Research Interests

My research focuses on the development of diagnostics based on tumor DNA/RNA deep sequencing (also known as next generation sequencing) to improve breast cancer treatment and survival. Most of my projects are embedded in the Sweden Cancerome Analysis Network–Breast (SCAN-B) study. I am also interested in improving open source bioinformatics and reproducible research infrastructure by contributing to projects such as Bioconda and Biopython.


Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson C, Proukakis C, Clarke W, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, Kolora SRR, Alexander N, Wolujewicz P, Ahmed A, Smith G, Shehreen S, Wenger AM, Salit M, Zook J. SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome. bioRxiv, 2019. doi:

Brueffer C*, Vallon-Christersson J*, Grabau D, Ehinger A, Häkkinen J, Hegardt C, Malina J, Chen Y, Bendahl PO, Manjer J, Malmberg M, Larsson C, Loman N, Rydén L, Borg Å, Saal LH. Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network–Breast Initiative. JCO Precision Oncology, 2018. 2:1-18. doi: 10.1200/PO.17.00135

Grüning B*, Dale R*, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch C, Valieris R, Caprez A, Batut B, Haudgaard M, Cokelaer T, Beauchamp KA, Pedersen BS, Hoogstrate Y, Ryan D, Bretaudeau A, Le Corguillé G, Brueffer C, …, Köster J. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 2018. 15: 475-476. doi: 10.1038/s41592-018-0046-7 [Preprint]

Brueffer C and Saal LH. TopHat-Recondition: A post-processor for TopHat unmapped reads. BMC Bioinformatics, 2016. 17(1):199. doi: 10.1186/s12859-016-1058-x [Preprint]

Tang MHE*, Dahlgren M*, Brueffer C, Tjitrowirjo T, Winter C, Chen Y, Olsson E, Wang K, Törngren T, Sjöström M, Grabau D, Bendahl PO, Rydén L, Niméus E, Saal LH, Borg Å, Gruvberger-Saal SK. Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing. Oncotarget, 2015. 6(35): 37169–37184. doi: 10.18632/oncotarget.5951

Alkner S*, Tang MHE*, Brueffer C, Dahlgren M, Chen Y, Olsson E, Winter C, Baker S, Ehinger A, Rydén L, Saal LH, Fernö M, Gruvberger-Saal SK. Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing. Breast Cancer Res, 2015. 17:102. doi: 10.1186/s13058-015-0608-x

Saal LH, Vallon-Christersson J, Häkkinen J, Hegardt C, Grabau D, Winter C, Brueffer C, Tang MHE, Reuterswärd C, Schulz R, Karlsson A, Ehinger A, Malina J, Manjer J, Malmberg M, Larsson C, Rydén L, Loman N, Borg Å. The Sweden Cancerome Analysis Network-Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine. Genome Medicine, 2015. 7(1):20. doi: 10.1186/s13073-015-0131-9

Conference Contributions

Bioinformatics Open Source Conference (BOSC) 2017, Prague, Czech Republic – Biopython Status Update 2017 [abstract and PDF] [video]

Bioinformatics Open Source Conference (BOSC) 2016, Orlando, USA – Biopython Status Update 2016 [abstract and PDF] [video]

Lund University Research Portal

Saal lab at Lund University

ORCID: 0000-0002-3826-0989



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