Abstract A23: Comprehensive next-generation sequencing-based genomic profiling identifies actionable genomic alterations in diverse pediatric tumor types: The Foundation Medicine (FMI) experience
Authors: Hawryluk Matthew J. , Wang Kai , Chmielecki Juliann , Ali Siraj M. , Palmer Gary , Garcia Lazaro , White Emily , Yelensky Roman , Stephens Philip J. , Ross Jeffrey S. , Miller Vincent A. 
Published: May 2015

Background: Solid tumor oncology is amidst a paradigm shift with the advent and increasingly successful utilization of targeted therapies that inhibit specific genomic alterations driving an individual patient's disease. Unfortunately, many pediatric tumors lack approved targeted therapies, and routine genomic profiling of pediatric tumors has yet to be applied in a widespread manner. More comprehensive testing platforms are required to determine the landscape of genomic alterations in pediatric solid tumors and thereby broaden targeted treatment options. We have developed a solid tumor next-generation sequencing (NGS)-based diagnostic test, optimized for routine clinical FFPE specimens including needle biopsies and malignant effusions, and report here on 193 pediatric patients' tumors analyzed to date in our CLIA-certified and CAP-accredited laboratory.

Methods: Hybridization capture of 3,320 exons from 182 cancer-related genes and 37 introns of 14 genes commonly rearranged in cancer (previous version of the test) or 3,769 exons from 236 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer (current version of the test) was applied to ≥ 50ng of DNA extracted from over 190 pediatric FFPE tumor specimens and sequenced to high, uniform coverage. Genomic alterations (base substitutions, small indels, rearrangements, copy number alterations) were determined and then reported for these patient samples.

Results: Successful profiles were generated from 193 pediatric patient specimens from individuals ≤21 years old at the time of biopsy. A total of 361 genomic alterations were identified, with 145/193 (75%, 95% CI 68%-81%) of cases harboring at least one genomic alteration, for an average of 2.5 genomic alterations per case (range 0-14). The number of genomic alterations varied widely depending on tumor type (average alterations per sample): 4 colon cancer samples (9.0), 11 bone sarcoma samples (3.7), 13 leukemia samples (3.1), 23 brain cancer samples (2.4), 27 soft tissue sarcoma samples (2.2), 6 liver samples (2.0), 26 neuroblastoma samples (1.7), 6 lung cancer samples (1.2), 5 kidney cancer samples (1.2), and 24 other tumor types. These alterations included 146 base substitutions, 54 indels, 133 copy number alterations, and 28 rearrangements. This corresponded to alterations within 102 genes with recurrent alterations observed in 61 genes. We identified 249 actionable alterations with 109/193 (56%) of these pediatric patients found to have at least one actionable alteration. Seventy one percent (176/249) of the actionable genomic alterations would not be detected by available tumor type specific tests or hotspot panels. This approach has led to novel insights into pediatric cancers including: novel potentially druggable kinase gene fusions (e.g. ALK, RET) and non-fusion alterations in known drug targets (e.g. EGFR, BRAF, ALK, MET, PTCH1, PIK3CA, KIT, PDGFRA, FGFR1).

Conclusions: Comprehensive NGS-based genomic profiling identified alterations in 75% of 193 unselected pediatric cancer clinical cases; and 56% of these patients (N=109) were found to have at least one therapeutically actionable alteration. Widespread deployment of this approach may provide treatment options for pediatric cancer patients.

Citation Format: Matthew J. Hawryluk, Kai Wang, Juliann Chmielecki, Siraj M. Ali, Gary Palmer, Lazaro Garcia, Emily White, Roman Yelensky, Philip J. Stephens, Jeffrey S. Ross, Vincent A. Miller. Comprehensive next-generation sequencing-based genomic profiling identifies actionable genomic alterations in diverse pediatric tumor types: The Foundation Medicine (FMI) experience. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A23.