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Identification of Multiple Novel Oncogenic Mutations in Thyroid Cancer
Susan Pitt1, Roland Hernandez2, Daniel Ruan2, Francis Moore2, Matthew Nehs2, Atul Gawande2, Nancy Cho2
1University of Wisconsin Hospital and Clinics, Madison, WI, 2Brigham and Women's Hospital, Boston, MA

Background:
Innovative therapies are needed for patients with advanced thyroid cancer refractory to conventional treatments. We sought to identify novel oncogenic mutations in human thyroid cancers with newly developed genomic assays not yet applied in this population.

Methods:
Samples from 239 human thyroid cancers were collected between January 2009 and September 2014 and analyzed with OncoMap-4 or OncoPanel multiplexed cancer assays detecting somatic mutations and variants in exonic DNA structure and copy number. The sequencing surveyed up to 275 cancer genes (91 introns across 30 genes) for DNA rearrangement.

Results:
We identified 351 unique oncogenic mutations in a total of 129 oncogenes or tumor suppressors. Mutations occurred in 85% of papillary (PTC), 4% of follicular (FTC), 7% of medullary (MTC), and 4% of anaplastic (ATC) thyroid cancers. Analysis revealed that 17% of the somatic mutations were novel. Three of the gene alterations occurred in both PTC and MTC (TET2, CIITA, and RHPN2), and consisted of 10 individual single nucleotide polymorphisms (SNPs). Two other unique mutations were identified in PTC and ATC specimens, EXT1 and EXT2, respectively. Additional novel oncogenic mutations discovered only in PTC involved: CBL, AR, BLM, BRD4, EP300, MPL, PRAME, SBDS, CD274, GSTM5, LMO2, SF1, SUZ12, TNFAIP3, XPO1, ZRSR2, and PARK2.

Conclusions:
This analysis revealed several previously unreported unique gene alterations in thyroid cancers that may be targets for the development of future therapies. In addition, we identified two novel oncogenic mutations in the EXT gene family that may play a role in dedifferentiation of PTCs.



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