scholarly journals Revised guidelines for Australian laboratories performing mycobacteriology testing

2020 ◽  
Vol 44 ◽  
Author(s):  
Ivan Bastian ◽  
Lisa Shephard ◽  
Richard Lumb ◽  
Keyword(s):  
Peer Review Process ◽  
Contact Tracing ◽  
Molecular Testing ◽  
Reference Laboratory ◽  
Work Practices ◽  
Quality Work ◽  
Molecular Tests ◽  
Assessment Approach ◽  
National Tuberculosis ◽  
Risk Categorisation

Mycobacteriology laboratories play a key role in tuberculosis (TB) control by providing phenotypic and molecular diagnostics, by performing molecular typing to aid contact tracing, and by supporting research and similar laboratories in Australia’s neighbouring countries where TB is prevalent. The National Tuberculosis Advisory Committee (NTAC) published a set of laboratory guidelines in 2006 aiming to document the infrastructure, equipment, staffing and work practices required for safe high-quality work in Australian mycobacteriology laboratories. These revised guidelines have the same aims and have been through a similar extensive consultative peer-review process involving the Mycobacterium Reference Laboratory (MRL) network, the Mycobacterium Special Interest Group (SIG) of the Australian Society for Microbiology (ASM), and other relevant national bodies. This revised document contains several significant changes reflecting the publication of new biosafety guidelines and tuberculosis standards by various national and international organisations, technology developments – such as the MPT64-based immunochromatographic tests (ICTs) and the Xpert MTB/RIF assay, and updated work practices in mycobacteriology laboratories. The biosafety recommendations affirm the latest Australian/New Zealand Standard 2243.3: 2010 and promote a biorisk assessment approach that, in addition to the risk categorisation of the organism, also considers the characteristics of the procedure being performed. Using this biorisk assessment approach, limited manipulations, such as Ziehl-Neelsen (ZN) microscopy, MPT64 ICTs, and culture inactivation/DNA extraction for molecular testing, may be performed on a positive TB culture in a PC2 laboratory with additional features and work practices. Other significant changes include recommendations on the integration of MPT64 ICTs and novel molecular tests into TB laboratory workflows to provide rapid accurate results that improve the care of TB patients. This revised document supersedes the original 2006 publication. NTAC will periodically review these guidelines and provide updates as new laboratory technologies become available.

Clinical Requests for Molecular Tests: The 3-Step Evidence Check

2012 ◽  
Vol 136 (12) ◽  
pp. 1585-1592 ◽  
Author(s):  
Alexis B Carter
Keyword(s):  
Laboratory Tests ◽  
Digital Age ◽  
Molecular Methods ◽  
Molecular Medicine ◽  
Molecular Testing ◽  
Reference Laboratory ◽  
New Wave ◽  
Molecular Test ◽  
Molecular Tests ◽  
The Individual

Laboratory tests performed by molecular methods are increasing in volume and complexity at an unprecedented rate. Molecular tests have a broad set of applications, and most recently have been advocated as the mechanism by which providers can further tailor treatments to the individual patient. As the momentum behind molecular testing continues to increase, pathology practices may find themselves unprepared for the new wave of molecular medicine. This special article has been developed in an effort to provide pathologists who have limited molecular training with a simple and quick algorithm for determining whether a requested molecular test is appropriate for a patient. Additional recommendations for a more intensive and proactive review and management of molecular requests also are included. The principles discussed can easily be applied to requests for any test, including those not using molecular methods, which would be sent to an outside reference laboratory. This special article was developed from a Webinar for the College of American Pathologists targeting education for pathologists about the transformation of pathology practice in the new molecular and digital age.

scholarly journals IFCC interim guidelines on molecular testing of SARS-CoV-2 infection

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Mary Kathryn Bohn ◽  
Nicasio Mancini ◽  
Tze Ping Loh ◽  
Cheng-Bin Wang ◽  
Matthias Grimmler ◽  
...  
Keyword(s):  
Task Force ◽  
Clinical Chemistry ◽  
Laboratory Medicine ◽  
Control Measures ◽  
Contact Tracing ◽  
Molecular Testing ◽  
Case Identification ◽  
Molecular Tests ◽  
Infection Control Measures ◽  
Clinical Laboratories

AbstractThe diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection globally has relied extensively on molecular testing, contributing vitally to case identification, isolation, contact tracing, and rationalization of infection control measures during the coronavirus disease 2019 (COVID-19) pandemic. Clinical laboratories have thus needed to verify newly developed molecular tests and increase testing capacity at an unprecedented rate. As the COVID-19 pandemic continues to pose a global health threat, laboratories continue to encounter challenges in the selection, verification, and interpretation of these tests. This document by the International Federation for Clinical Chemistry and Laboratory Medicine (IFCC) Task Force on COVID-19 provides interim guidance on: (A) clinical indications and target populations, (B) assay selection, (C) assay verification, and (D) test interpretation and limitations for molecular testing of SARS-CoV-2 infection. These evidence-based recommendations will provide practical guidance to clinical laboratories worldwide and highlight the continued importance of laboratory medicine in our collective pandemic response.

What Every Neuropathologist Needs to Know: Practical Aspects and Pitfalls in Molecular Diagnosis of Brain Tumors

2021 ◽  
Author(s):  
J Stephen Nix ◽  
Cristiane M Ida
Keyword(s):  
Brain Tumors ◽  
Molecular Diagnosis ◽  
Genetic Alterations ◽  
Genetic Alteration ◽  
Molecular Testing ◽  
Test Results ◽  
Molecular Test ◽  
Molecular Tests ◽  
Clinically Significant ◽  
Selection Of

Abstract Molecular testing has become part of the routine diagnostic workup of brain tumors after the implementation of integrated histomolecular diagnoses in the 2016 WHO classification update. It is important for every neuropathologist to be aware of practical preanalytical, analytical, and postanalytical factors that impact the performance and interpretation of molecular tests. Prior to testing, optimizing tumor purity and tumor amount increases the ability of the molecular test to detect the genetic alteration of interest. Recognizing basic molecular testing platform analytical characteristics allows selection of the optimal platform for each clinicopathological scenario. Finally, postanalytical considerations to properly interpret molecular test results include understanding the clinical significance of the detected genetic alteration, recognizing that detected clinically significant genetic alterations are occasionally germline constitutional rather than somatic tumor-specific, and being cognizant that recommended and commonly used genetic nomenclature may differ. Potential pitfalls in brain tumor molecular diagnosis are also discussed.

Molecular Testing in the Diagnosis and Management of Hepatitis C Virus Infection

2002 ◽  
Vol 126 (3) ◽  
pp. 285-290 ◽  
Author(s):  
Raymond P. Podzorski
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Nucleic Acid ◽  
The United States ◽  
Nucleic Acid Amplification ◽  
Diagnosis And Treatment ◽  
Molecular Testing ◽  
Nucleic Acid Amplification Tests ◽  
Diagnosis And Management ◽  
Molecular Tests

Abstract Objectives.—To review hepatitis C virus (HCV), describe the types of molecular-based tests available for the diagnosis and management of HCV infection, and discuss the appropriate utilization of these tests. Data Sources.—Current information is presented from the published literature, as well as new information where available. Study Selection.—A major cause of posttransfusion and community-acquired non-A, non-B hepatitis worldwide is HCV. Approximately 4 million people in the United States are infected with HCV, resulting in 8000 to 10 000 deaths annually. Because HCV is not readily cultured, in vitro molecular-based tests have been developed for use in the diagnosis and treatment of HCV-infected patients. Molecular tests include qualitative and quantitative nucleic acid amplification tests, branched DNA tests, and HCV genotyping assays. Qualitative HCV nucleic acid amplification tests are used routinely in association with serologic tests to help make a diagnosis of infection with HCV. Quantitative HCV testing and genotyping methods have been found to be valuable tools in the treatment of infected patients. A patient's pretreatment HCV viral load and the rate of virus decline during therapy have been shown to correlate with the likelihood of long-term response to antiviral therapy. Information pertaining to the genotype of HCV infecting patients has been shown to be helpful in making recommendations regarding treatment. Certain genotypes of HCV are much more responsive to therapy, allowing a shorter course of treatment. Conclusions.—Molecular tests are valuable tools for use in the diagnosis and treatment of patients infected with HCV.

scholarly journals Molecular Testing Strategies for Pulmonary Adenocarcinoma: An Optimal Approach With Cost Analysis

2018 ◽  
Vol 143 (5) ◽  
pp. 628-633 ◽  
Author(s):  
Lester J. Layfield ◽  
Richard D. Hammer ◽  
Sandra K. White ◽  
Larissa V. Furtado ◽  
Robert L. Schmidt
Keyword(s):  
Essential Genes ◽  
Professional Organizations ◽  
Sequential Testing ◽  
Molecular Testing ◽  
Optimal Sequence ◽  
Expected Cost ◽  
Molecular Tests ◽  
Gene Testing ◽  
Few Data ◽  
Optimal Approach

Context.— Molecular analysis of lung adenocarcinoma for therapeutically important genes is standard of practice, with multiple professional organizations recommending testing of all adenocarcinomas for mutations in EGFR, ALK, and ROS1. Some organizations recommend analyzing these genes in association with a panel. Few data exist as to optimal testing method or optimal sequence of testing from a cost perspective. Objective.— To determine which order of gene testing was least costly and whether sequential, small panel, or next-generation sequencing (NGS) was cheapest. Design.— Recent recommendations propose a set of essential molecular tests (EGFR, ALK, and ROS1) and an optional set of molecular tests that may be useful for selection of clinical trials. We compared the costs of different testing sequencing strategies for both the 3 essential genes and for 5 optimal genes. Testing costs were determined by a survey of prices from large laboratories. The strategy most frequently rated as the lowest cost strategy was designated the optimal testing strategy. Results.— Sequential testing of the essential genes in the order EGFR-ROS1-ALK was optimal from a cost perspective. The expected cost of sequential testing was $2227 (95% CI, $1733–$2794). The cost of NGS was $2500. The expected cost per positive result was $11,362 using this strategy. Conclusions.— Molecular testing of lung adenocarcinomas for the set of 3 essential genes and 5 optional genes can be performed by a variety of methods and in a variety of sequences. From a cost perspective, sequential testing in the order EGFR, ROS1, then ALK is optimal. NGS would be competitive if the price was less than $2200. NGS is optimal if testing for the 3 essential genes will be followed by testing for the 5 optional genes. NGS testing is optimal if the clinician plans to test both essential and optional genes.

scholarly journals Molecular Diagnostic Testing for Aspergillus

2016 ◽  
Vol 54 (11) ◽  
pp. 2655-2660 ◽  
Author(s):  
Margaret V. Powers-Fletcher ◽  
Kimberly E. Hanson
Keyword(s):  
Direct Detection ◽  
Diagnostic Testing ◽  
Molecular Diagnostic ◽  
Molecular Testing ◽  
Content Type ◽  
Clinical Specimens ◽  
Molecular Tests ◽  
Assay Performance ◽  
Clinical Mycology ◽  
Invasive Infections

The direct detection ofAspergillusnucleic acid in clinical specimens has the potential to improve the diagnosis of aspergillosis by offering more rapid and sensitive identification of invasive infections than is possible with traditional techniques, such as culture or histopathology. Molecular tests forAspergillushave been limited historically by lack of standardization and variable sensitivities and specificities. Recent efforts have been directed at addressing these limitations and optimizing assay performance using a variety of specimen types. This review provides a summary of standardization efforts and outlines the complexities of molecular testing forAspergillusin clinical mycology.

scholarly journals Practical Molecular Testing in a Clinical Genitourinary Service

2019 ◽  
Vol 144 (3) ◽  
pp. 277-289 ◽  
Author(s):  
Martin J. Magers ◽  
Liang Cheng
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Germ Cell Tumors ◽  
Genitourinary Tract ◽  
Molecular Testing ◽  
Testicular Germ Cell ◽  
Molecular Tests ◽  
Molecular Oncology ◽  
Ets Family

Context.— Molecular testing is increasingly playing a key role in the diagnosis, prognosis, and treatment of neoplasms of the genitourinary system. Objective.— To provide a general overview of the clinically relevant molecular tests available for neoplasms of the genitourinary tract. Data Sources.— Relevant medical literature indexed on PubMed. Conclusions.— Understanding of the molecular oncology of genitourinary neoplasms is rapidly advancing, and the pathologist must be aware of the practical implications of molecular testing. While many genomic abnormalities are not yet clinically relevant, there is an increasing library of ancillary tests that may guide diagnosis, prognosis, and/or treatment of many neoplasms. Recurrent genomic abnormalities have been identified in many types of renal cell carcinoma, and some types of renal cell carcinoma are specifically defined by the molecular abnormality. Two major routes of developing urothelial carcinoma have been molecularly described. Recurrent translocations involving ETS family genes are found in approximately half of prostate cancer cases. Testicular germ cell tumors typically harbor i(12p). Penile neoplasms are often high-risk human papillomavirus–driven cancers. Nonetheless, even as genitourinary neoplasms are increasingly better understood at the molecular level, further research with eventual clinical validation is needed for optimal diagnosis, prognosis, and treatment of aggressive malignancies in the genitourinary tract.

Overview of Molecular Testing of Cytology Specimens

2019 ◽  
Vol 64 (1-2) ◽  
pp. 136-146 ◽  
Author(s):  
Min Huang ◽  
Shuanzeng Wei
Keyword(s):  
Personalized Medicine ◽  
Clinical Laboratory ◽  
Molecular Testing ◽  
Molecular Tests ◽  
Dna And Rna ◽  
Tissue Degradation ◽  
Pertinent Information ◽  
The Common ◽  
Short Time

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.

scholarly journals Utility of molecular tests in cytopathology

CytoJournal ◽  
2014 ◽  
Vol 11 ◽  
pp. 5 ◽  
Author(s):  
Arthur David Somoza ◽  
F. Zahra Aly
Keyword(s):  
Molecular Analysis ◽  
Diagnostic Information ◽  
Classification Systems ◽  
Cervical Cytology ◽  
Pancreatic Cysts ◽  
Molecular Testing ◽  
Thyroid Cytology ◽  
Anaplastic Lymphoma ◽  
Molecular Tests ◽  
Test Kit

With the popularity of interventional radiology, diagnostic material obtained can be limited requiring critical decisions on making the best use of it. Molecular testing using nanogram amounts of tissue can add useful diagnostic information by improving sensitivity and/or specificity of the diagnosis. This review examines the use of molecular tests in cervical cytology, “indeterminate” thyroid cytology specimens, pancreatic cyst fluid, urinary tract and pulmonary adenocarcinoma cytologic material. Molecular human papillomavirus (HPV) testing combined with cervical cytology increases sensitivity of detection of high grade lesions. In cytologically negative cases, the HPV negative predictive value endorses longer screening intervals. With the high prevalence of benign thyroid nodules, cytology plays a vital role in screening. However, 10-40% of the specimens obtained are cytologically indeterminate. Molecular analysis of these specimens can predict the malignant risk in these cases. Increased detection of pancreatic cysts has necessitated accurate pre-operative diagnosis delineating non-mucinous from mucinous cysts, which have a potential for progression to adenocarcinoma. Multimodal diagnosis of pancreatic cysts and molecular analysis help to clarify neoplastic risk; and in cases of limited fluid, may be the only available diagnostic information. Urothelial carcinoma (UC) of the bladder, a common cancer with frequent recurrences, requires lifelong surveillance. The UroVysion ™ test kit can increase the sensitivity of detection of UC especially in cases of residual/recurrent carcinoma after therapy. Subsets of lung adenocarcinomas are now commonly targeted by therapies based on molecular mutation results of epidermal growth factor receptor, KRAS or echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase re-arrangements. The move toward standardization of reporting of cytology specimens commencing with cervical smears and more recently, thyroid cytology specimens is also changing the practice of cytopathology. Combining the stringent cytology criteria with ancillary molecular testing is expected to yield more discrete and diagnostic categories for research and reporting. The profession is at an exciting point of implementing novel molecular markers to refine diagnostic criteria and create clinically relevant classification systems.

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