Abstract A36: Integrated sequencing of pediatric thyroid carcinoma reveals frequent targetable alterations
Authors: Potter Samara L. , Reuther Jacquelyn , Gandhi Ilavarasi , Hollingsworth Faith , Sayeed Hadi , Voicu Horatiu , Kakkar Nipun , Baksi Koel Sen , Sarabia Stephen F. , Lopez Monica E. , Chelius Daniel C. , Athanassaki Ioanna D. , Venkatramani Rajkumar , Quintanilla Norma M. , Lopez-Terrada Dolores , Roy Angshumoy , Parsons Donald Williams 
Published: February 2019

Abstract
Background: Papillary thyroid carcinomas (PTC) comprise 90% of thyroid cancers in children. Pediatric PTC is known to be clinically and biologically different than adult PTC, with pediatric tumors more likely to present with metastases and less likely to have the typical alterations found in adult tumors, including BRAF V600E mutations and RET alterations. While the prognosis for pediatric PTC is generally good, some patients with metastatic and/or refractory disease have poorer outcomes and novel treatment approaches are needed. Given the relative lack of genomic information available for pediatric PTC, we sought to perform integrated DNA and RNA-based sequencing of a cohort of clinically annotated tumors in order to identify genetic alterations that might inform improved diagnostic and therapeutic approaches for these patients.
Methods: Potential cases were identified through review of the Texas Children’s Hospital Pathology archives for the years 2005-2016. Clinical review of each patient chart was performed, with metastatic and treatment-refractory tumors prioritized for analysis. Nucleic acids (DNA/RNA) were extracted from FFPE tumor samples with sufficient tissue available. Tumor DNA was captured using a custom-designed next-generation mutation panel that includes the entire coding regions and select noncoding regions of 124 genes implicated in pediatric solid tumors. Tumor RNA was assessed for fusions using a commercially available multiplex gene fusion panel (Archer Oncology Research panel) targeting 75 pediatric solid tumor genes. Sequencing was performed on an Illumina MiSeq. After completion of DNA/RNA mutation panel testing in all available cases, more comprehensive analyses (exome sequencing, capture transcriptome sequencing) will be performed on cases in which driver alterations are not identified. Putative driver alterations will be confirmed by targeted DNA/RNA testing.
Results: A total of 41 pediatric PTC cases were prioritized for analysis. Of those, 40 were from patients of age 8-18 years, with a single sample from a 23-year-old. The majority of patients were metastatic to cervical lymph nodes (31/40, 77.5%), and just over one third of those patients were found to have additional pulmonary metastases (11/31, 35.5%). The male-to-female ratio was 1:3. Relapsed or refractory disease occurred in 18 patients (18/41, 44%). Nucleic acid extractions have been completed for 29 cases. DNA sequencing has been performed for 11 cases, revealing potentially targetable mutations in 6 tumors (54%): BRAF p.V600E x 4, PIK3R1 p.Y29fs, and PTPN11 p.S502T. RNA samples have been successfully sequenced for 16 cases, identifying potentially targetable fusions in 8 tumors (50%): NTRK3 x 4 (both known and novel fusions), BRAF x 2, and RET x 2. All driver alterations detected in cases successfully subjected to both DNA and RNA sequencing to date are mutually exclusive, with a single alteration per tumor.
Conclusions: Frequent alterations were identified in known cancer genes in pediatric PTC cases, many of which are currently targetable with FDA-approved or investigational agents (e.g., MAPK pathway inhibitors; PI3K pathway inhibitors, other kinase inhibitors). Use of both DNA and RNA panel sequencing targeting genes known to be altered in pediatric solid tumors has the potential to identify alterations of clinical relevance in a majority of pediatric PTC patients.
Citation Format: Samara L. Potter, Jacquelyn Reuther, Ilavarasi Gandhi, Faith Hollingsworth, Hadi Sayeed, Horatiu Voicu, Nipun Kakkar, Koel Sen Baksi, Stephen F. Sarabia, Monica E. Lopez, Daniel C. Chelius, Ioanna D. Athanassaki, Rajkumar Venkatramani, Norma M. Quintanilla, Dolores Lopez-Terrada, Angshumoy Roy, Donald Williams Parsons. Integrated sequencing of pediatric thyroid carcinoma reveals frequent targetable alterations [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A36.