In 2020, the Cancer Informatics project group was established as part of Rolf Skotheim’s Genome Biology group within the Department of Molecular Oncology.

The project group has three main focus areas:

• On the research side, we are involved in various projects, primarily on prostate, colorectal and ovarian cancer. In the department, we have access to comprehensive research biobanks for various types of solid tumors, and researchers with different types of expertise and background complement eachother in a multi-disciplinary research environment. In the Cancer Informatics project group, we make use of programming (primarily Python and R) and informatics tools to develop methods and implement algorithms that are aiming to increase our knowledge of how solid tumors progress. We also try to develop biomarkers and to classify cancers into various risk-groups based on molecular data.
• Teaching. We give lectures in bioinformatics and are involved in supervision of bioinformatics students at the MSc and PhD level.
• We offer cross-group bioinformatics services within the Department of Molecular Oncology. Recent advances in sequencing technology, and extensive collaboration with the in-house core facility section that offer a well-functioning sequencing infrastructure, have made it possible to analyze numerous molecular properties pan-cancer. In our project group, we have implemented several downstream analysis pipelines for management and analysis of genomic, transcriptomic and methylation data, with the aim to translate raw data into meaningful bio-medical knowledge.

We collaborate with Sigma2/NRIS (Norwegian Research Infrastructure Services), and are grateful for the opportunity to use their large Linux clusters for management of sensitive data, and also for offering computational resources.

Selected publications:

Sveen A, Johannessen B, Klokkerud SM, Kraggerud SM, Meza-Zepeda LA, Bjørnslett M, Bischof K, Myklebost O, Taskén K, Skotheim RI, Dørum A, Davidson B, Lothe RA (2024)
Evolutionary mode and timing of dissemination of high-grade serous carcinomas
JCI Insight, 9 (3)
DOI 10.1172/jci.insight.170423, PubMed 38175731

Meier Strømme J, Johannessen B, Skotheim RI (2023)
Deviating Alternative Splicing as a Molecular Subtype of Microsatellite Stable Colorectal Cancer
JCO Clin Cancer Inform, 7, e2200159
DOI 10.1200/CCI.22.00159, PubMed 36821799

Carm KT, Johannessen B, Bogaard M, Bakken AC, Maltau AV, Hoff AM, Axcrona U, Axcrona K, Lothe RA, Skotheim RI (2022)
Somatic mutations reveal complex metastatic seeding from multifocal primary prostate cancer
Int J Cancer, 152 (5), 945-951
DOI 10.1002/ijc.34226, PubMed 35880692

Strømme JM, Johannessen B, Kidd SG, Bogaard M, Carm KT, Zhang X, Sveen A, Mathelier A, Lothe RA, Axcrona U, Axcrona K, Skotheim RI (2022)
Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity
Cancer Gene Ther, 29 (8-9), 1276-1284
DOI 10.1038/s41417-022-00444-7, PubMed 35194199

Sveen A, Johannessen B, Eilertsen IA, Røsok BI, Gulla M, Eide PW, Bruun J, Kryeziu K, Meza-Zepeda LA, Myklebost O, Bjørnbeth BA, Skotheim RI, Nesbakken A, Lothe RA (2021)
The expressed mutational landscape of microsatellite stable colorectal cancers
Genome Med, 13 (1), 142
DOI 10.1186/s13073-021-00955-2, PubMed 34470667

Sveen A*, Johannessen B*, Tengs T*, Danielsen SA, Eilertsen IA, Lind GE, Berg KCG, Leithe E, Meza-Zepeda LA, Domingo E, Myklebost O, Kerr D, Tomlinson I, Nesbakken A, Skotheim RI, Lothe RA (2017)
Multilevel genomics of colorectal cancers with microsatellite instability-clinical impact of JAK1 mutations and consensus molecular subtype 1
*Equal contributors
Genome Med, 9 (1), 46
DOI 10.1186/s13073-017-0434-0, PubMed 28539123

Johannessen B, Sveen A, Skotheim RI (2015)
TIN: An R Package for Transcriptome Instability Analysis
Cancer Inform, 14, 109-12
DOI 10.4137/CIN.S31363, PubMed 26448683

Outreach – Popular science

Johannessen, Strømme, Skotheim, The quest for biomarkers in prostate cancer: Multi-sample transcriptomics overcomes heterogeneity and reveals genes with prognostic biomarker potential, Nature Portfolio Communities (2022)

Johannessen, Berg, Bruk av udødelige cellelinjer på tarmkreft, Best Practice (2017)

Johannessen, Skotheim, From numbers and sequences to personalized cancer treatment: Challenges and opportunities as medicine enters the era of big data, Meta Magazine (2015)