Molecular markers
Polymerase chain reaction
Current applications



Topic Completed: 1 January 2010

Revised: 15 February 2019

Copyright: 2008-2018, PathologyOutlines.com, Inc.

PubMed Search: Polymerase chain reaction[TI] current applications

Note: as PCR applications are voluminous, references are meant to be illustrative and not complete

Rodney E. Shackelford, D.O., Ph.D.
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Cite this page: Shackelford R. Polymerase chain reaction - current applications. PathologyOutlines.com website. http://www.pathologyoutlines.com/topic/MolecularPCRapplications.html. Accessed August 21st, 2019.
Archeology and evolution
  • DNA that has survived in ancient tissue up to 45,000 years old can be amplified to provide large quantities for sequencing
  • Analysis of DNA from ancient organisms is used to study ancient species, as well as evolution (Genome Res 1991;1:107)
DNA sequencing
  • Determining the order of DNA bases
  • Traditional Sanger method is not based on PCR but some newer sequencing methods use PCR to make copies of the DNA before the sequencing begins (Wikipedia: DNA Sequencing [Accessed 4 June 2018])
  • Although PCR introduces replication errors, DNA sequencing of the total PCR product may give the correct sequence because
    1. Errors occur in only a small percentage of the bases
    2. Incorporation of incorrect bases is essentially random
    3. New DNA polymerases have lower frequencies of mutations due to proofreading capabilities (Strachan: Human Molecular Genetics, 4th Edition, 2010)
Forensic identification
  • To identify individuals, forensic scientists scan 13 DNA regions or loci that vary from person to person and use the data to create a DNA profile of that individual ("DNA fingerprint")
  • Information is stored in the CODIS database, funded by U.S. FBI (Wikipedia: Combined DNA Index System [Accessed 4 June 2018])
  • There is an extremely small chance that another person has the same DNA profile for a particular set of 13 regions
  • PCR is used to make millions of exact copies of DNA from a biological sample, which allows use of biological samples as small as a few skin cells
  • Note: great care must be taken to prevent contamination with other biological materials during the identifying, collecting and preserving of a sample
Medical and pathogen diagnosis
Molecular genetics
Molecular pathology
Paternity testing
  • Use of genetic fingerprinting to determine if a man is the biological father of an individual
  • Current techniques use PCR and restriction fragment length polymorphisms
  • Older techniques used ABO blood group typing, analysis of other proteins or HLA antigens
  • In a DNA parentage test, the probability of parentage is 0% if the alleged parent is not biologically related to the child and typically > 99.9% if the alleged parent is biologically related to the child (Wikipedia: DNA Paternity Testing [Accessed 4 June 2018])
Tissue identification
Transplant engraftment analysis
  • Transplant engraftment studies are used to evaluate the level of donor versus recipient cells in posttransplant specimens
  • Unique DNA fingerprints from recipient and donor are used to determine the proportion of each contained within the total DNA extracted from the posttransplant specimen; these percentages correspond to relative amounts of donor and recipient cells in the specimen
  • Engraftment studies are sequentially performed on transplant patients to monitor closely the levels of donor and recipient cells so that appropriate therapeutic intervention can proceed, if necessary
  • Analysis often uses short tandem repeats (STRs) as part of the "fingerprint" (Bone Marrow Transplant 2002;29:243)
Tumorigenesis
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