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Johan Lindberg

Researcher

Research description

I am working at Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet, as a senior researcher with a focus on cancer genomics. 

I have established and is responsible for an infrastructure serving large biomarker driven randomised clinical trials. The infrastructure encompasses reception and storage of biomaterial, subsequent processing for Illumina sequencing and analysis using an in-house developed bioinformatics pipeline.

Continuous assay- and informatics development is essential to ensure that state of the art profiling is available for the clinical trials we are running. My team is therefore devoted to pushing the boundaries of assay development and incorporating new knowledge generated from other research groups into our infrastructure. We were first to develop an assay capable of identifying the microsatellite instability phenotype by analysis of dying cancer cell DNA debris extracted from plasma (circulating tumor DNA). In addition, the androgen receptor is the key transcription factor in metastatic prostate cancer. Treatment targeting the androgen receptor gives rise to multiple types of somatic perturbations associated with poor prognosis. These have commonly been investigated individually in retrospective studies with doubtful clinical utility. Therefore we have established a comprehensive liquid biopsy profile investigating all types of somatic perturbations simultaneously and found that multi-level profiling of the androgen receptor is required for improved patient stratification

My team consist of two bioinformaticians, three research engineers and one postdoc. We are currently responsible for prospective genomic profiling in several projects including:

ALASCCA

ALASCCA is a randomized prospective clinical trial investigating the effect of adjuvant aspirin treatment of PI3K mutated localized colorectal cancer. Patients are included from a network of 32 hospitals in Sweden, Denmark, Finland and Norway. Inclusion was initiated in the fall of 2016 and currently (2020-05-21) 2741 colorectal cancer cases have been profiled by broad panel sequencing with two weeks turnover. The trial will run until approximately 4000 study participants have been included.

ProBio

ProBio is a biomarker driven prospective clinical trial addressing the unmet need for treatment predictive biomarkers in advanced prostate cancer. ProBio is currently including patients from a nation-wide network of hospitals in Sweden and will soon open sites Belgium and Norway. Due to the difficulty of obtaining metastatic biopsies in metastatic prostate cancer we developed a circulating tumor DNA sequencing profile tailored for advanced prostate cancer that is applied in ProBio. The circulating tumor DNA sequencing profile enables detection of:

  • Mutations, amplifications and genomic rearrangements in the androgen receptor.
  • Mutations, genomic rearrangements and amplifications/deletions in key genes involved in prostate cancer.
  • DNA-repair deficiency.
  • Microsatellite instability and hypermutated cancers.

PSFF (Pre-screening for phase I clinical trials)

PSFF is a pilot project conducted together with the Personalised Cancer Medicine Program at Karolinska Institutet (PCM) with the goal to establish a routine molecular screening program for patients with advanced cancer in Stockholm. Currently (2020-05-21), 71 of 200 planned patients have been profiled using prospective broad panel sequencing of circulating tumor DNA. 

Teaching portfolio

I am teaching whenever I get the chance with a focus on cancer genomics and bioinformatics.

Education

  • 2003 Master of Science in Engineering Biology, Umeå University, Umeå.
  • 2008 PhD in Biotechnology, Royal Institute of Technology, Stockholm.
  • 2009-2013 Postdoc at Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm.
  • 2013-2017 Assistant Professor at Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm.
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