CLSI MM06—Quantitative Molecular Methods for Infectious Diseases recognizes the increased use of quantitative molecular methods for measuring and monitoring the concentration of pathogens in patient specimens. CLSI MM06 provides guidance for the development and use of quantitative molecular methods, such as nucleic acid probes and nucleic acid amplification techniques of the target sequences specific to particular microorganisms, and presents recommendations for quality assurance, proficiency testing, and interpretation of results. Issues specific to the quantification of nucleic acid in diagnostic testing and monitoring, particularly in viral diseases, include an update on technologies used in molecular quantification; specimen handling and preparation; standards, calibrators, and reference materials; analytical and clinical verification/validation; reporting and interpreting results; clinical utility; and recommendations for manufacturers and clinical laboratories.

CLSI MM06-Ed3 replaces CLSI MM06-Ed2 published in 2010. Several changes were made to this edition, including:

• Updating Chapter 3 to bring awareness to newer applications, including vector monitoring during gene therapy and drug resistance mutations using next-generation sequencing.
• Updating all chapters for procedural, technological, and regulatory aspects that specifically cover considerations when developing quantitative molecular methods for infectious diseases.
• Updating important aspects of matrix selection, technology selection, verification and validation, and quality assurance unique to quantitative molecular-based testing have been updated to include the latest guidelines and best practices.

CLSI MM06 is to be used for the implementation of tests for diagnostic purposes after the benefits and potential risks associated with the use of the test in clinical practice have been considered. Specimen handling and preparation; standards, calibrators, and reference materials; analytical and clinical verification/validation; reporting and interpreting results; and QC and clinical utility are the focus of CLSI MM06. CLSI MM06 does not establish a clinically acceptable limit of quantification (LoQ) because consensus for most assays is currently lacking on this issue. 

CLSI MM06 is intended for manufacturers or laboratories that develop tests, laboratories that perform or intend to implement such tests, clinicians that use the results to diagnose or manage patients, and agencies that regulate their use. 

Nucleic acid testing for infectious agents poses unique issues; quantification introduces additional complexity. With the advent of commercially available quantitative kits and the increase in quantitative laboratory-developed testing, a guideline for the development, verification, validation, implementation, and quality assurance of these assays is warranted. At the time of the development of CLSI MM06, clinical use of quantitative molecular assays was primarily applicable to viral diseases. CLSI MM06 applies to assays used to identify clinical disease and monitor disease progression and prognosis, therapeutic efficacy, and the emergence of active disease in chronic viral infections or during reactivation. In principle, the methodologies can also be applied to other infectious agents and disease processes.