title: Silent genetic alterations identified by targeted next-generation sequencing in pheochromocytoma/paraganglioma: A clinicopathological correlations.
abstract: The goal of this pilot study was to develop a customized, cost-effective amplicon panel (Ampliseq) for target sequencing in a cohort of patients with sporadic phaeochromocytoma/paraganglioma.
  
  
  
  Phaeochromocytoma/paragangliomas from 25 patients were analysed by targeted next-generation sequencing approach using an Ion Torrent PGM instrument. Primers for 15 target genes (NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, MAX, MEN1, KIF1Bβ, EPAS1, CDKN2 & PHD2) were designed using ion ampliseq designer. Ion Reporter software and Ingenuity® Variant Analysis™ software (www.ingenuity.com/variants) from Ingenuity Systems were used to analysis these results.
  
  
  
  Overall, 713 variants were identified. The variants identified from the Ion Reporter ranged from 64 to 161 per patient. Single nucleotide variants (SNV) were the most common. Further annotation with the help of Ingenuity variant analysis revealed 29 of these 713variants were deletions. Of these, six variants were non-pathogenic and four were likely to be pathogenic. The remaining 19 variants were of uncertain significance. The most frequently altered gene in the cohort was KIF1B followed by NF1. Novel KIF1B pathogenic variant c.3375+1G>A was identified. The mutation was noted in a patient with clinically confirmed neurofibromatosis. Chromosome 1 showed the presence of maximum number of variants.
  
  
  
  Use of targeted next-generation sequencing is a sensitive method for the detecting genetic changes in patients with phaeochromocytoma/paraganglioma. The precise detection of these genetic changes helps in understanding the pathogenesis of these tumours.
authors.affiliation: Cancer Molecular Pathology, School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.
authors.forename: Suja
authors.initials: S
authors.lastname: Pillai
authors.affiliation: Cancer Molecular Pathology, School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.
authors.forename: Vinod
authors.initials: V
authors.lastname: Gopalan
authors.affiliation: Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong.
authors.forename: Chung Y
authors.initials: CY
authors.lastname: Lo
authors.affiliation: Department of Surgery, Gold Coast University Hospital, Gold Coast, Australia.
authors.forename: Victor
authors.initials: V
authors.lastname: Liew
authors.affiliation: Cancer Molecular Pathology, School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia; Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Smith
authors.affiliation: Cancer Molecular Pathology, School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia. Electronic address: a.lam@griffith.edu.au.
authors.forename: Alfred King Y
authors.initials: AK
authors.lastname: Lam
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease / Q000235:genetics; D018095:Germ-Line Mutation; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D016547:Kinesins / Q000235:genetics; D008297:Male; D008875:Middle Aged; D009154:Mutation; D025542:Neurofibromin 1 / Q000235:genetics; D010235:Paraganglioma / Q000235:genetics* / Q000473:pathology; D010673:Pheochromocytoma / Q000235:genetics* / Q000473:pathology; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies; D013385:Succinate Dehydrogenase / Q000235:genetics; D055815:Young Adult
chemical_list: C091053:KIF1B protein, human; D025542:Neurofibromin 1; D013385:Succinate Dehydrogenase; D016547:Kinesins
keywords: Next generation sequencing; Paraganglioma; Phaeochromocytoma