Helping lab professionals GoMolecular.

What is Molecular Diagnostics?


In this article:

  • The three steps of a molecular assay
  • Regulated and approved molecular tests
  • The economics of molecular assays

By Frederick L. Kiechle, M.D., Ph.D.

Molecular diagnostics is growing rapidly.  Molecular diagnostic tests detect specific sequences in DNA or RNA that may or may not be associated with disease, including single nucleotide polymorphism (SNP), deletions, rearrangements, insertions and others. Clinical applications can be found in at least six general areas: infectious diseases; oncology; pharmacogenomics; genetic disease screening; human leukocyte antigen typing; and coagulation.1

Each molecular assay requires three basic steps:

    1. The extraction and purification of nucleic acid.

    2. The amplification or making copies of the nucleic acid of interest (target) or
        attaching multiple copies of a dye to a single target copy.

    3. The detection of the amplified target using real time polymerase chain reaction
        (PCR) or end product detection including microarrays, Luminex (similar to flow
        cytometry), or sequencing.

These three steps can be performed by three separate devices or combined into one device.

The Federal Drug Administration (FDA) and Clinical Laboratory Improvement Act (CLIA) regulate clinical molecular tests like all other clinical laboratory tests.2,3

FDA Approved/Cleared

     • The current FDA approved or cleared molecular test list can be found at the       
        Association of Molecular Pathology (AMP) website under Publications
        and Resources.

     • FDA-cleared molecular tests may be modified by a laboratory. For example, a
        nucleic acid extractor that differs from the extractor(s) listed in the FDA approval
        may be validated. Another common example is laboratory validation of a specimen
        type not on the list already approved by the FDA.

ASR (Analyte Specific Reagents)

     • These are FDA-regulated and can be used for patient specimens after
        in-house validation. The components of the assay cannot be sold in a “kit” form
        or purchased from the same manufacturer.  Many manufacturers are either preparing
        their current list of ASRs for FDA clearance or are discontinuing their production.

RUO (Research Use Only)

     • This term usually refers to tests and rarely to devices. The assays are not FDA 
       regulated, but the FDA does define the category (research, not diagnosis).

     • “RUO products are, in fact, used diagnostically.  Laboratories buy products labeled
       as RUO and then use the results in generating diagnoses.”3

LDT (Laboratory Developed Tests)

     • These tests are not FDA regulated, but must be validated using CLIA standards       
        before they can be used to generate clinically used results.2

Molecular diagnostic testing usually generates a profit margin that increases as the testing volume goes up. In general, there is greater clinical demand for tests that produce results in less than one day. The infectious disease applications are among the most common area of clinical interest.

The number of commercially available assays is always increasing.1,4  Screening for hospital acquired infections (HAIs) — like methicillin-resistant Staphylococcus aureus, Clostridium difficile or Vancomycin-resistant enterococci — represent a second set of applications of interest to infectious disease surveillance and hospital administration.5

Molecular assays may be qualitative — to see if the virus exist — or quantitative — to see how much of the virus exists.  Basic molecular assay economics suggest two other categories of assays.  The first are assays that may be reported in the same patient including recurrence of an infectious disease or cancer, and detection of minimal residual disease.  The second category refers to tests that only need to be performed once in a patient’s lifetime including mutations that modify Clopidogrel (Plavix) or the activity of Factor V (the Leiden mutation) or Warfarin metabolism or prothrombin [the Factor II (G20210A) mutation].


  1. Grody WW, Nakamura RM, Strom CM, Kiechle FL (eds). Molecular Diagnostics: Techniques and Applications for the Clinical Laboratory. Academic Press, Inc.; Boston, MA. 2010.

  2. Gibbs JN. Regulatory pathways for molecular diagnosis. Detailing the various options available and what each requires. Genetic Eng Biotech News 2008: 28(14)

  3. Gibbs JN. Uncertainty persists with RUO products. FDA may be considering more restrictive approach with research use only assays. Genetics Eng Biotech News 2011; 31(7)

  4. Espy MJ, Uhl JR, Sloan LM, Brickwatter SP, Jones MF, Vetter EA, et al. Real-time PCR in clinical microbiology: Applications for routine laboratory testing. Clin Microbiol Rev 2006; 19:165-256.

  5. Rao A, Fader B, Hocker K. Molecular detection and surveillance of healthcare-associated infections. Molecular Diagnostics: Techniques and Applications for the Clinical Laboratory. (Eds: Grody WW, Nakamura RM, Strom CM, Kiechle FL). Academic Press, Inc.; Boston, MA. 2010: pp 327-346.