Formalin‐fixed paraffin‐embedded clinical tissues show spurious copy number changes in array‐CGH profiles

Formalin‐fixed paraffin‐embedded (FFPE) archival clinical specimens are invaluable in discovery of prognostic and therapeutic targets for diseases such as cancer. However, the suitability of FFPE‐derived genetic material for array‐based comparative genomic hybridization (array‐CGH) studies is underexplored. In this study, genetic profiles of matched FFPE and fresh‐frozen specimens were examined to investigate DNA integrity differences between these sample types and determine the impact this may have on genetic profiles. Genomic DNA was extracted from three patient‐matched FFPE and fresh‐frozen clinical tissue samples. T47D breast cancer control cells were also grown in culture and processed to yield a fresh T47D sample, a fresh‐frozen T47D sample and a FFPE T47D sample. DNA was extracted from all the samples; array‐CGH conducted and genetic profiles of matched samples were then compared. A loss of high molecular weight DNA was observed in the FFPE clinical tissues and FFPE T47D samples. A dramatic increase in absolute number of genetic alterations was observed in all FFPE tissues relative to matched fresh‐frozen counterparts. In future, alternative fixation and tissue‐processing procedures, and/or new DNA extraction and CGH profiling protocols, may be implemented, enabling identification of changes involved in disease progression using stored clinical specimens.