Abstract 3167: CNV patterns in 822 routine diagnostic cases of NSCLC, melanoma, and colorectal cancer
Authors: Stenzinger Albrecht , Penzel Roland , Klauschen Frederick , Warth Arne , Brandt Regine , Heim Daniel , Schirmacher Peter , Weichert Wilko , Endris Volker , Pfarr Nicole 
Published: July 2016

Targeted deep massive parallel sequencing (MPS) has been implemented in routine molecular diagnostics for high-throughput genetic profiling of formalin-fixed paraffin-embedded cancer samples. This approach is now widely used to interrogate simple somatic mutations but experience with the analysis of copy number variations (CNV) is still limited. Here, we retrospectively analyzed CNVs in 822 cancer cases (n = 135 melanoma, n = 468 non-small cell lung cancers (NSCLC), n = 219 colorectal cancers (CRC)) that were sent to our institution for routine molecular profiling using a semiconductor based sequencing platform. Amplifications and deletions inferred by MPS coverage data were independently validated by a qPCR assay. We observed a decreasing frequency of CNV in clinically actionable genes from melanoma to NSCLC to colorectal cancer.

Of 56 melanomas with genetic aberrations in BRAF, 31 showed co-occurring CNV in other genes, mainly affecting CDKN2A. Some tumors (5 cases each) revealed clustered deletions affecting either ABL1, NOTCH1, and RET or STK11, GNA11, and JAK3. 8.1% of the cases had amplifications in clinically actionable genes. In the group of NRAS mutant tumors (n = 39), 26 showed co-occurring CNVs in other genes, such as CDKN2A and FGFR3, and 9 NRAS mutant cases were additionally mutated in BRAF. 19.1% had amplifications in clinically actionable genes. In contrast to BRAF mutant tumors, we did not see any specific CNV clusters. In the group of BRAF/NRASwt tumors (n = 11), we observed 5 cases with co-amplification of KDR, KIT, PDGFRA and another 6 cases with KIT mutations. While co-amplified cases had many gene deletions, KIT mutated tumors harbored only very few genetic aberrations in other genes.

Across both NSCLC data sets, we identified 14 cases with amplified EGFR (10 of them harboring co-occurring EGFR mutations) and detected 8 NSCLC with KRAS amplifications (of which 7 had co-occurring mutations of KRAS). KRAS mutated tumors displayed frequent amplifications in MYC (n = 10) and MDM2 (n = 5). Of the 22 BRAF mutant tumors, two harbored mutated KRAS. In contrast to melanoma, we observed no clustering of CNVs in BRAFmut NSCLCs. Within the group of KRAS/EGFR/BRAFwt tumors, we identified 15 cases harboring genetic aberrations in MET (n = 8 mutations, n = 7 amplifications).

Compared to melanoma and NSCLC, the number of CNV in CRC was rather low. IGF2 amplifications were most prevalent (n = 13) followed by MYC (n = 9). Two cases showed amplified wild-type alleles of KRAS. Two KRAS mutant tumors showed concomitant amplification of NRAS and three cases harbored amplified EGFR.

In conclusion we demonstrate that i) detection of CNVs by targeted MPS data obtained from FFPE material is feasible and ii) could be validated independently, iii) this approach enables detection of known CNV patterns, and iv) uncovers new CNV patterns in clinically actionable targets across cancers.

Citation Format: Albrecht Stenzinger, Roland Penzel, Frederick Klauschen, Arne Warth, Regine Brandt, Daniel Heim, Peter Schirmacher, Wilko Weichert, Volker Endris, Nicole Pfarr. CNV patterns in 822 routine diagnostic cases of NSCLC, melanoma, and colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3167.