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Molecular Pathology

Polymerase Chain Reaction

Current applications

Author: Rodney E. Shackelford, D.O., Ph.D. (see Reviewers page)
Revised: 13 October 2014, last major update January 2010
Copyright: (c) 2008-2014, PathologyOutlines.com, Inc.

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

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
● The 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)
● Although PCR introduces replication errors, DNA sequencing of the total PCR product may give the correct sequence because (a) errors occur in only a small percentage of the bases, (b) the incorporation of incorrect bases is essentially random, (c) new DNA polymerases have lower frequencies of mutations due to proofreading capabilities (Human Molecular Genetics 2; Garland Science 1999, Chapter 6)

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 US FBI (Wikipedia)
● 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

● Hemoglobinopathies (Clin Lab Haematol 2004;26:159)
● Measuring residual disease post-treatment (Clin Lymphoma Myeloma 2009;9 Suppl 3:S266)
● Prenatal diagnosis of aneuploidy (Folia Histochem Cytobiol 2007;45 Suppl 1:S11)
● Diagnosis of specific infectious disorders, including Aspergillosis / fungi (Rev Iberoam Micol 2007;24:89); BK virus (Clin J Am Soc Nephrol 2006;1:374) or other viruses (Curr Issues Mol Biol 2007;9:87); Salmonella / bacteria (J Infect Dev Ctries 2008;2:421); Schistosomiasis / parasites (Mem Inst Oswaldo Cruz 2006;101 Suppl 1:145)

Molecular genetics

● Study of the structure and function of genes at the molecular level
● Includes study of how genes are transferred from generation to generation (Wikipedia)

Molecular pathology

● Identification of gene rearrangements associated with specific tumor types (Jpn J Clin Oncol 2007;37:79)
● Molecular classification of leukemia (Br J Cancer 2007;96:535)

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)

Tissue identification

● PCR is part of a process of tissue fingerprinting to identify specimen mix-up, cross contamination, floaters or carry-over artifacts (Adv Anat Pathol 2008;15:211, J Mol Diagn 2007;9:205, Am J Clin Pathol 1993;100:666)

Transplant engraftment analysis

● Transplant engraftment studies are used to evaluate the level of donor versus recipient cells in post-transplant specimens
● Unique DNA fingerprints from recipient and donor are used to determine the proportion of each contained within the total DNA extracted from the post-transplant 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)


● PCR helps understand the importance of particular molecules and pathways that may be involved in tumorigenesis (J Histochem Cytochem 2010 Mar;58:277, BMC Cancer 2009;9:315)

End of Molecular Pathology > Polymerase Chain Reaction > Current applications

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