Clinicial Cancer Genomics – Johan Lindberg's research group

The Cancer Genomics research team is focused on biomarker discovery and assay- and informatics development with a special interest in liquid biopsies. The team is responsible for genomic analysis of prospective research projects and randomized trials.

DNA genetic code

Our research

My team has established and is responsible for a sample- and analysis process at KI/SciLife to enable biomarker driven randomized clinical trials and prospective research projects. The process encompasses reception and storage of biomaterial, subsequent processing for Illumina sequencing and analysis using an in-house developed bioinformatics pipeline and curation software. The setup is made possible through collaboration with KI biobank and Clinical Genomics at SciLife lab. Since 2016 >5500 samples from >50 hospitals in 6 European countries has been analysed and reported. The main studies have been ALASCCA and ProBio. The first result from the ProBio trial was published in Nature Medicine and the ALASCCA trial met its primary endpoint which was recently presented at ASCO-GI.

The sample- and analysis process has been optimized, enabling a two-week turnover of results even to trial sites in other countries such as Belgium. Consequently, the weekly team activities have strong similarities to a routine diagnostic setting with tight timelines and uptime requirements. To give patients in clinical routine access to improved diagnostics and state-of-the art genomics the iPCM (implementation of Personalized Cancer Medicine) project was launched in late 2020 with the goal to implement the research infrastructure for genomic profiling in clinical routine at Clinical Pathology, Karolinska Hospital. Hitherto, genomic analysis of prostate cancer and ovarian cancer has been implemented as routine diagnostic tests with many more yet to come.

Collectively, the large prospective research projects provides a unique resource for cancer genomics assay development and retrospective biomarker discovery projects. 

Publications

All publications from group members

Funding

Grants

  • Swedish Cancer Society
    1 January 2024
    This project was started to develop precision medicine for disseminated prostate cancer. All healthy individuals have DNA from dead cells in their blood. In patients with cancer, some of the free-floating DNA in blood comes from the cancer cells. This DNA is called circulating tumor DNA. In this project, new technology will be used to explore different uses for circulating tumor DNA, for example whether it can be used to follow treatment response and determine treatment choices. The project will study disseminated prostate cancer and all treatments used to treat this disease. The project is about using newly developed technology to identify biomarkers through analysis of circulating tumor DNA. The goal of this project is to provide oncologists with a tool to better follow and understand whether a patient is responding or not responding to a treatment by monitoring ctDNA levels in blood over time. Another goal is to improve treatment choices through analysis of circulating tumor DNA.
  • Swedish Cancer Society
    1 January 2021
    Prostate cancer is the most common form of cancer in Sweden. Although survival is 92% after 5 years, prostate cancer takes the most lives of all cancer types. A challenge with prostate cancer is that many men carry a completely harmless cancer that will not cause any symptoms if left undetected. The widespread PSA testing therefore leads to unnecessary side effects and costs to society. The Stockholm3 test is a blood test based on a combination of biomarkers that was developed to meet these challenges. Combined with new technology that improves the precision of biopsy, the problems have decreased but there is room for improvement. To reduce the problems in screening for prostate cancer, new types of biomarkers are needed. One such biomarker is DNA remnants from dying cancer cells which can be purified and analyzed from plasma. Such DNA residues are called circulating tumor DNA. In this research project, circulating tumor DNA will be analyzed from patients diagnosed with prostate cancer as well as healthy individuals to investigate whether circulating tumor DNA has the potential to identify those men who need treatment and those who should not. The goal of this research is to develop a diagnostic test to improve screening for prostate cancer.

Staff and contact

Group leader

All members of the group

Visiting address

Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Nobels väg 12A, Stockholm, 171 77, Sweden

Postal address

Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, PO Box 281, Stockholm, 171 77, Sweden

Keywords:
Bioinformatics (Computational Biology) (Applications at 10610) Biomarkers Biomarkers, Tumor Cancer and Oncology Genes, Neoplasm Genomics Liquid Biopsy Medical Bioinformatics and Systems Biology Medical Genetics and Genomics Prospective Studies Show all
Content reviewer:
04-09-2025