Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples

Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Here, we have validated TaqMan based quantitative PCR (qPCR) assays to detect CNAs in genes of high clinical importance in formalin-fixed, paraffin-embedded (FFPE) samples. A cohort of 22 tumors of various types that harbor 67 CNAs in 13 genes was assessed. The abnormalities in these tumors were detected by using a NGS-based 50 gene hotspot panel on Ion Torrent PGM and molecular inversion probe (MIP) array. The CNAs included ERBB2 (n = 6), PDGFRA (n = 6), KIT (n = 7), NRAS (n = 3), PIK3CA (n = 6), MYC (n = 7), MET (n = 4), FLT3 (n = 6), FGFR3 (n = 3), FGFR2 (n = 3), EGFR (n = 7), KRAS (n = 6) and FGFR1 (n = 5). Different amounts of input DNA were tested and 5 ng FFPE DNA was found to be adequate without limiting detection sensitivity. All 22 (100%) positive tumor samples revealed by MIP array were confirmed by real time qPCR and 17 of 22 (77.2%) samples tested by NGS were confirmed. The limit of detection of the qPCR assay was determined by serial dilution of SKBR3 cell line DNA (with amplified ERBB2) and showed an ability to detect 3 copies consistently up to 0.75% dilution. The ability to use low input of FFPE DNA, high sensitivity, and short turnaround time makes qPCR a valuable and economically viable platform for detecting single gene CNAs as well as for confirmation of CNAs detected by high throughput screening assays.