Circulating tumour DNA, a new tool for personalized cancer treatment
Sirkulerende tumor DNA, et nytt verktøy for persontilpasset kreftbehandling
The project aims to offer biomarkers in liquid biopsies in clinical cancer related studies in our hospital region to better measure treatment response and guide treatment choices. Routines for biobanking have been established in clinical trials. Circulating tumor DNA has been searched for in operable pancreatic cancer and melanomas with success.
The project has included funding for two of the sub-projects of the larger «Persontilpassa kreftbehandling – biomarkørar og kliniske studier»; sub-project 4) Biobanking and Logistics, and sub-project 1) Circulating Tumor DNA. In this project a biobank connected to the research facilities for clinical studies is to be established. This includes creation of an EK document, tracking system, health register as well as physical storage of samples and establishment of administrative solutions. To facilitate this, a project group consisting of clinicians, study nurses and unique personnel processing samples before and after biobanking has been created. The project group has been involved in testing and adjusting of the biobanking protocol using several small clinical studies, and the major pilot of the protocol for larger studies will be BGBIL006 initiating in 2017. The biobanking system established at Helse Bergen will be used actively in the “Persontilpassa kreftbehandling”-project. In order to perform the project we need biobanked material and as this will take some time we have through collaboration had access to already biobanked material. For detection of circulating tumor DNA new methodologies have to be established. For an NGS based approached samples from 147 leukemia patients were used as a pilot to establish sample logistics, library preparation, as well as bioinformatical processing of data and sequence interpretation for a 54-gene panel (sequencing performed at the Mohn laboratories). The results from this analysis are included in several different projects, submitted article (Reikvam et al., Genome Medicine, 2016), two other manucscripts in preparation. Data generated from this gene panel has been used to further develop the web-based NGS analysis software CoreMine Oncology (PubGene). We have in 2016 increased the security, and developed the analysis module to include more severity prediction algorithms, higher levels of filtering and in general highly increasing the user friendliness for scientists. For operable pancreatic ductal adenocarcinoma different methodologies were evaluated for its ability to detect mutations in KRAS and TP53 in different sample materials from 14 patients (collaboration with Prof A. Molven). Mutations where found in 13/14 samples when using dissected FFPE. Cell free DNA was isolated from pancreatic juice and plasma. ctDNA was present all of the pancreatic juice samples but none of the I not detected by PNA-clamp in any plasma sample despite high levels of cell free DNA present. One master student graduated on this project in 2016, and this will be further developed by a recruited PhD candidate in 2017. Our collaborators in Stavanger (Nordgård and Tjensvoll) are currently developing a pancreas gene panel for ctDNA, and our samples will be sequenced at SUS in the future. The study of malignant melanoma treated with Avastin (collaboration with Prof O.Straume) cell free DNA from 39/44 patients was explored guided by results from Sanger and/or NGS gene panel sequencing. By digital droplet PCR ctDNA was detected in 20/24 patients samples, and a significant change in ctDNA was shown to correlate with clinical data. (manuscript in preparation). A broader mutation profiling of ctDNA will be performed on 10 patients (collaboration with Prof. L. Meza-Zapeda).