Anal Biochem. 2009 Mar 15;386(2):288-90. Epub 2008 Dec 7.

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

Cukier HN, Pericak-Vance MA, Gilbert JR, Hedges DJ.

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Miami Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.

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.

PMID:: 19121619; [PubMed - indexed for MEDLINE]

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