423P - A targeted cancer clinical sequencing system based on a clinical biobank in Hokkaido University Hospital

Date 17 December 2016
Event ESMO Asia 2016 Congress
Session Poster lunch
Topics Diagnostics
Personalised Medicine
Presenter Hiroshi Nishihara
Citation Annals of Oncology (2016) 27 (suppl_9): ix132-ix133. 10.1093/annonc/mdw591
Authors H. Nishihara1, H. Hayashi2, S. Tanishima3, R. Mori3, I. Kinoshita4, Y. Komatsu5, H. Dosaka-Akita4
  • 1Division Of Clinical Cancer Genomics, Hokkaido University Hospital, 060-8648 - Sapporo/JP
  • 2Division Of Clinical Cancer Genomics, Hokkaido University Hospital, 060-8638 - Sapporo/JP
  • 3Biomedical Informatics, Mitsubishi Space Software, 661-0001 - Amagasaki/JP
  • 4Medical Oncology, Hokkaido University Hospital, 060-8648 - Sapporo/JP
  • 5Cancer Center, Hokkaido University Hospital, 060-8638 - Sapporo/JP

Abstract

Background

Development of genomic medicine enables us to perform contemporary clinical sequencing, while the acquision of high quality biospecimen and the appropriate handling of these materials are indispensable. In Hokkaido University, we have started Clinical Biobank, a novel system for On-Demand type banking in 2014. We obtain biospecimens including blood and tissue fixed by PAXgene Tissue system, and extract DNA and RNA from PAX-fixed paraffin embedded sample with the high quality and enough amounts for clinical sequencing after the pathological evaluation. Using this clinical biobank workflow, we have established the Division of Clinical Cancer Genomics for cancer personalized medicine, and started cancer clinical sequencing as a clinical examination.

Methods

We developed a novel cancer clinical sequencing system by amplicon exome sequence targeting 160 cancer genes; CLHURC (Clinical Sequence System in Hokkaido University Hospital for Cancer Individualized Medicine) collaborating with Mitsubishi Space Software Co. Ltd (MSS). In our system, genomic DNA was extracted from both tumor tissue and peripheral blood mononuclear cells as a normal control, and perform deep sequencing using MiSeq. FastQ files were analyzed by MSS using original bioinformatics pipeline within 3 business days, and we identified cancer-specific somatic gene alteration such as SNV, Ins/Del and CNV. Finally, cancer board conference consisting of medical oncologists, pathologists, clinical laboratory technologists, bioinformaticians and clinical geneticists proposes the personalized treatment strategies based on the gene profiles.

Results

During 4 months, we examined 43 cancer patients and perform targeted exome sequence. As a result, detection rate of actionable gene mutation and druggable gene mutation was around 86% and 44%, respectively.

Conclusions

We believe that our novel clinical sequencing system using biospecimen based on Clinical Biobank will vigorously promote cancer individualized medicine throughout Japan and also Asia.

Clinical trial indentification

Legal entity responsible for the study

N/A

Funding

Hokkaido University

Disclosure

All authors have declared no conflicts of interest.