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 R. Gilbert, Dale J. Hedges

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

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

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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