Investigating the role of somatic sequencing platforms for phaeochromocytoma and paraganglioma in a large UK cohort

Abstract

Objectives: Phaeochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumours with malignant potential and a hereditary basis in almost 40% of patients. Germline genetic testing has transformed the management of PPGL enabling stratification of surveillance approaches, earlier diagnosis and predictive testing of at-risk family members. Recent studies have identified somatic mutations in a further subset of patients, indicating that molecular drivers at either a germline or tumour level can be identified in up to 80% of PPGL cases. The aim of this study was to investigate the clinical utility of somatic sequencing in a large cohort of patients with PPGL in the United Kingdom.

Design and patients: Prospectively collected matched germline and tumour samples (development cohort) and retrospectively collected tumour samples (validation cohort) of patients with PPGL were investigated.

Measurements: Clinical characteristics of patients were assessed and tumour and germline DNA was analysed using a next-generation sequencing strategy. A screen for variants within 'mutation hotspots' in 68 human cancer genes was performed.

Results: Of 141 included patients, 45 (32%) had a germline mutation. In 37 (26%) patients one or more driver somatic variants were identified including 26 likely pathogenic or pathogenic variants and 19 variants of uncertain significance. Pathogenic somatic variants, observed in 25 (18%) patients, were most commonly identified in the VHL, NF1, HRAS and RET genes. Pathogenic somatic variants were almost exclusively identified in patients without a germline mutation (all but one), suggesting that somatic sequencing is likely to be most informative for those patients with negative germline genetic test results.

Conclusions: Somatic sequencing may further stratify surveillance approaches for patients without a germline genetic driver and may also inform targeted therapeutic strategies for patients with metastatic disease.

Keywords: paraganglioma; phaeochromocytoma; somatic variant.

Figure 1

Flowchart for variant filtering and classification. *Minimum base quality below 20. **On the basis of the data from the Catalogue of Somatic Mutations in Cancer (COSMIC) (https://cancer.sanger.ac.uk/cosmic) or ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/). ***<500 reads was less than two standard deviations below the mean coverage). °Including multiple variants in the same tumour. ^Validation of suspected driver variants was performed using; (i) Sanger sequencing for 10 cases (D73,D77,D78,D79,D84,D87,D88,D95,D97,D98), (ii) Nuclear magnetic resonance spectroscopy to detect 2‐hydroxyglutarate for case D84, (iii) hybrid capture‐based sequencing for case D87, and (iv) SDHB immunohistochemistry for case D77, D86)

Figure 2

Distribution of somatic and germline variants according to molecular clusters. Only pathogenic and likely pathogenic variants of the pooled cohort are shown. Cluster 1: Pseudohypoxia. Cluster 2: Kinase signalling

Figure 3

Clinical and molecular characterisation of cases with identified driver somatic variants. Please note that only patients of the development cohort were included, as detailed clinical information was missing for patients of the validation cohort

Figure 4

Gene wish list for a targeted PPGL (phaeochromocytomas and paragangliomas) gene panel. Gene wish list was selected based on published literature, , , , and the top 20 mutated genes in PPGL on COSMIC (Catalogue of Somatic Mutations in Cancer)