem-solving strategies that expert pathologists use in making a diagnosis and to state them in the logical terms of computer science. Our approach has been to build systems first for experimentation and then for use. The result of our work is an integrated computer-based approach that handles expert knowledge as formal relationships and morphologic images and that uses a number of logical strategies to provide multiple perspectives on diagnostic tasks. Configured as a pathologist's workstation, this approach can be expected to enhance the performance of trained general pathologists and pathologists in training. Lymph node pathology has been used as the prototype domain for this research, but care has been taken to seek a generalized authoring and inference structure that can be applied to other areas of pathology by changing the contents but not the structure itself. Excursions into various surgical pathology specialties suggest that the ways the system is constructed and exercised is fundamentally robust. Such computer-based expert systems can be expected to generate a new standard in the practice of pathology--based on the "gold standard" of classical morphology, but including the coordinated use of new methods from immunology and molecular biology in a multidisciplinary approach to diagnosis when these techniques are relevant. The benefits from this technology can be expected to be widespread with the evolution, refinement, and diffusion of these systems.     

Critical diagnoses (critical values) in anatomic pathology

Similar to critical values in clinical pathology, occasional diagnoses in surgical pathology and cytology may require urgent contact of the physician to facilitate rapid intervention or treatment. However, there are no established critical value (critical diagnosis) guidelines in anatomic pathology. As discussed herein, the Association of Directors of Anatomic and Surgical Pathology (ADASP) believes that establishing anatomic pathology critical diagnosis guidelines represents a practice improvement and patient safety initiative. ADASP also recognizes that a generic anatomic pathology critical diagnosis guideline such as this should be used only as a template because the list needs to be customized at each individual hospital following consultation with relevant clinical services. Based on surveys of the membership of the ADASP, this document provides examples of possible critical diagnoses in anatomic pathology.     

Critical diagnoses (critical values) in anatomic pathology

Similar to critical values in clinical pathology, occasional diagnoses in surgical pathology and cytology may require urgent contact of the physician to facilitate rapid intervention or treatment. However, there are no established critical value (critical diagnosis) guidelines in anatomic pathology. As discussed herein, the Association of Directors of Anatomic and Surgical Pathology (ADASP) believes that establishing anatomic pathology critical diagnosis guidelines represents a practice improvement and patient safety initiative. The ADASP also recognizes that a generic anatomic pathology critical diagnosis guideline such as this should only be used as a template because the list needs to be customized at each individual hospital after consultation with relevant clinical services. Based on surveys of the membership of the ADASP, this document provides examples of possible critical diagnoses in anatomic pathology.     

Current concepts on the molecular pathology of non-small cell lung carcinoma

Recent advances in the understanding of the complex biology of non-small cell lung carcinoma (NSCLC), particularly activation of oncogenes by mutation, translocation and amplification, have provided new treatment targets for this disease, and allowed the identification of subsets of NSCLC tumors, mostly with adenocarcinoma histology, having unique molecular profiles that can predict response to targeted therapy. The identification of specific genetic and molecular targetable abnormalities using tumor tissue and cytology specimens followed by the administration of a specific inhibitor to the target, are the basis of personalized lung cancer treatment. In this new paradigm, the role of a precise pathology diagnosis of lung cancer and the proper handling of tissue and cytology samples for molecular testing is becoming increasingly important. These changes have posed multiple new challenges for pathologists to adequately integrate routine histopathology analysis and molecular testing into the clinical pathology practice for tumor diagnosis and subsequent selection of the most appropriate therapy.     

Molecular assays in breast cancer pathology

Recent advances in understanding the molecular pathology of breast cancer offer significant potential to identify patients who may benefit from adjuvant therapies. To date, few of these advances are utilised in a routine setting. We review molecular assays that are currently in use or are in the advanced stages of development, which may be used as predictive or prognostic biomarkers in breast cancer.The only widely used breast cancer molecular assay is in situ hybridisation (ISH) for human epidermal growth factor receptor 2 (HER2) gene amplification and we highlight key issues with the interpretation of this assay, with particular attention to the difficulties of the equivocal category. New molecular assays such as ISH for the topoisomerase II alpha (TOP2A) gene and for the aberrations in the copy number of the centromeric region of chromosome 17 are readily performed in a standard histopathology laboratory, but to date there are insufficient data to support their routine use. We also review the current data on two commercially available multigene expression assays, Oncotype DX and MammaPrint and discuss their potential use. Overall, while new molecular assays have significant potential to improve patient selection for therapy, well-performed histopathology with reliable interpretation of standard hormone and HER2 assays provides the most important predictive and prognostic information in early breast cancer.     

Molecular testing for infectious diseases should be done in the clinical microbiology laboratory

Over the past decade, there has been an explosion in the use of molecular tests to diagnose and manage infectious diseases. HIV is a prime example of an infectious agent whose diagnosis at least in the acute stage, susceptibility testing, and management are all dependent on molecular diagnostics. The ability to accurately diagnose a plethora of respiratory pathogens quickly, simply, and relatively inexpensively compared to traditional methods is becoming a reality. Direct sequencing and microarray analysis holds great promise for directly detecting a wide variety of organisms from clinical specimens. The question is where this testing should be done in the clinical laboratory. There are at least four models that have emerged: Molecular infectious disease testing as an arm of the clinical microbiology laboratory. Molecular infectious disease testing done in a central molecular pathology laboratory under the leadership of a clinical microbiologist. Molecular infectious disease testing done in a central molecular pathology laboratory under the leadership of an individual whose primary interest is in another area of molecular pathology. Molecular infectious disease testing sent to a reference laboratory and not done on site or within the institution's health care system. We have asked three individuals who have thought about this very complex issue to share their rationale for supporting one of these models. Frederick Nolte is the Director of Clinical Laboratories and Director of Molecular Pathology at the Medical University of South Carolina, is active in and held several positions of responsibility in AMP (Association of Molecular Pathology) and is Chair of the CLSI's Area Committee for Molecular Methods, Alex McAdam is the Director of the Infectious Diseases Diagnostic Division at Children's Hospital Boston and an editor of this journal, and his colleague, Nima Mosammaparast, is the Assistant Director of the Infectious Diseases Diagnostic Laboratory at Children's Hospital Boston.     

Molecular pathology in lung cancer: a guide to the techniques used in clinical practice

Five year survival rates for lung cancer patients are poor; however the development of new therapeutic options, which benefit subsets of the population, offer hope of improvement. These novel therapies frequently rely upon the analysis of biomarkers in pathology samples; in lung cancer patients, testing is now routinely carried out to identify small mutations and chromosomal rearrangements in order to predict response to treatment. The recent increase in biomarker analyses in pathology samples has lead to the development of a new specialty, molecular pathology. The use of molecular pathology assays in clinical samples is largely under the control of the histopathologist; who is likely to be asked, as a minimum, to select tissue sections for molecular analysis and mark areas of H&E stained slides for macro or microdissection. Many histopathologists will also be involved in the sourcing and implementation of new assays. This review aims to provide a guide to some of the most commonly used molecular pathology methods – their advantages and their limitations.     

Best practices for clinical pathology testing in carcinogenicity studies

The Society of Toxicologic Pathology (STP) and American Society for Veterinary Clinical Pathology (ASCVP) convened a Clinical Pathology in Carcinogenicity Studies Working Group to recommend best practices for inclusion of clinical pathology testing in carcinogenicity studies. Regulatory guidance documents and literature were reviewed, and veterinary pathologists from North America, Japan, and Europe were surveyed regarding current practices, perceived value, and recommendations for clinical pathology testing in carcinogenicity studies. For two-year rodent carcinogenicity studies, the Working Group recommends that clinical pathology testing be limited to collection of blood smears at scheduled and unscheduled sacrifices to be examined only if indicated to aid in the diagnosis of possible hematopoietic neoplasia following histopathologic evaluation. Additional clinical pathology testing is most appropriately used to address specific issues from prior toxicity studies or known test article-related class effects. Inadequate data were available to make a recommendation concerning clinical pathology testing for alternative six-month carcinogenicity assays using genetically modified mice, although the Working Group suggests that it may be appropriate to use the same approach as for two-year carcinogenicity studies since the study goal is the same.     

Molecular testing in cytology

In the era of personalized medicine, molecular testing plays a critical role in patient care. The rapid advance of molecular techniques, especially next-generation sequencing, makes molecular diagnosis feasible in daily practice. Molecular testing can be used as a valuable ancillary test to increase diagnostic sensitivity and specificity, especially in small biopsy or cytology samples. In addition, molecular testing plays an important role in selecting patients for appropriate treatment by detecting therapeutic and predictive biomarkers in tissue or cytology samples. Molecular studies can be applied in all cytology samples, sometimes with better results than histology. As molecular testing has become essential for patient care and is often requested to be performed in cytology samples, it is critical for cytopathologists to understand the basics of molecular diagnostic methods, indications for molecular testing, and how to best utilize different cytologic samples for this purpose. In this special issue, experts in various areas of cytopathology and molecular pathology review the literature and discuss the basics of molecular techniques and the application of molecular testing in various types of cytology samples. It is our hope that after reading the articles in this special issue, the readers can know better about the possibilities of molecular cytology, a very exciting field of pathology.     

Anatomical pathology and molecular diagnosis

150 years ago, R. Virchow proposed a "cellular pathology" theory that forced one to revise many concepts of the mechanisms responsible for the development of disease and marked the beginning and further development of anatomical pathology as an independent discipline. Rapid progress in immunology, genetics, biotechnology, and cellular and molecular biology in the late 1980s to the early 1990s gave rise to a new field, namely molecular medicine. Damage changes the profile of expression some genes, activates various signal systems, and, due to of intercellular and cellular-matrix interactions, then spreads first at the level of organs, then at that of the whole body if a pathological process cannot localize. By involving some cells, the pathological process cannot cause characteristic morphological changes and therefore traditional studies yield a negative result. Molecular pathology became a necessary additional tool in the work of a pathologist, by allowing him to obtain the information that had been earlier beyond the reach, which increased the validity of diagnosis. Some points of the Virchow "cellular pathology" theory are supported by molecular pathology.     

Molecular genetic methods in the diagnosis of lower respiratory tract infections

Molecular diagnostic techniques, such as PCR, have become useful tools for the rapid etiological diagnosis of lower respiratory tract infections. Nucleic acid amplification tests (NAATs) have been evaluated for detecting most respiratory pathogens, and commercial assays are available for some pathogens. However, standardized protocols are needed before these assays are introduced into routine diagnostic use. For pneumonia, NAATs offer advantages over conventional tests for the detection of Mycoplasma pneumoniae, Legionella spp. and Chlamydia pneumoniae. For pneumococcal pneumonia in adults, PCR adds little to existing diagnostic tests, and is unable to distinguish pneumococcal colonization from infection when testing respiratory samples. Although less sensitive than culture-based methods, several commercial molecular diagnostic assays have been developed for tuberculosis and are useful rapid tests for selected patients. PCR can now be considered the rapid diagnostic test of choice for pertussis and some respiratory virus infections. Further work is required to better characterize the role of molecular diagnostic tests for diagnosing lower respiratory tract infections, and to develop standard assays that can be readily adopted by routine diagnostic laboratories.     

Pitfalls in molecular diagnostics

Molecular diagnostic techniques are part of the ancillary arsenal of anatomic pathologists. Advances in technology and knowledge regarding disease pathogenesis, tumorigenesis, and immune function contribute to the development of these assays. However, each technique, if applied incorrectly or in ignorance, can lead to difficulties in execution or errors in interpretation. In this review of commonly used molecular diagnostic tests, including immunohistochemistry, microsatellite instability testing, chromosomal microarray testing, and conventional and next-generation sequencing, the emphasis will be on potential pitfalls and considerations for each platform. Emerging technologies that may be used in clinical applications in the near future will also be discussed. An understanding of the methodologies, advantages, and drawbacks of molecular assays will help pathologists aid in diagnostic and therapeutic decisions.     

Microdissection-based genotyping assists discrimination of reactive gliosis from glioma

We used molecular anatomic pathology to determine the mutational status (loss of heterozygosity [LOH]) to make the distinction between reactive gliosis and glial neoplasia. LOH has been shown to be absent in reactive states and present in neoplastic cellular proliferations. Three groups of patient specimens were analyzed: group 1, reactive gliosis (n = 15); group 2, gliomas of varying histologic type and grade (n = 54); group 3, diagnostically challenging reactive gliosis vs glioma (n = 16). No group 1 cases (0/15 [0%]) showed allelic loss, whereas all high-grade glial neoplasms, a subset of group 2 (35/35 [100%]) manifested at least 1 allelic loss alteration, with most cases (33/35 [94%]) displaying 2 or more such changes. During a look forward at the group 3 patients, clinical history clarified the problematic diagnosis in a subset of 11 patients: 8 (73%) of 11 clinical outcomes were predicted correctly by our analysis. The molecular anatomic pathology approach outlined herein is designed for minute, formalin-fixed, paraffin-embedded specimens, which are encountered in everyday surgical pathology practice. Molecular anatomic pathology opens the possibilities of molecular analysis to everyday pathology practice.     

Quality assurance indicators in anatomic pathology

Quality assurance indicators in anatomic pathology focus on both technical and cognitive processes that result in a written report. The written report serves as both an intermediate outcome, which, in part, determines patient care outcomes, and a source of information for quality assurance studies. General requirements of a program include procedures that meet Joint Commission on Accreditation of Healthcare Organizations requirements for data gathering, data analysis, action, and effectiveness evaluation; documentation; and personnel standards. Specific indicators in surgical pathology and cytopathology focus on timeliness of reports, diagnostic accuracy, relevance of information in reports to the care of the patient, and proficiency testing. Cytopathology requires some unique indicators because of its dual screening and diagnostic role, including detection of false-negative results and comparison of cytotechnologist and cytopathologist diagnoses. Quality assurance indicators for the autopsy include those for the autopsy pathology as a subdiscipline of pathology as well as those that integrate autopsy information into a program of clinical quality assurance.     

Expectations and essentials for the community practice of pathology

In 3 surveys during the past 10 years, community hospital pathologists were asked what they want, need, or look for when employing a pathologist and, more specifically, what skills and knowledge a newly minted pathologist should have to be successful in the community practice of pathology. The most recent survey, done in spring of 2005, cited surgical pathology diagnosis, frozen section diagnosis, gross dissection, cytology, and fine-needle aspiration as essentials in anatomic pathology. For clinical pathology, knowledge of clinical medicine and test strategies that use the laboratory for clinical problem solving was paramount. New expectations in the latest survey were knowledge of molecular pathology and experience in quality assurance procedures. New pathologists generally meet the expectations of the community hospital workplace; however, there were some deficiencies: they were not proficient in gross pathology or autopsy pathology, they were slow, and many lack the clinical knowledge and experience to be effective consultants. The principal attribute that determines success in the practice of pathology, however, is skill in communication and interpersonal relations, and this remains the major deficiency of the fledgling pathologist.