Integrated DNA and RNA sequencing reveals targetable alterations in
metastatic pediatric papillary thyroid carcinoma
Background: Pediatric papillary thyroid carcinoma (PTC) is clinically
and biologically distinct from adult PTC. We sequenced a cohort of
clinically-annotated pediatric PTC cases enriched for high-risk tumors
to identify genetic alterations of relevance for diagnosis and therapy.
Methods: Tumor DNA and RNA were extracted from FFPE tissue and subjected
to next generation sequencing (NGS) library preparation using a custom
124 gene hybridization capture panel and the 75 gene Archer Oncology
Research Panel, respectively. NGS libraries were sequenced on an
Illumina MiSeq. Results: Thirty-six pediatric PTC cases were analyzed.
Metastases were frequently observed to cervical lymph nodes (29/36,
81%), with pulmonary metastases less commonly found (10/36, 28%).
Relapsed or refractory disease occurred in 18 patients (18/36, 50%).
DNA sequencing revealed targetable mutations in 8 of 31 tumors tested
(26%), most commonly BRAF p.V600E (n=6). RNA sequencing identified
targetable fusions in 13 of 25 tumors tested (52%): RET (n=8), NTRK3
(n=4), and BRAF. Mutually-exclusive targetable alterations were
discovered in 15 of the 20 tumors (75%) with both DNA and RNA analyzed.
Fusion positive PTC was associated with multifocal disease, higher tumor
staging, and higher American Thyroid Association (ATA) risk levels. Both
BRAF V600E mutations and gene fusions were correlated with the presence
of cervical metastases. Conclusions: Targetable alterations were
identified in 75% of pediatric PTC cases with both DNA and RNA
evaluated. Inclusion of RNA sequencing for detection of fusion genes is
critical for evaluation of these tumors. Patients with fusion positive
tumors were more likely to have features of high-risk disease.