Using Next Generation DNA Sequencing (NGS) To Select Targeted Therapies and Predict Resistance to Standard Therapies in Colorectal Cancer (CRC)
Christine E Sheehan, Alex Parker, Mirna Jarosz, Sean Downing, Roman Yelensky, Doron Lipson, Geoff Otto, Amy Donahue, Sohail Balasubramanian, Philip Stephens, Gary Palmer, Maureen Cronin, Jeffrey S Ross. Albany Medical College, Albany, NY; Foundation Medicine Inc., Cambridge, MA
Background: The recent introduction of massively parallel (NGS) DNA sequencing to clinical samples has enabled the discovery of novel and unanticipated genomic-derived drug targets of therapy for patients with relapsed and metastatic CRC. NGS can also identify markers of chemoresistance to standard therapies for CRC.
Design: DNA was extracted from 4 X 10 μ FFPE sections from 49 cases of primary CRC (52% male; 48% female; mean age 60 years; 10% Stages I/II; 40% Stage III; 40% Stage IV; 10% Stage unknown). NGS wasperformed on the primary tumor in 80% and on metastases in 20% of the CRC. The exons of 145 cancer-related genes were fully sequenced by NGS technology using the Illumina HiSeq 2000 (Illumina Inc. San Diego, CA) to at an average sequencing depth of 253X. Tumoral DNA was evaluated for point mutations, insertions/deletions (indels), translocations and copy number alterations (CNA).
Results: NGS revealed 156 genomic alterations in the 49 CRC samples including base substitutions (58%), indels (28%), CNAs (12.7%) and translocations/rearrangements (1.3%). NGS derived gene mutation frequencies were similar to the COSMIC database with the exceptions of higher NGS rates of TP53 mutation (71% vs 48%) and APC alterations (75% vs 29%). NGS derived alterations associated with sensitivity or resistance to targeted therapies were identified in 27 (55%) of CRCs including FBXW7 (6 tumors); BRAF (5 tumors); (SMAD4 (5 tumors); PIK3CA (4 tumors); BRCA1 (3 tumors); STK11 (2 tumors); ATM (2 tumors) BRCA2 (2 tumors); GNAS (2 tumors) CDK8 (1 tumor) and HER2 (1 tumor). 2 tumors had 3 alterations each associated with potential treatment decisions. In one CRC, genomic sequences suggestive of a novel chromosome 2 rearrangement adjacent to the ALK kinase domain was identified and confirmed by analyzing a cDNA library constructed from the patient's FFPE tumor RNA. This in-frame fusion, not currently detectable by FISH, starts at the canonical exon 20 recombination site previously reported for the majority of ALK fusion genes and contains the same intracellular domain as other ALK rearrangements including EML4-ALK, known to be ALK kinase inhibitor sensitive.
Conclusions: NGS can be performed on FFPE CRC samples in a highly sensitive deep sequencing of genomic DNA which, when applied to a broad cancer-related gene survey, uncovers an unexpectedly high frequency of genomic alterations in CRC patients that can reveal actionable genetic events that inform treatment decisions.
Monday, March 4, 2013 1:00 PM
Poster Session II # 138, Monday Afternoon