Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays

Holly N Cukier, Margaret A Pericak-Vance, John Gilbert, Dale J. Hedges

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

The recent implication of genomic copy number variations (CNVs) in multiple human genetic disorders has led to increased interest in CNV discovery technologies. There is a growing consensus that, in addition to the method used for detection, at least one additional technology should be employed for validation. Real-time quantitative polymerase chain reaction (qPCR) analysis, incorporating a normal (2N) copy number standard, is commonly used as a means of validating CNVs. Whereas it has previously been reported that formalin-fixed paraffin-embedded (FFPE) DNA samples can yield spurious CNV calls in real-time qPCR assays, here we report that sample degradation under standard laboratory storage conditions generates a significant increase in false-positive CNV results. Results suggest the possibility of biased degradation among genomic regions and emphasize the need to assess sample integrity immediately prior to real-time qPCR experiments.

Original languageEnglish
Pages (from-to)288-290
Number of pages3
JournalAnalytical Biochemistry
Volume386
Issue number2
DOIs
StatePublished - Mar 15 2009

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Multiplex Polymerase Chain Reaction
Polymerase chain reaction
Real-Time Polymerase Chain Reaction
Assays
Degradation
Technology
Inborn Genetic Diseases
Medical Genetics
Paraffin
Formaldehyde
DNA
Experiments

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology
  • Cell Biology

Cite this

Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays. / Cukier, Holly N; Pericak-Vance, Margaret A; Gilbert, John; Hedges, Dale J.

In: Analytical Biochemistry, Vol. 386, No. 2, 15.03.2009, p. 288-290.

Research output: Contribution to journalArticle

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