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

Research description

I am heading the Cancer Genomics team at MEB.  The team consists currently of two bioinformaticians, three research engineers and one postdoc. The team has a translational focus, with the goal to pursue clinically relevant research questions. We have developed an informatics infrastructure consisting of in-house developed- and publically available tools to enable live processing of sequencing based data. 

The Cancer Genomics team is responsible for targeted sequencing in a prospective clinical trial investigating the effect of adjuvant aspirin treatment of PI3K mutated localized colorectal cancer. Patient inclusion was initiated in the fall 2016 and during the first year 542 colorectal cancers were profiled with two weeks turnover. Reports with randomization information is being sent on a weekly basis to a national network of 27 participating hospitals. The trial will run until approximately 4000 study participants have been included.

We are conducting large studies in prostate cancer where genomic profiling is used to address tumor grading, prognostication at diagnosis and optimization of treatment in the metastatic setting. 

We have developed a targeted circulating tumour DNA-based profile that enables us to detect:

  • 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 instable and hypermutated cancers.

We are currently preparing to enable live profiling of circulating tumor DNA in metastatic prostate cancer in a clinical trial setting.  The goal is to initiate the clinical trial (ProBio-II) during the fall 2018. 

The Cancer Genomics team is part of a larger research environment with 20-25 persons focused on different aspects of prostate cancer, which is lead by Henrik Grönberg.


Teaching portfolio

I am teaching whenever I get the chance. I am currently co-responsible for the course "Biobanking as a resource for biomedical research".




Somatic alterations detected in diagnostic prostate biopsies provide an inadequate representation of multifocal prostate cancer
Kristiansen A, Bergström R, Delahunt B, Samaratunga H, Guðjónsdóttir J, Grönberg H, et al
The Prostate 2019;():-

TP53 Outperforms Other Androgen Receptor Biomarkers to Predict Abiraterone or Enzalutamide Outcome in Metastatic Castration-Resistant Prostate Cancer
De Laere B, Oeyen S, Mayrhofer M, Whitington T, Van Dam Pj, Van Oyen P, et al
Clinical cancer research : an official journal of the American Association for Cancer Research 2019;25(6):1766-1773

A novel technique for biobanking of large sections of radical prostatectomy specimens
Lindh C, Delahunt B, Samaratunga H, Yaxley J, Gudjónsdóttir J, Clements M, et al
Histopathology 2018;72(3):481-489

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis
Mayrhofer M, De Laere B, Whitington T, Van Oyen P, Ghysel C, Ampe J, et al
Genome medicine 2018;10(1):85-

Development and Validation of a Novel RNA Sequencing-Based Prognostic Score for Acute Myeloid Leukemia
Wang M, Lindberg J, Klevebring D, Nilsson C, Lehmann S, Grönberg H, et al
Journal of the National Cancer Institute 2018;110(10):1094-1101

Differential impact of RB status on E2F1 reprogramming in human cancer
Mcnair C, Xu K, Mandigo Ac, Benelli M, Leiby B, Rodrigues D, et al
The Journal of clinical investigation 2018;128(1):341-358

Expression levels of long non-coding RNAs are prognostic for AML outcome
Mer As, Lindberg J, Nilsson C, Klevebring D, Wang M, Grönberg H, et al
Journal of hematology & oncology 2018;11(1):52-

The Stockholm-3 (STHLM3) Model can Improve Prostate Cancer Diagnostics in Men Aged 50-69 yr Compared with Current Prostate Cancer Testing
Eklund M, Nordström T, Aly M, Adolfsson J, Wiklund P, Brandberg Y, et al
European urology focus 2018;4(5):707-710

Towards Next-generation Urine-based Prostate Cancer Risk Stratification
Nordström T, Lindberg J, Eklund M
European urology 2018;74(6):739-740

Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer
Malgerud L, Lindberg J, Wirta V, Gustafsson-liljefors M, Karimi M, Moro Cf, et al
Molecular oncology 2017;11(10):1413-1429

Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns
De Laere B, Van Dam Pj, Whitington T, Mayrhofer M, Diaz Eh, Van Den Eynden G, et al
European urology 2017;72(2):192-200

Corrigendum to "Integration of Copy Number and Transcriptomics Provides Risk Stratification in Prostate Cancer: A Discovery and Validation Cohort Study" [EBioMedicine 2 (9) (2015) 1133-1144]
Camcap Study Group, Ross-adams H, Lamb Ad, Dunning Mj, Halim S, Lindberg J, et al
EBioMedicine 2017;17():238-

Genetic profile of ductal adenocarcinoma of the prostate
Seipel Ah, Whitington T, Delahunt B, Samaratunga H, Mayrhofer M, Wiklund P, et al
Human pathology 2017;69():1-7

Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling
Karthik Gm, Rantalainen M, Stålhammar G, Lövrot J, Ullah I, Alkodsi A, et al
BMC cancer 2017;17(1):802-

Molecular Differences between Screen-Detected and Interval Breast Cancers Are Largely Explained by PAM50 Subtypes
Li J, Ivansson E, Klevebring D, Tobin Np, Lindström Ls, Holm J, et al
Clinical cancer research : an official journal of the American Association for Cancer Research 2017;23(10):2584-2592

Translating a Prognostic DNA Genomic Classifier into the Clinic: Retrospective Validation in 563 Localized Prostate Tumors
Lalonde E, Alkallas R, Chua Mlk, Fraser M, Haider S, Meng A, et al
European urology 2017;72(1):22-31

Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling
Wang M, Lindberg J, Klevebring D, Nilsson C, Mer As, Rantalainen M, et al
Leukemia 2017;31(10):2029-2036

Determining breast cancer histological grade from RNA-sequencing data
Wang M, Klevebring D, Lindberg J, Czene K, Grönberg H, Rantalainen M
Breast cancer research : BCR 2016;18(1):48-

Gene regulatory mechanisms underpinning prostate cancer susceptibility
Whitington T, Gao P, Song W, Ross-adams H, Lamb Ad, Yang Y, et al
Nature genetics 2016;48(4):387-97

Large-scale evaluation of SLC18A2 in prostate cancer reveals diagnostic and prognostic biomarker potential at three molecular levels
Haldrup C, Lynnerup As, Storebjerg Tm, Vang S, Wild P, Visakorpi T, et al
Molecular oncology 2016;10(6):825-37

Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers
Rantalainen M, Klevebring D, Lindberg J, Ivansson E, Rosin G, Kis L, et al
Scientific reports 2016;6():38037-

The In Vitro Stability of Circulating Tumour DNA
Henao Diaz E, Yachnin J, Grönberg H, Lindberg J
PloS one 2016;11(12):e0168153-

Exome sequencing of contralateral breast cancer identifies metastatic disease
Klevebring D, Lindberg J, Rockberg J, Hilliges C, Hall P, Sandberg M, et al
Breast cancer research and treatment 2015;151(2):319-24

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study
Camcap Study Group, Ross-adams H, Lamb Ad, Dunning Mj, Halim S, Lindberg J, et al
EBioMedicine 2015;2(9):1133-44

Prostate cancer screening in men aged 50-69 years (STHLM3): a prospective population-based diagnostic study
Grönberg H, Adolfsson J, Aly M, Nordström T, Wiklund P, Brandberg Y, et al
The Lancet. Oncology 2015;16(16):1667-76

The RNA-binding protein Sam68 regulates expression and transcription function of the androgen receptor splice variant AR-V7
Stockley J, Markert E, Zhou Y, Robson Cn, Elliott Dj, Lindberg J, et al
Scientific reports 2015;5():13426-

Tracking the origin of metastatic prostate cancer
Lindberg J, Kristiansen A, Wiklund P, Grönberg H, Egevad L
European urology 2015;67(5):819-22

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding
Huang Q, Whitington T, Gao P, Lindberg Jf, Yang Y, Sun J, et al
Nature genetics 2014;46(2):126-35

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence
Genovese G, Kahler Ak, Handsaker Re, Lindberg J, Rose Sa, Bakhoum Sf, et al

Evaluation of exome sequencing to estimate tumor burden in plasma
Klevebring D, Neiman M, Sundling S, Eriksson L, Darai Ramqvist E, Celebioglu F, et al
PloS one 2014;9(8):e104417-

Hypermethylation of the GABRE~miR-452~miR-224 promoter in prostate cancer predicts biochemical recurrence after radical prostatectomy
Kristensen H, Haldrup C, Strand S, Mundbjerg K, Mortensen Mm, Thorsen K, et al
Clinical cancer research : an official journal of the American Association for Cancer Research 2014;20(8):2169-81

Immunohistochemical profile of ductal adenocarcinoma of the prostate
Seipel Ah, Samaratunga H, Delahunt B, Wiklund F, Wiklund P, Lindberg J, et al
Virchows Archiv : an international journal of pathology 2014;465(5):559-65

Sequencing of breast cancer stem cell populations indicates a dynamic conversion between differentiation states in vivo
Klevebring D, Rosin G, Ma R, Lindberg J, Czene K, Kere J, et al

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins
Lindberg J, Klevebring D, Liu W, Neiman M, Xu J, Wiklund P, et al
European urology 2013;63(2):347-53

Genetic markers associated with early cancer-specific mortality following prostatectomy
Liu Wn, Xie Cmc, Thomas Cy, Kim St, Lindberg J, Egevad L, et al
CANCER 2013;119(13):2405-12

The mitochondrial and autosomal mutation landscapes of prostate cancer
Lindberg J, Mills Ig, Klevebring D, Liu W, Neiman M, Xu J, et al
European urology 2013;63(4):702-8

Identification of new differentially methylated genes that have potential functional consequences in prostate cancer
Kim Jw, Kim St, Turner Ar, Young T, Smith S, Liu W, et al
PloS one 2012;7(10):e48455-

Identification of novel CHD1-associated collaborative alterations of genomic structure and functional assessment of CHD1 in prostate cancer
Liu W, Lindberg J, Sui G, Luo J, Egevad L, Li T, et al
Oncogene 2012;31(35):3939-48

Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy
Neiman M, Sundling S, Grönberg H, Hall P, Czene K, Lindberg J, et al
PloS one 2012;7(11):e48616-

Signaling pathways involved in the regulation of TNF alpha-induced toll-like receptor 2 expression in human gingival fibroblasts
Davanian H, Bage T, Lindberg J, Lundeberg J, Concha Hq, Chen Ms, et al
CYTOKINE 2012;57(3):406-16

Antibodies to Several Citrullinated Antigens Are Enriched in the Joints of Rheumatoid Arthritis Patients
Snir O, Widhe M, Hermansson M, Von Spee C, Lindberg J, Hensen S, et al

Signal pathways JNK and NF-kappa B, identified by global gene expression profiling, are involved in regulation of TNF alpha-induced mPGES-1 and COX-2 expression in gingival fibroblasts
Bage T, Lindberg J, Lundeberg J, Modeer T, Yucel-lindberg T
BMC GENOMICS 2010;:241-

The Gene Expression Profile in the Synovium as a Predictor of the Clinical Response to Infliximab Treatment in Rheumatoid Arthritis
Lindberg J, Wijbrandts Ca, Van Baarsen Lg, Nader G, Klareskog L, Catrina A, et al
PLOS ONE 2010;5(6):e11310-

The plasticity of the mammalian transcriptome
Lindberg J, Lundeberg J
GENOMICS 2010;95(1):1-6

Automation of cDNA Synthesis and Labelling Improves Reproducibility
Klevebring D, Gry M, Lindberg J, Eidefors A, Lundeberg J

Extremely Different Behaviours in High and Low Body Weight Lines of Chicken are Associated with Differential Expression of Genes Involved in Neuronal Plasticity
Ka S, Lindberg J, Stromstedt L, Fitzsimmons C, Lindqvist N, Lundeberg J, et al

Multiple antibody reactivities to citrullinated antigens in sera from patients with rheumatoid arthritis: association with HLA-DRB1 alleles
Snir O, Widhe M, Von Spee C, Lindberg J, Padyukov L, Lundberg K, et al

Systemic TNF blockade does not modulate synovial expression of the pro-inflammatory mediator HMGB1 in rheumatoid arthritis patients - a prospective clinical study
Sundberg E, Grundtman C, Klint Eaf, Lindberg J, Ernestam S, Ulfgren Ak, et al

Determination of binding specificities in highly multiplexed bead-based assays for antibody proteomics
Schwenk Jm, Lindberg J, Sundberg M, Uhlen M, Nilsson P

Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits
Rubin Cj, Lindberg J, Fitzsimmons C, Savolainen P, Jensen P, Lundeberg J, et al
BMC GENOMICS 2007;:208-

Transmission of Stress-Induced Learning Impairment and Associated Brain Gene Expression from Parents to Offspring in Chickens
Lindqvist C, Janczak Am, Natt D, Baranowska I, Lindqvist N, Wichman A, et al
PLOS ONE 2007;2(4):e364-

Effect of infliximab on mRNA expression profiles in synovial tissue of rheumatoid arthritis patients
Lindberg J, Af Klint E, Catrina Ai, Nilsson P, Klareskog L, Ulfgren Ak, et al

Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
Lindberg J, Af Klint E, Ulfgren Ak, Stark A, Andersson T, Nilsson P, et al

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