What is Nucleic Acid-based Diagnostics?

Nucleic acid-based diagnostics detect the presence of a pathogen either by directly detecting the presence of DNA or RNA nucleic acids in the host or by first amplifying the pathogen DNA or RNA. Nucleic acid-based diagnostics are a standard central laboratory technique, although simplified nucleic acid-based diagnostics that may be useful in resource-poor settings are emerging.

Overview

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Nucleic acid-based diagnostics detect specific nucleic acid (i.e. DNA or RNA). In the case of infectious diseases, nucleic acid-based diagnostics detect DNA or RNA from the infecting organism. For non-infectious diseases, nucleic acid-based diagnostics may be used to detect a specific gene or the expression of a gene associated with disease. Common nucleic-acid based diagnostic techniques used to diagnose infectious diseases are summarized in the table below.1-2

  Description Strengths Weaknesses
PCR/RT-PCR DNA (or RNA reverse transcribed to cDNA) is amplified to detect the presence of a pathogen or host gene of interest DNA is amplified which allows for sensitive detection Requires highly skilled technician and laboratory equipment, amplified material can contaminate subsequent samples
Isothermal amplification Similar to PCR, but uses simplified amplification techniques that operate at a single temperature DNA is amplified which allows for sensitive detection, simplified isothermal amplification is more amenable to point-of-care devices/low-resource settings Newer technology that has not been extensively clinically validated, amplified material can contaminate subsequent samples
Hybridization DNA probes bind directly to DNA of pathogen or host gene of interest No risk of contamination of new samples with amplified material Because the target DNA is not amplified, technique can be less sensitive, requires highly skilled technician and laboratory equipment
Sequencing The specific genetic code is determined for an amplified piece of DNA or the full genome of an organism Beyond confirming the presence of a pathogen, sequencing can provide detailed information about the original and unique characteristics of the pathogen in a specific patient, not practical for low-resource settings Sequencing techniques are expensive, time consuming, and require both a highly skilled technician and expensive laboratory equipment

Nucleic acid-based diagnostics have an advantage over immunoassays in that they can detect genetic markers, such as those for drug resistance in bacteria, beyond detecting the presence of a pathogen. However, for infectious organisms that are able to hide in host organs or other areas of the body where obtaining an infected sample is difficult, nucleic acid-based diagnostics may fail to detect disease. In contrast, when a sample containing an infectious organism cannot be obtained, immunoassays that can detect the host immune response reactions to a pathogen can provide an indirect measure of the presence of an infection.

Existing Products

Nucleic acid-based diagnostics are widely used in centralized laboratory settings to diagnose both infectious and non-infectious conditions. A full list of FDA cleared/approved nucleic acid-based diagnostics is available from the Association of Molecular Pathology.3

Nucleic Acid-based Diagnostics for Non-Neglected Diseases

Nucleic acid-based diagnostics are used to diagnose a wide range of conditions, including cancer, genetic markers associated with a high risk of cancer, and genetic diseases (e.g. cystic fibrosis). Nucleic acid-based diagnostics are also used to detect a variety of infectious diseases, including anthrax, Clostridium difficile (a common hospital acquired bacterial infection), chlamydia, and gonorrhea.

Nucleic Acid-based Diagnostics for Neglected Diseases

Nucleic acid-based diagnostics are used to diagnose a wide range of neglected diseases including leishmaniasis, tuberculosis, and HIV. FDA approved molecular tests for neglected diseases are summarized in the table below.3

 Disease Manufacturer Test Name Method
Leishmaniasis Cepheid - Sunnyvale, CA Smart Leish PCR assay RT-PCR
Tuberculosis Gen-Probe, Inc. - San Diego, CA AMPLIFIED™ Mycobacterium tuberculosis Direct Test (MTD) Transcription mediated amplification (TMA)
HIV Abbott Molecular, Inc. - Des Plaines, IL Abbott Real-time HIV-1 Real-time RT-PCR
Roche Molecular Diagnostics - Pleasanton, CA AMPLICOR HIV-1 MONITOR™ Test, v1.5
COBAS AMPLICOR HIV-1 MONITOR™ Test, v1.5
COBAS® AmpliPrep/
COBAS® TaqMan HIV-1 Test
Real-time RT-PCR
Siemens Healthcare Diagnostics - Deerfield, IL VERSANT® HIV-1 RNA 3.0 Assay (bDNA) Branched Chain DNA Signal Amplification

References

  1. Weile J and Knabbe C (2009). “Current application and future trends of molecular diagnostics in clinical bacteriology”. Anal Bioanal Chem394: 731-742.
  2. Muldrew KL (2009). “Molecular diagnostics of infectious diseases”. Curr Opin Pediatr 21: 102-111.
  3. Association of Molecular Pathology (2011). FDA cleared/approved nucleic acid-based diagnostics.

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Pipline

Analysis

Nucleic acid-based diagnostics are already in use for many neglected diseases, especially PCR-based assays in centralized laboratory settings. However, there are several nucleic acid-based diagnostics in development for neglected diseases. These include newer methods such as Loop-Mediated Isothermal Amplification (LAMP) methods that are amenable to use at the point of patient care in low resource settings.

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There are numerous publications and manuals with detailed protocols and explanations of the principles of nucleic-acid based assays, many written specifically focused on the diagnosis of infectious diseases.

  • Roche. Applications of PCR
  • Journal of Molecular Diagnostics
  • Weile J and Knabbe C (2009). “Current application and future trends of molecular diagnostics in clinical bacteriology”. Anal Bioanal Chem394: 731-742.
  • Muldrew KL (2009). “Molecular diagnostics of infectious diseases”. Curr Opin Pediatr 21: 102-111.

Get Involved

To learn how you can get involved in neglected disease drug, vaccine or diagnostic research and development, or to provide updates, changes, or corrections to the Global Health Primer website, please view our FAQs.