Aberrant Splicing of in Families With Unexplained Succinate Dehydrogenase-Deficient Paragangliomas.

Context: Germline mutations in the succinate dehydrogenase genes (///, -collectively, "") have been implicated in paraganglioma (PGL), renal cell carcinoma (RCC), gastrointestinal stromal tumor (GIST), and pituitary adenoma (PA). Negative SDHB tumor staining is indicative of SDH-deficient tumors, usually reflecting an underlying germline mutation. However, approximately 20% of individuals with SDH-deficient tumors lack an identifiable germline mutation.

Methods: We performed whole-exome sequencing (WES) of germline and tumor DNA followed by Sanger sequencing validation, transcriptome analysis, metabolomic studies, and haplotype analysis in 2 Italian-Australian families with SDH-deficient PGLs and various neoplasms, including RCC, GIST, and PA.

Results: Germline WES revealed a novel intronic variant, which had been missed during previous routine testing, in 4 affected siblings of the index family. Transcriptome analysis demonstrated aberrant splicing, with the retained intronic segment introducing a premature stop codon. WES of available tumors in this family showed chromosome 1 deletion with loss of wild-type in a PGL and a somatic gain-of-function mutation in a GIST. The intronic variant identified was subsequently detected in the second family, with haplotype analysis indicating a founder effect.

Conclusions: This is the deepest intronic variant to be reported among the genes. Intronic variants beyond the limits of standard gene sequencing analysis should be considered in patients with SDH-deficient tumors but negative genetic test results.