Abstract 1384: A comprehensive gene panel for precise diagnosis and treatment of childhood cancer

• Published in: Cancer research (Chicago, Ill.) Vol. 76; no. 14_Supplement; p. 1384
• Main Authors: Triche, Timothy J., Biegel, Jackie, Judkins, Alex, Busse, Tracy, Wayne, Alan, Bhojwani, Deepa, Asgharzadeh, Shahab, Oberley, Matthew, Parham, David
• Format: Journal Article
• Language: English
• Published: 15-07-2016
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2016-1384

We have created and are validating a targeted gene panel that utilizes 20ng of FFPE DNA and 10 ng of FFPE RNA in a simple, 3-tube Ion AmpliSeq assay suitable for sequencing on the Ion Torrent platform with rapid turn around time (<3 days in lab) and automated report generation that is designed specifically to improve pediatric cancer diagnosis, identify prognostic features, and detect genomic alterations (including mutations, insertions, deletions, gene amplification, and RNA expression levels) that match current targeted therapeutic targets. The core content is identical to the Oncomine Comprehensive Assay as employed by the NCI MATCH program. In addition, a total of 128 genes known to be genomically altered in pediatric cancer are interrogated (either hotspots or coding exons), 21 genes frequently amplified in pediatric cancer, and 157 gene fusions (including over 1,500 variants) unique to these tumors are included. Unique to this panel are 22 pharmacogenomic gene polymorphisms that influence cytotoxic drug metabolism, to guide patient-specific dosing. Content was chosen to cover all common pediatric malignancies, including pediatric leukemia (ALL, AML, and multiple variants within each), lymphoma, brain tumors, neuroblastoma, and sarcomas, by a working group composed of pediatric oncologists and pathologists. Specific genomic alterations were identified from a comprehensive search of the pediatric cancer literature by the panel and categorized by level of evidence (FDA approved drug, open clinical trial, or peer-reviewed literature identifying a feature in a pediatric cancer). This panel includes 45 of the 51 gene targets identified by the COG TAP committee for pediatric cancer specific gene target-therapeutic agent matching. In contrast to the NCI MATCH program, which currently employs the Ion Torrent Personal Genome Machine and Ion 318 Chip, this panel is intended for use on the newly available Ion S5 platform, due to its significantly enlarged content. Verification of individual feature identification by orthogonal assays (Sanger sequencing, PCR, FISH, SNP arrays) is in process. The assay will be released initially as an LDP, with intended updated content as new features and therapeutics are identified. Unlike current panels for specific features like single gene mutations or known gene translocations, this panel is intended to detect all currently known genomic alterations with level I, II, or III evidence in pediatric cancer, as well as the ability to detect new gene mutations and fusion variants (subject to secondary assay validation). Also unique is the ability to measure gene amplification and RNA expression levels in one comprehensive panel starting with 30 ng or less of nucleic acid extracted from routine clinical FFPE specimens. This is the only comprehensive gene panel for pediatric cancer that encompasses diagnostic, prognostic, pharmacogenomic, and therapeutic targets in one assay.
Citation Format: Timothy J. Triche, Jackie Biegel, Alex Judkins, Tracy Busse, Alan Wayne, Deepa Bhojwani, Shahab Asgharzadeh, Matthew Oberley, David Parham. A comprehensive gene panel for precise diagnosis and treatment of childhood 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 1384.