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The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome

View ORCID ProfileChristian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
doi: https://doi.org/10.1101/2020.01.30.926733
Christian Brueffer
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
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  • ORCID record for Christian Brueffer
Sergii Gladchuk
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
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Christof Winter
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
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Johan Vallon-Christersson
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
3CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
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Cecilia Hegardt
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
3CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
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Jari Häkkinen
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
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Anthony M. George
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
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Yilun Chen
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
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Anna Ehinger
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
4Department of Pathology, Skåne University Hospital, Lund, Sweden
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Christer Larsson
2Lund University Cancer Center, Medicon Village, Lund, Sweden
5Division of Molecular Pathology, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Niklas Loman
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
6Department of Oncology, Skåne University Hospital, Lund, Sweden
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Martin Malmberg
6Department of Oncology, Skåne University Hospital, Lund, Sweden
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Lisa Rydén
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
7Department of Surgery, Skåne University Hospital, Lund, Sweden
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Åke Borg
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
3CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
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Lao H. Saal
1Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
2Lund University Cancer Center, Medicon Village, Lund, Sweden
3CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
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  • For correspondence: lao.saal@med.lu.se
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Abstract

Breast cancer is a disease of genomic alterations, of which the complete panorama of somatic mutations and how these relate to molecular subtypes and therapy response is incompletely understood. Within the Sweden Cancerome Analysis Network–Breast project (SCAN-B; ClinicalTrials.gov NCT02306096), an ongoing study elucidating the tumor transcriptomic profiles for thousands of breast cancers prospectively, we developed an optimized pipeline for detection of single nucleotide variants and small insertions and deletions from RNA sequencing (RNA-seq) data, and profiled a large real-world population-based cohort of 3,217 breast tumors. We use it to describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population-based cohort of patients, and relate it to patient overall survival. We demonstrate that RNA-seq can be used to call mutations in important breast cancer genes such as PIK3CA, TP53, and ERBB2, as well as the status of key molecular pathways and tumor mutational burden, and identify potentially druggable genes in 86.8% percent of tumors. To make this rich and growing mutational portraiture of breast cancer available for the wider research community, we developed an open source web-based application, the SCAN-B MutationExplorer, accessible at http://oncogenomics.bmc.lu.se/MutationExplorer. These results add another dimension to the use of RNA-seq as a potential clinical tool, where both gene expression-based and gene mutation-based biomarkers can be interrogated simultaneously and in real-time within one week of tumor sampling.

Footnotes

  • http://oncogenomics.bmc.lu.se/MutationExplorer

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 31, 2020.
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The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome
Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
bioRxiv 2020.01.30.926733; doi: https://doi.org/10.1101/2020.01.30.926733
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The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome
Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
bioRxiv 2020.01.30.926733; doi: https://doi.org/10.1101/2020.01.30.926733

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