Whole Exome Sequencing is an Efficient and Accurate Technique to Detect Germline Mutations in Patients with Phaeochromocytomas and Paraganglionomas

Program: Abstracts - Orals, Featured Poster Presentations, and Posters
Session: MON 37-82-Pheochromocytoma & Paraganglioma
Monday, June 17, 2013: 1:45 PM-3:45 PM
Expo Halls ABC (Moscone Center)

Poster Board MON-43
Aideen Mcinerney-Leo1, Mhairi Marshall1, Paul J Leo1, Brooke Gardiner1, Diana Benn2, Warrick J Inder3, Matthew A Brown1, Roderick John Clifton-Bligh4 and Emma L Duncan*1
1University of Queensland Diamantina Institute, Woolloongabba, Australia, 2Kolling Inst of Medical Res, St Leonards, Australia, 3Princess Alexandra Hospital, Woolloongabba QLD, Australia, 4Royal North Shore Hospital, Sydney, Australia
Background and Aim: The American College of Clinical Oncology guidelines suggest genetic testing should be offered to individuals with an a priorichance of >10% of carrying a mutation.  A person diagnosed with a phaeochromocytoma (PCC) or paraganglioma (PGL) has a much higher chance of carrying a germline mutation than this.  However, genetic testing is not routine in all patients with PCC/PGL.  In part this may be due to genetic heterogeneity and the prohibitive number of exons requiring sequencing, resulting in high costs.  Some experts recommend taking a targeted approach based on phenotypic features to limit costs, with sequential sequencing of potential genes; however, this frequently results in significant delays in diagnosis.  We aimed to determine whether whole exome sequencing using an off-the-shelf exome chip was an efficient, cost effective and sensitive means of detecting causative mutations in this population.

Methods:  Whole exome sequencing was performed on blinded samples from 7 unrelated individuals with PCC/PGL with mutations previously identified by Sanger sequencing, using the Illumina/TruSeq Exome capture platform. Data was filtered looking for protein coding variants in a gene panel (RET, NF1, VHL, SDHD, SDHB, SDHC, SDHA, SDHAF2, KIF1B, TMEM127, EGLN1 and MAX) and all samples were analysed blindly.

Results: Six out of seven mutations were detected using the Illumina/TruSeq exome capture. The remaining sample in which a mutation was not detected had a mutation in SDHC.  The Illumina/TruSeq exome capture platform has no targeted capture for exons 2, 4, 5 and 6. In contrast, Roche/NimbleGen SeqCap EZ platform captures all exons of SDHC.  The sample has now been re-run using this capture technology.  In comparing the targeted capture regions from the respective companies using R script, Roche/NimbleGen SeqCapEZ captures a greater percentage of the exons in the panel of causative genes compared with the Illumina/TruSeq.

The costs of exome sequencing is approximately $AU1,500 per sample to sequence all known PCC/PGL genes (currently 13) compared to $AU4,100 to sequence only the four most common genes.  The time from receipt of blinded samples to analysed results was less than five weeks.

Conclusions: Whole exome sequencing is a sensitive, rapid, cost-effective method of screening candidate genes for PCC and PGL.  However, platform selection is critical to maximize sensitivity.

Nothing to Disclose: AM, MM, PJL, BG, DB, WJI, MAB, RJC, ELD

*Please take note of The Endocrine Society's News Embargo Policy at http://www.endo-society.org/endo2013/media.cfm

Sources of Research Support: Royal Brisbane and Women's Hospital Foundation