Search

Because the clinical impact of cancer genomics is being increasingly recognized, tumor sequencing will likely continue to expand in breadth and scope. Therefore, it is vital for laboratory professionals to adopt the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists guidelines and create a standardized system of classification and nomenclature for somatic variants. Combining robust bioinformatics pipelines with thorough data analysis is necessary to efficiently and reproducibly identify and assess the impact of clinically relevant variants.

The COVID-19 pandemic remains a significant problem involving health systems worldwide. Several diagnostic methods are reported for detecting the coronavirus in clinical, research, and public health laboratories. rRT-PCR is considered the gold standard; however, as it required skilled personnel and special equipment, rapid antigen tests have been developed and used as first-line screening. The serologic testing of antibodies can also be used to enhance the detection sensitivity and accuracy, which are used to assess the overall infection rate. This review summarizes the molecular techniques and serologic assays widely used in China and discusses the advantages and disadvantages of these techniques.

The COVID-19 pandemic has led to the rapid development of a plethora of molecular diagnostic assays with real-time polymerase chain reaction (RT-PCR) at the forefront. In this review, we will discuss the history and utility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) molecular diagnostics and the associated current and future regulatory process in Europe. We will assess the performance characteristics of a range of the most common SARS-CoV-2 molecular tests currently used in Europe with a focus on as rapid molecular platforms, stand-alone RT-PCR kits, the role of low-throughput and high-throughput end-to-end testing platforms, and the rapidly evolving field of SARS-CoV-2 variant of concern identification.

Pediatric neoplasms have unique demands, including triaging of small biopsies for multiple testing modalities, and a pediatric cancer genome that is notably different from the adult cancer genome. Pediatric cancers are more likely to be driven by gene fusions and typically have a lower tumor mutational burden. Clinically relevant unique molecular targets exist within pediatric cancers, with important implications for diagnosis, prognosis, and treatment selection. Hence, assays and interpretation workflows must be designed thoughtfully to support molecular tumor profiling for children with cancer, including accommodation of small samples, detection of gene fusions, and consideration of potential germline associations.

Molecular pathology techniques continue to evolve. Although polymerase chain reaction (PCR) remains the cornerstone methodology for nucleic acid amplification, improvements in nucleic acid detection methodologies (i.e. PCR) have increased the detection sensitivity by using fluorescent and bead based array technologies. Single base pair lesions can be detected via sequencing and related techniques to discern point mutations in disease pathogenesis. Novel technologies, such as high- resolution melting analysis, provide fast high throughput post PCR analysis of genetic mutations or variance in nucleic acid sequences. These and other technologies such as hybrid capture, fluorohore and chemiluminescence detections assays allow for rapid diagnosis and prognosis for expeditious and personalized patient management.

Virtually all the red blood cell and platelet antigen systems have been characterized at the molecular level. Highly reliable methods for red blood cell and platelet antigen genotyping are now available. Genotyping is a useful adjunct to traditional serology and can help resolve complex serologic problems. Although red blood cell and platelet phenotypes can be inferred from genotype, knowledge of the molecular basis is essential for accurate assignment. Genotyping of blood donors is an effective method of identifying antigen-negative and/or particularly rare donors. Cell-free DNA analysis provides a promising noninvasive method of assessing fetal genotypes of blood group alloantigens.

MicroRNAs (miRNAs) are poised to provide diagnostic, prognostic, and therapeutic targets for several diseases including malignancies for precision medicine applications. The miRNAs have immense potential in the clinical arena because they can be detected in the blood, serum, tissues (fresh and formalin-fixed paraffin-embedded), and fine-needle aspirate specimens. The most attractive feature of miRNA-based therapy is that a single miRNA could be useful for targeting multiple genes that are deregulated in cancers, which can be further investigated through systems biology and network analysis that may provide cancer-specific personalized therapy.

Ovarian carcinoma continues to be a concern for woman and maintains significant morbidity and mortality. Emerging molecular markers are providing additional opportunities for effective diagnosis and prognosis of disease. An integrated clinicopathologic and molecular classification of gynecologic malignancies has the potential to refine the clinical risk prediction of patients with cancer and to provide more tailored treatment recommendations.

The unprecedented expansion of molecular pathology continues to affect and influence the clinical laboratory. Technological advances in high-throughput automation, cost containment, and refined methodology have improved the understanding of pathobiology through application of molecular pathology to multiple disease spaces. Incorporation of this field to emerging omics platforms, pharmacovigilance and biomarker discovery, and accessibility by lay consumers demonstrates the widespread reach of molecular pathology in the clinical marketplace. Pathologists should remain the stewards of this powerful and adaptable technology to provide guidance and appropriate laboratory application toward effective patient monitoring with respect to disease diagnosis and management.

Molecular pathology techniques continue to evolve. Although polymerase chain reaction (PCR) remains the cornerstone methodology for nucleic acid amplification, improvements in nucleic acid detection methodologies (i.e. PCR) have increased the detection sensitivity by using fluorescent and bead based array technologies. Single base pair lesions can be detected via sequencing and related techniques to discern point mutations in disease pathogenesis. Novel technologies, such as high- resolution melting analysis, provide fast high throughput post PCR analysis of genetic mutations or variance in nucleic acid sequences. These and other technologies such as hybrid capture, fluorohore and chemiluminescence detections assays allow for rapid diagnosis and prognosis for expeditious and personalized patient management.

MicroRNAs are small endogenous noncoding RNAs that are critical regulators of several physiologic and pathologic processes including cancers. Variations in the level of microRNA expression have been linked with the development, progression, and spread of cancer to distant organs. These tiny molecules may play a role in accurate and early diagnosis, and also as prognostic determinants. Modulating their activity provides opportunities for developing and designing novel cancer therapeutics. Recent studies indicate their detection in a wide variety of human biologic specimens including blood, serum, fine-needle aspirates, and tissues, making them clinically useful biomarkers of disease for early detection, prognosis, and for designing personalized therapies.

This article provides an overview of the application of molecular diagnostic methods to red cell and platelet compatibility testing. The advantages and limitations of molecular methods are evaluated compared with traditional serologic methods. The molecular bases of clinically significant red cell and platelet antigens are presented. Current recommendations for reporting molecular assay results and distinctions between genotype and phenotype are discussed.

New technologies, analytic techniques, and computer-assisted diagnosis algorithms will change the way pathologists and clinicians interact with and use clinical data. Simultaneously, the artisanal nature of the culture and clinical practice of medicine have made them resistant to change. An understanding of workflow science will help pathologists prepare for the changes that lie ahead in anatomic and clinical pathology, better care for patients, and make better and more respectful use of existing human and other resources. This article provides a primer on workflow science, including historical perspective, review of current literature, and extrapolation of future trends.

Molecular informatics (MI) is an evolving discipline that will support the dynamic landscape of molecular pathology and personalized medicine. MI provides a fertile ground for development of clinical solutions to bridge the gap between clinical informatics and bioinformatics. Rapid adoption of next generation sequencing (NGS) in the clinical arena has triggered major endeavors in MI that are expected to bring a paradigm shift in the practice of pathology. This brief review presents a broad overview of various aspects of MI, particularly in the context of NGS based testing.

The success of the Human Genome Project 1 has expanded the field of molecular biology in an exponential manner. It has facilitated the identification of numerous novel genes of unknown function whose functions can now be determined and whose expressions can be monitored in different disease states. Whereas the discipline of pathology often refers to the rubric of the study of disease in general, molecular pathology refers to the analysis of nucleic acids and proteins to diagnose disease, predict the occurrence of disease, and predict the prognosis of diagnosed disease and guide therapy. Furthermore, recent advances in molecular pathology have positively affected the practice of medicine, especially diagnostic medicine. These changes result from abilities to clone disease-causing genes and the proteins that they encode and to detect the presence of these genes and proteins in the serum and other body fluids and tissues of patients, even though they may be present in minute quantities. This detection has been made possible by a veritable explosion of new, highly sensitive techniques involving amplification methods, such as polymerase chain reaction, branched DNA

Pancreatic neoplasms, including ductal adenocarcinoma, intraductal papillary mucinous neoplasm, solid pseudopapillary neoplasm, pancreatic endocrine neoplasms, acinar cell carcinoma, and ampullary carcinoma, are associated with different genetic abnormalities. Liver neoplasms, including hepatic adenomas, hepatocellular carcinomas, and cholangiocarcinomas, are associated with identifiable risk factors and genetic changes. Gall bladder adenomas and adenocarcinomas arise from distinct molecular pathways. The molecular abnormalities seen in these tumors are not used routinely in the molecular diagnostic laboratory.

Molecular testing has a large and increasing role in the diagnosis of infectious diseases. It has evolved significantly since the first probe tests were FDA approved in the early 1990s. This article highlights the uses of molecular techniques in diagnostic microbiology, including “older,” as well as innovative, probe techniques, qualitative and quantitative RT-PCR, highly multiplexed PCR panels, some of which use sealed microfluidic test cartridges, MALDI TOF, and nuclear magnetic resonance. Tests are grouped together by technique and target. Tests with similar roles for similar analytes are compared with respect to benefits, drawbacks, and possible problems.

This article reviews the molecular features and pathogenesis of gynecologic malignancies. Understanding the molecular basis of endometrial carcinoma helps to provide an explanation for the prognosis of these tumors and opens up avenues for research into novel therapies that may prove beneficial.

The biomarkers galactomannan and 1,3-β-d-glucan have been well studied over the past years and are gaining a role in the diagnosis of invasive fungal infections. Although not as well studied until recently, molecular methods for the diagnosis of invasive fungal infection are also being evaluated. Outcomes data for molecular testing are expanding, but have not yet provided enough evidence for inclusion of molecular diagnostics in formal clinical guidelines. Lack of standardization and validation of the various molecular assays and platforms has hindered their widespread acceptance in the evaluation of invasive fungal infections, although the future is promising.