Lymphoma and plasma cell neoplasms
Molecular analysis
Polymerase chain reaction (PCR)

Author: Nikhil Sangle, M.D. (see Authors page)

Revised: 3 April 2017, last major update February 2011

Copyright: (c) 2001-2017,, Inc.

PubMed Search: polymerase chain reaction lymphoma

See also Molecular Pathology chapter
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Cite this page: Polymerase chain reaction (PCR). website. Accessed August 21st, 2019.
Definition / general
  • 10,000 times more sensitive than Southern blot
  • Clones appear as 1 - 2 bands (if 1 or 2 alleles were rearranged); polyclonal cells appear as a smear since no amplification usually occurs due to wide separation of V and J regions
  • Faster than Southern blot and minimal tissue required
Uses by pathologists
  1. Add sample DNA, 4 nucleotides, buffer with magnesium, primers and Taq DNA polymerase to test tube
  2. Use PCR cycler with 3 reactions: (a) denature double stranded DNA, (b) allow annealing of primers, (c) allow DNA polymerase activity to extend primer
  3. Use multiple cycles, to provide exponential expansion of DNA
  4. Analyze products by gel electrophoresis, then stain gel with ethidium bromide OR transfer gel to nylon membrane by Southern blotting and hybridize membrane with labeled probe

  • False negatives are due to imperfect consensus primers, inability to detect partial DJ rearrangements; mutations of Ig genes that prevent annealing of primers; lymphomas that arise from B cell precursors prior to rearrangement
PCR and Temperature Gradient Gel Electrophoresis
Reverse Transcriptase PCR (RT-PCR)
  • Used to detect chimeric fusion mRNA transcripts translocations
  • Highly sensitive technique by which a very low copy number of RNA molecules can be detected
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