Defining diagnostic tissue in the era of personalized medicine

Dick van Velzen and the Burnside warehouse organ scandal in Nova Scotia, Canada

Dick van Velzen practiced as a pediatric pathologist at Alder Hey Children's Hospital in Liverpool, England from September 1988 until December 1995; he then relocated to the IWK-Grace Health Centre, a children's and maternity hospital in Halifax, Nova Scotia, Canada, where he practiced until he was fired for cause in January 1998. About a year and a half later, his practice in Liverpool came under increasing scrutiny, with the initial focus on the massive collection of post-mortem pediatric organs he had accumulated for planned future research on sudden infant death syndrome. Soon, a Parliamentary Inquiry began investigating the full scope of his Liverpool practice. During the Inquiry, another organ-hoarding scandal erupted; van Velzen, when leaving Halifax after his dismissal, had put his family's personal belongings into a storage facility at Burnside Industrial Park and then did not pay bills. As his belongings were being prepared for auction, formalin-fixed organs were found, and a Canada-wide arrest warrant for disrespect for human remains was issued by the Halifax Police. While the Alder Hey scandal resulted in a 535-page-long Parliamentary Report and the Human Tissue Act, van Velzen was never charged criminally in the UK. The largely unknown story of his second organ scandal in Halifax, is related here. Although he had obtained the body parts with the consent of the parents of the child to which they had belonged, his failure to properly identify and store them traumatized parents already impacted by his organ-hoarding in the UK, traumatized additional parents in Halifax, and resulted in significant waste of public resources in investigating the case. He pled guilty to "indignity to a human body" in Canada and was fined and placed on 12 months' probation.

A deep learning model to classify neoplastic state and tissue origin from transcriptomic data

Application of deep learning methods to transcriptomic data has the potential to enhance the accuracy and efficiency of tissue classification and cell state identification. Herein, we developed a multitask deep learning model for tissue classification combining publicly available whole transcriptomic (RNA-seq) datasets of non-neoplastic, neoplastic and peri-neoplastic tissue to classify disease state, tissue origin and neoplastic subclass. RNA-seq data from a total of 10,116 patient samples processed through a common pipeline were used for model training and validation. The model achieved 99% accuracy for disease state classification (ROC-AUC of 0.98) and 97% accuracy for tissue origin (ROC-AUC of 0.99). Moreover, the model achieved an accuracy of 92% (ROC-AUC 0.95) for neoplastic subclassification. This is the first multitask deep learning algorithm developed for tissue classification employing a uniform pipeline analysis of transcriptomic data with multiple tissue classifiers. This model serves as a framework for incorporating large transcriptomic datasets across conditions to facilitate clinical diagnosis and cell-based treatment strategies.

Vibrational Spectroscopy for Identification of Metabolites in Biologic Samples

Vibrational spectroscopy (mid-infrared (IR) and Raman) and its fingerprinting capabilities offer rapid, high-throughput, and non-destructive analysis of a wide range of sample types producing a characteristic chemical "fingerprint" with a unique signature profile. Nuclear magnetic resonance (NMR) spectroscopy and an array of mass spectrometry (MS) techniques provide selectivity and specificity for screening metabolites, but demand costly instrumentation, complex sample pretreatment, are labor-intensive, require well-trained technicians to operate the instrumentation, and are less amenable for implementation in clinics. The potential for vibration spectroscopy techniques to be brought to the bedside gives hope for huge cost savings and potential revolutionary advances in diagnostics in the clinic. We discuss the utilization of current vibrational spectroscopy methodologies on biologic samples as an avenue towards rapid cost saving diagnostics.

Factors that drive the increasing use of FFPE tissue in basic and translational cancer research

The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.

Integrated Pathology Informatics Enables High-Quality Personalized and Precision Medicine: Digital Pathology and Beyond

CONTEXT

- The critical role of pathology in diagnosis, prognosis, and prediction demands high-quality subspecialty diagnostics that integrates information from multiple laboratories.

OBJECTIVE

- To identify key requirements and to establish a systematic approach to providing high-quality pathology in a health care system that is responsible for services across a large geographic area.

DESIGN

- This report focuses on the development of a multisite pathology informatics platform to support high-quality surgical pathology and hematopathology using a sophisticated laboratory information system and whole slide imaging for histology and immunohistochemistry, integrated with ancillary tools, including electron microscopy, flow cytometry, cytogenetics, and molecular diagnostics.

RESULTS

- These tools enable patients in numerous geographic locations access to a model of subspecialty pathology that allows reporting of every specimen by the right pathologist at the right time. The use of whole slide imaging for multidisciplinary case conferences enables better communication among members of patient care teams. The system encourages data collection using a discrete data synoptic reporting module, has implemented documentation of quality assurance activities, and allows workload measurement, providing examples of additional benefits that can be gained by this electronic approach to pathology.

CONCLUSION

- This approach builds the foundation for accurate big data collection and high-quality personalized and precision medicine.

Clinical Applications of Whole-slide Imaging in Anatomic Pathology

The development of whole-slide imaging has paved the way for digitizing of glass slides that are the basis for surgical pathology. This transformative technology has changed the landscape in research applications and education but despite its tremendous potential, its adoption for clinical use has been slow. We review the various niche applications that initiated awareness of this technology, provide examples of clinical use cases, and discuss the requirements and challenges for full adoption in clinical diagnosis. The opportunities for applications of image analysis tools in a workflow will be changed by integration of whole-slide imaging into routine diagnosis.

To Share or Not to Share: Ethical Acquisition and Use of Medical Data

The Health Information Technology for Economic and Clinical Health (HITECH) Act proposes the meaningful use of interoperable electronic health records throughout the United States health care delivery system as a critical national goal. As we have moved from medical records on paper to interoperable electronic health records, the rapid and easy sharing of medical data through the Internet makes medical data insecure. Electronic data is easy to share but many steps to ensure security of the data need to be taken. Beyond medical data security, we need to ethically acquire, use and manage data so that all people involved with the data from producer to data manager are recognized and respected. This paper advocates that sharing medical data can be ethically the right choice for everyone in health care if data sharing guidelines are available for people to use, modify and strengthen for specific purposes.

Standardization of negative controls in diagnostic immunohistochemistry: recommendations from the international ad hoc expert panel

Standardization of controls, both positive and negative controls, is needed for diagnostic immunohistochemistry (dIHC). The use of IHC-negative controls, irrespective of type, although well established, is not standardized. As such, the relevance and applicability of negative controls continues to challenge both pathologists and laboratory budgets. Despite the clear theoretical notion that appropriate controls serve to demonstrate the sensitivity and specificity of the dIHC test, it remains unclear which types of positive and negative controls are applicable and/or useful in day-to-day clinical practice. There is a perceived need to provide "best practice recommendations" for the use of negative controls. This perception is driven not only by logistics and cost issues, but also by increased pressure for accurate IHC testing, especially when IHC is performed for predictive markers, the number of which is rising as personalized medicine continues to develop. Herein, an international ad hoc expert panel reviews classification of negative controls relevant to clinical practice, proposes standard terminology for negative controls, considers the total evidence of IHC specificity that is available to pathologists, and develops a set of recommendations for the use of negative controls in dIHC based on "fit-for-use" principles.

Canadian Association of Pathologists-Association canadienne des pathologistes National Standards Committee for High Complexity Testing/Immunohistochemistry: guidelines for the preparation, release, and storage of unstained archived diagnostic tissue sections for immunohistochemistry

OBJECTIVES

Formalin-fixed, paraffin-embedded unstained archived diagnostic tissue sections are frequently exchanged between clinical laboratories for immunohistochemical staining. The manner in which such sections are prepared represents a type of preanalytical variable that must be taken into account given the growing importance of immunohistochemical assays, especially predictive and prognostic tests, in personalized medicine.

METHODS

Recommendations were derived from review of the literature and expert consensus of the Canadian Association of Pathologists-Association canadienne des pathologists National Standards Committee for High Complexity Testing/Immunohistochemistry.

RESULTS

Relevant considerations include the type of glass slide on which to mount the unstained sections; the thickness of the tissue sections; the time from slide preparation to testing; the environment, particularly the temperature at which the unstained sections will be maintained prior to testing; the inclusion of on-slide positive control tissue where possible; and whether patient identifier(s) should be included on slide labels.

CONCLUSIONS

Clear communication between requesting and releasing laboratories will facilitate the proper preparation of unstained sections and also ensure that applicable privacy considerations are addressed.

The role of diagnostic tissue in research

There are two broad classes (or categories) of excised human tissue: diagnostic tissue (DT) and research tissue (RT). Classification of excised human tissue does not define its ultimate use and ultimate use of excised human tissue does not define its classification. While both DT and RT can be used for research, DT has specific requirements with respect to how it must be handled if and when being accessed for research. We highlight distinguishing features of DT: (1) it is a clinical record, (2) it must be identifiable to a specific individual, (3) it is stewarded by pathology departments/clinical laboratories and (4) it has a mandatory retention period. We discuss how the further sub-classification of DT into archived DT (aDT) and excess DT (eDT) impacts the nature of its role in research. We examine the concept of DT as a clinical record and emphasize the impact of mandatory retention as it applies to how DT may be accessed for research purposes. We explain the role of post-retention eDT as a source of RT as well as procedures for access to in-retention aDT for research. Clarity of such issues will facilitate responsible access to DT for research.