PheoSeq

Abstract

Genetic diagnosis is recommended for all pheochromocytoma and paraganglioma (PPGL) cases, as driver mutations are identified in approximately 80% of the cases. As the list of related genes expands, genetic diagnosis becomes more time-consuming, and targeted next-generation sequencing (NGS) has emerged as a cost-effective tool. This study aimed to optimize targeted NGS in PPGL genetic diagnostics. A workflow based on two customized targeted NGS assays was validated to study the 18 main PPGL genes in germline and frozen tumor DNA, with one of them specifically directed toward formalin-fixed paraffin-embedded tissue. The series involved 453 unrelated PPGL patients, of whom 30 had known mutations and were used as controls. Partial screening using Sanger had been performed in 275 patients. NGS results were complemented with the study of gross deletions. NGS assay showed a sensitivity ≥99.4%, regardless of DNA source. We identified 45 variants of unknown significance and 89 pathogenic mutations, the latter being germline in 29 (7.2%) and somatic in 58 (31.7%) of the 183 tumors studied. In 37 patients previously studied by Sanger sequencing, the causal mutation could be identified. We demonstrated that both assays are an efficient and accurate alternative to conventional sequencing. Their application facilitates the study of minor PPGL genes, and enables genetic diagnoses in patients with incongruent or missing clinical data, who would otherwise be missed.

A Next-Generation Sequencing Primer—How Does It Work and What Can It Do?

“…Test results can be helpful for the initial diagnosis, tumor classification, determining the origin of the cancer, and prognosis. 76 Table 2 77 – 130 provides a partial list of cancers where NGS information has provided value for managing patients. Thyroid nodules are a specific example where fine needle aspiration and cytologic examination may not yield a definitive diagnosis, while NGS has been shown to have high specificity and sensitivity for cancer detection.…”

Metabolic implications of hypoxia and pseudohypoxia in pheochromocytoma and paraganglioma

“…Approximately 40% of the PPGL tumours carry a germ line mutation in one of a number of susceptibility genes, which makes PPGL the cancer syndrome with the highest reported degree of heritability (Dahia 2014 ). More recently, apparently sporadic cases were shown to harbour somatic mutations in known susceptibility genes (and some newly defined genes) which raises the number of a genetic driver event in these cancers to up to 70–80% (Burnichon et al 2016 ; Curras-Freixes et al 2017 ).…”

Next-generation panel sequencing identifies NF1 germline mutations in three patients with pheochromocytoma but no clinical diagnosis of neurofibromatosis type 1

“…Since no mutation could be detected, DNA derived from the thyroid carcinoma was analyzed with regards to somatic mutations in RET, NRAS, KRAS and MERTK. When again the analysis did not confirm a mutation, a panel-based NGS approach, using a customized panel including all PPGL-associated genes, was applied to the pheochromocytoma-derived DNA (30).…”