Genetic classification is gaining increasing traction in refining the diagnosis and prognosis of thyroid cancer. Comprehensive mutation analysis is currently only available at specialized overseas centers. We sought to develop a suitable next generation sequencing (NGS) platform and to examine the mutation profile of a group of aggressive tumours.
Previously published platforms for targeted analysis of thyroid cancer were collated with findings from The Cancer Genome Atlas project. DNA and RNA panels were designed to detect point mutations and indels in 58 genes; and 52 gene fusions respectively.
Nucleic acids were extracted from frozen and formalin-fixed paraffin-embedded (FFPE) tissue. DNA was initially analysed using the Agilent Haloplex® system and subsequently the Agilent SureSelect® system. RNA was analysed using the NuGEN Ovation® system. Sequencing was performed on the Illumina MiSeq platform and data analysed using proprietary software.
DNA analysis on 23 tumours with the Agilent Haloplex® system identified most previously known mutations but showed inconsistent coverage across target regions. Subsequent analysis with the SureSelect® system showed consistent coverage for all 16 samples; mutations were identified in 12/16 (75%). In a group of aggressive tumours, dual TERT C282T and BRAFV600E or NRASQ61R mutations were identified in 8/16 (50%). Additional mutations were identified in KRAS, RET, TP53, PIK3CA and ARID1B.
RNA analysis was performed on 31 tumours (19 frozen; 12 FFPE) that had previously tested negative for point mutations in BRAF or RAS. Analysis was possible in 23/31 (74%). Gene fusions were identified in 8/31 (26%) and included RET/PTC1, PAX/PPARgamma, ETV6/NTRK3, TPM3/NTRK1 and BRAF/CCNY.
In this study, we demonstrated the feasibility of comprehensive genetic analysis of thyroid tumours using NGS. This approach is efficient and cost effective. Further work will be required to test its suitability for FNA analysis and to integrate genetic testing into clinical practice.