J Endocr Soc.  2020  Dec  01.  4(12): bvaa071
Sunita M C De Sousa, 
John Toubia, 
Tristan S E Hardy, 
Jinghua Feng, 
Paul Wang, 
Andreas W Schreiber, 
Joel Geoghegan, 
Rachel Hall, 
Lesley Rawlings, 
Michael Buckland, 
Catherine Luxford, 
Talia Novos, 
Roderick J Clifton-Bligh, 
Nicola K Poplawski, 
Hamish S Scott, 
David J Torpy.
 
  
Context: Germline mutations in the succinate dehydrogenase genes (SDHA/B/C/D, SDHAF2-collectively, "SDHx") 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 SDHx mutation. However, approximately 20% of individuals with SDH-deficient tumors lack an identifiable germline SDHx 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 SDHC intronic variant, which had been missed during previous routine testing, in 4 affected siblings of the index family. Transcriptome analysis demonstrated aberrant SDHC 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 SDHC in a PGL and a somatic gain-of-function KIT mutation in a GIST. The SDHC 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 SDHx 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.
Keywords:  SDHC; intronic mutation; paraganglioma; succinate dehydrogenase; whole-exome sequencing