The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer: A Report of the Association for Molecular Pathology

Clinical utility describes the benefits of each laboratory test for that patient. Many stakeholders have adopted narrow definitions for the clinical utility of molecular testing as applied to targeted pharmacotherapy in oncology, regardless of the population tested or the purpose of the testing. This definition does not address all of the important applications of molecular diagnostic testing. Definitions consistent with a patient-centered approach emphasize and recognize that a clinical test result\u27s utility depends on the context in which it is used and are particularly relevant to molecular diagnostic testing because of the nature of the information they provide. Debates surrounding levels and types of evidence needed to properly evaluate the clinical value of molecular diagnostics are increasingly important because the growing body of knowledge, stemming from the increase of genomic medicine, provides many new opportunities for molecular testing to improve health care. We address the challenges in defining the clinical utility of molecular diagnostics for inherited diseases or cancer and provide assessment recommendations. Starting with a modified analytic validity, clinical validity, clinical utility, and ethical, legal, and social implications model for addressing clinical utility of molecular diagnostics with a variety of testing purposes, we recommend promotion of patient-centered definitions of clinical utility that appropriately recognize the valuable contribution of molecular diagnostic testing to improve patient care

Review The Henry Ford Production System: LEAN Process Redesign Improves Service in the Molecular Diagnostic Laboratory A Paper from the 2008 William Beaumont Hospital Symposium on Molecular Pathology

Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here , we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps , approaching the ideal of a one-piece flow for specimens through collection/ retrieval , transport , and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement. Molecular diagnostic laboratories, just as for other areas of pathology, face challenges associated with increasing testing volumes, decreasing reimbursement, and maintaining and improving quality levels. Diagnostic accuracy is crucial in pathology; nucleic acid-based diagnostic test results are often important for subsequent therapeutic decision making. Accurate and timely molecular testing can add a great deal of value to total patient management. Specimen types such as peripheral blood, bone marrow aspirates, and formalin-fixed, paraffin-embedded (FFPE) tissue, are routinely evaluated using molecular techniques. For tissue-based nucleic acid assays to enter a clinical setting, nucleic acids must be obtainable through current practices of diagnostic pathology. This might involve dealing with individuals who are based at off-site locations, have different priorities, and often have very little understanding of molecular testing requirements. Finally, the isolation of nucleic acids from FFPE tissue, which makes it possible to bring molecular testing to surgical pathology, requires close collaboration between molecular and histology personnel. For accurate and reliable test results, FFPE tissue must be handled in a standardized fashion, similar to how blood an

Do Circulating Tumor Cells, Exosomes, and Circulating Tumor Nucleic Acids Have Clinical Utility? a Report of the Association for Molecular Pathology

Diagnosing and screening for tumors through noninvasive means represent an important paradigm shift in precision medicine. In contrast to tissue biopsy, detection of circulating tumor cells (CTCs) and circulating tumor nucleic acids provides a minimally invasive method for predictive and prognostic marker detection. This allows early and serial assessment of metastatic disease, including follow-up during remission, characterization of treatment effects, and clonal evolution. Isolation and characterization of CTCs and circulating tumor DNA (ctDNA) are likely to improve cancer diagnosis, treatment, and minimal residual disease monitoring. However, more trials are required to validate the clinical utility of precise molecular markers for a variety of tumor types. This review focuses on the clinical utility of CTCs and ctDNA testing in patients with solid tumors, including somatic and epigenetic alterations that can be detected. A comparison of methods used to isolate and detect CTCs and some of the intricacies of the characterization of the ctDNA are also provided

Fast and Molecular Friendly Heat and Mechanical Agitation Based EDTA Decalcification of Bone Marrow Trephine Biopsies Provides High Quality DNA with Preserved Histology and Immunohistochemistry

Background: Modern hematopathology relies heavily on molecular studies as diagnostic, prognostic and predictive ancillary studies, especially with the advent of next generation sequencing (NGS). While bone marrow (BM) aspirate smears continue to be used as the primary DNA source, hemodilution and BM fibrosis might make them non-representative of native BM including lack of potential sub clones. Traditional Hydrochloric acid (HCL) based decalcification (HD) makes bone marrow trephine biopsy non-amenable to DNA studies. We demonstrate a temperature and magnetic stirring based EDTA decal (ED) method that preserves DNA and provides a reasonable turnaround time. Design: BM biopsies were received in formalin and treated with HCL (RDO rapid decal, Apex, Aurora, IL) or 10% EDTA (Mol- Delcalcifier and BoneStation, Milestone Medical, Kalamazoo, MI) (at 37 and 50 °C) followed by regular processor vs. rapid processor (Tissue Tek VIP 300E vs. Tissue-Tex Xpress x50, Sakura, Torrance, CA). Immunohistochemistry (IHC) was performed for CD20, CD3, CD34, TdT, CD138 and Tryptase. DNA was evaluated by spectrophotometry and amplification of control size ladder mix generating amplicons of 100, 200, 300, and 400 base pairs (bp) (Invivoscribe, San Diego, CA). Student T test was used for statistical analyses. Results: BM histology and IHC was unaltered by ED (37 °C or 50 °C) or use of regular vs. rapid processor. When comparing ED method across all conditions, best results were obtained with ED at 50 °C + regular tissue processor with reliable amplification up to 300 bps. For 400 bp, this method reliably generated amplicons albeit at lower peak heights (as compared to 100-300 bp) while other conditions mostly failed to generate any 400 bp amplicons. In contrast, HD amplified DNA only up to 100 bp although mean peak amplicon height for 100 bp was substantially less than ED method (13732 vs. 24275). Surprisingly, DNA quality of ED was superior to clot section. ED (50 °C) with regular processor demonstrated statistically significant superiority over use of rapid processor at either 37 or 50 °C for 100- 300 bp (p\u3c0.05). Conclusions: We demonstrate that increasing temperature to 50 °C (with magnetic stirring) during ED does not alter histology or immunohistochemistry and yields good quality DNA with reasonable turnaround time (approximately 5 hours decalcification) as compared to the historically long decalcification periods (up to 24 hours) of EDTA based methods. NGS studies are in progress to further validate this process

Fast and molecular friendly heat and mechanical agitation based EDTA decalcification of bone marrow trephine biopsies provides high quality DNA with preserved histology and immunohistochemistry

Background: Modern hematopathology relies heavily on molecular studies as diagnostic, prognostic and predictive ancillary studies, especially with the advent of next generation sequencing (NGS). While bone marrow (BM) aspirate smears continue to be used as the primary DNA source, hemodilution and BM fibrosis might make them non-representative of native BM including lack of potential sub clones. Traditional Hydrochloric acid (HCL) based decalcification (HD) makes bone marrow trephine biopsy non-amenable to DNA studies. We demonstrate a temperature and magnetic stirring based EDTA decal (ED) method that preserves DNA and provides a reasonable turnaround time. Design: BM biopsies were received in formalin and treated with HCL (RDO rapid decal, Apex, Aurora, IL) or 10% EDTA (Mol- Delcalcifier and BoneStation, Milestone Medical, Kalamazoo, MI) (at 37 and 50 °C) followed by regular processor vs. rapid processor (Tissue Tek VIP 300E vs. Tissue-Tex Xpress x50, Sakura, Torrance, CA). Immunohistochemistry (IHC) was performed for CD20, CD3, CD34, TdT, CD138 and Tryptase. DNA was evaluated by spectrophotometry and amplification of control size ladder mix generating amplicons of 100, 200, 300, and 400 base pairs (bp) (Invivoscribe, San Diego, CA). Student T test was used for statistical analyses. Results: BM histology and IHC was unaltered by ED (37 °C or 50 °C) or use of regular vs. rapid processor. When comparing ED method across all conditions, best results were obtained with ED at 50 °C + regular tissue processor with reliable amplification up to 300 bps. For 400 bp, this method reliably generated amplicons albeit at lower peak heights (as compared to 100-300 bp) while other conditions mostly failed to generate any 400 bp amplicons. In contrast, HD amplified DNA only up to 100 bp although mean peak amplicon height for 100 bp was substantially less than ED method (13732 vs. 24275). Surprisingly, DNA quality of ED was superior to clot section. ED (50 °C) with regular processor demonstrated statistically significant superiority over use of rapid processor at either 37 or 50 °C for 100- 300 bp (p\u3c0.05). Conclusions: We demonstrate that increasing temperature to 50 °C (with magnetic stirring) during ED does not alter histology or immunohistochemistry and yields good quality DNA with reasonable turnaround time (approximately 5 hours decalcification) as compared to the historically long decalcification periods (up to 24 hours) of EDTA based methods. NGS studies are in progress to further validate this process

The Henry Ford Production System: LEAN Process Redesign Improves Service in the Molecular Diagnostic Laboratory: A Paper from the 2008 William Beaumont Hospital Symposium on Molecular Pathology

Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps, approaching the ideal of a one-piece flow for specimens through collection/retrieval, transport, and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement