Comprehensive genetic screening of pheochromocytoma and paraganglioma through targeted capture and next generation sequencing

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-42
Joakim Crona*, Peter StÃ¥lberg, Per Hellman and Peyman Björklund
Uppsala University, Uppsala, Sweden
Background: Recent studies show that up to 60% of Pheochromocytomas (PCC) and Paragangliomas (PGL) have germline or somatic mutations in one of the eleven described disease causing genes. These genes together comprise 24k bases in 142 exons and a genetic screening test can be both extensively time-consuming and expensive.

Methods; Frozen tumour samples from 88 PCC or PGL were included. An Illumina Truseq custom amplicon assay was designed to cover known PCC and PGL disease causing genes. Libraries were multiplexed and sequenced on a single run on an Illumina MiSEQ instrument. Previous results from Sanger sequencing of all fragments of SDHB, SDHC, SDHD, SDHAF2, VHL, RET (exons 10-11 and 13-16), TMEM127 and MAX had been utilized as control, including 32 patients with confirmed pathogenic mutations.

Results; Average coverage was 726 reads per base pair and 97% of bases achieved 10X coverage. For pathogenic single nucleotide variants (SNVs), the sensitivity and specificity compared to Sanger sequencing was 100 and 96% respectively. In addition, there were 40 unique non-synonymous SNVs in NF1. A second sequencing run has been performed, reproducibility between independent runs will be calculated.

Conclusion: Targeted capture and next generation sequencing offers powerful and cost-effective specifications in the clinical genetics screening of PCC and PGL. Although further optimization is required for clinical certification, there are immediate benefits if utilized as a research application.

Nothing to Disclose: JC, PS, PH, PB

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Sources of Research Support: Swedish Cancer Society; Swedish Society for Medical Research; Selander Foundation; Lions club Uppsala. PB is a Swedish Cancer Society Investigator