Endocrine Abstracts (2016) 46 P9 | DOI: 10.1530/endoabs.46.P9

Whole-exome sequencing (WES) of samples from patients with advanced pancreatic neuroendocrine tumours (pNETs) with exceptional responses vs. poor responders to targeted therapies; a TransNET study

Jorge Barriuso1, Angela Lamarca1, Mairéad McNamara1, Timothy Burgis2, Prakash Manoharan1, Andrew Hayes3, Wasat Mansoor1, Richard Hubner1 & Juan Valle1


1The Christie NHS Foundation Trust (ENETS Centre of Excellence), Manchester, UK; 2Bioinformatics Core Facility, Faculty of Biology, Medicine and Health, Manchester, UK; 3Genome Core Facility. Faculty of Biology, Medicine and Health, Manchester, UK.


Background: Despite encouraging advances in the systemic therapy options for patients with pNETs (sunitinib and everolimus), no predictive biomarkers have been established for these drugs. We aimed to identify distinctive genomic alterations associated with benefit from treatment in patients with pNETs, by comparing exceptional-responders (ER) to poor-responders (PO).

Methods: Patients who achieved an objective radiological response (complete or partial) by RECIST 1.1, due to its exceptionality (5% for everolimus and 9.3% for sunitinib) in landmark trials, were included in the ER group together with those with a progression-free survival (PFS) beyond the median reported in the registration trials. Patients with a similar PFS to the placebo groups in the pivotal trials were classified as PO.

Deoxyribonucleic acid (DNA) was extracted from archival formalin-fixed paraffin-embedded (FFPE) tumour samples (T) and normal tissue (NT) or blood (B). Paired-end libraries were prepared using Illumina’s Nextera Rapid Capture Expanded Exome enrichment kit. Illumina HiSeq2500 was used for the sequencing with a >100x coverage of the exomes. VarDict software was used for variant calling. Manchester Cancer Research Centre biobank approval for the study was obtained; all patients provided written informed consent.

Results: Thirty-one patients were screened; following review of availability and quality of the FFPE samples, 12 were found eligible to proceed with DNA extraction and sequencing. For these 12 cases, paired DNA extracted from T and NT or B was obtained. Five of the 12 patients received treatment with both drugs (everolimus and sunitinib, sequentially in either order). Overall, 11 received everolimus and 6 received sunitinib; 9 and 5 patients were classified as ER to everolimus and sunitinib, respectively. Only 3 PO were identified (everolimus (2 patients); sunitinib (1 patient)). All samples were sequenced and passed the standard quality check to proceed with the bioinformatic analysis. Interpretation of results is ongoing.

Conclusion: It is feasible to find patients with a pNET diagnosis phenotypically distinct in relation to their responses and to perform WES from FFPE samples. Final WES results of this TransNET study will be presented at the meeting.