Christian Brueffer

Christian Brueffer

Bioinformatics — Cancer Research —
Open Source Software — Software Engineering

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. Additionally I work on improving open source bioinformatics and reproducible research infrastructure by contributing to projects such as conda-forge, Bioconda and Biopython.

Publications

Detection of circulating tumor cells and circulating tumor DNA before and after mammographic breast compression in a cohort of breast cancer patients scheduled for neoadjuvant treatment. Förnvik D, Aaltonen KE, Chen Y, George AM, Brueffer C, Rigo R, Loman N, Saal LH, Rydén L. Breast Cancer Research and Treatment (2019). doi: 10.1007/s10549-019-05326-5

SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome. 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. bioRxiv (2019). doi: https://doi.org/10.1101/581264

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. 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. JCO Precision Oncology (2018). 2:1-18. doi: 10.1200/PO.17.00135

Bioconda: sustainable and comprehensive software distribution for the life sciences. 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. Nature Methods (2018). 15: 475-476. doi: 10.1038/s41592-018-0046-7 [Preprint]

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

Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing. 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. Oncotarget (2015). 6(35): 37169–37184. doi: 10.18632/oncotarget.5951

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. 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. Breast Cancer Res (2015). 17:102. doi: 10.1186/s13058-015-0608-x

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. 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. Genome Medicine (2015). 7(1):20. doi: 10.1186/s13073-015-0131-9

Conference Contributions

Swedish Cancer Research Meeting 2019, Umeå, Sweden – Defining the Mutational Landscape of the Primary Breast Cancer Transcriptome through large-scale RNA-seq in the Sweden Cancerome Analysis Network–Breast (SCAN-B) Project

Keystone Symposium on Precision Medicine in Cancer 2018, Stockholm, Sweden – RNA-seq-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers in the Population-Based Multicenter SCAN-B Study

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

ResearchGate

Impactstory

Google Scholar

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