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The mutational landscape of the SCAN‐B real‐world primary breast cancer transcriptome

Brueffer, Christian LU orcid ; Gladchuk, Sergii LU ; Winter, Christof LU ; Vallon-Christersson, Johan LU orcid ; Hegardt, Cecilia LU ; Häkkinen, Jari LU orcid ; George, Anthony LU ; Chen, Yilun LU ; Ehinger, Anna LU orcid and Larsson, Christer LU , et al. (2020) In EMBO Molecular Medicine 12(10).
Abstract
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. We describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population‐based cohort and relate it to patient survival. We demonstrate that RNA‐seq can be used to call mutations in genes such as PIK3CA, TP53, and ERBB2, as well as the status of molecular pathways and... (More)
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. We describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population‐based cohort and relate it to patient survival. We demonstrate that RNA‐seq can be used to call mutations in genes such as PIK3CA, TP53, and ERBB2, as well as the status of molecular pathways and mutational burden, and identify potentially druggable mutations in 86.8% of tumors. To make this rich dataset available for the research community, we developed an open source web application, the SCAN‐B MutationExplorer (http://oncogenomics.bmc.lu.se/MutationExplorer). These results add another dimension to the use of RNA‐seq as a clinical tool, where both gene expression‐ and mutation‐based biomarkers can be interrogated in real‐time within 1 week of tumor sampling. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
cancer, breast cancer, mutation, RNA-seq, survival, transcriptome
in
EMBO Molecular Medicine
volume
12
issue
10
article number
e12118
publisher
Wiley-Blackwell
external identifiers
  • pmid:32926574
  • scopus:85091252227
ISSN
1757-4684
DOI
10.15252/emmm.202012118
project
Sweden Cancerome Analysis Network - Breast (SCAN-B): a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine
RNA sequencing for molecular diagnostics in breast cancer
language
English
LU publication?
yes
id
53bd93b6-f816-4be8-818f-47aaab60690c
date added to LUP
2020-09-15 23:51:26
date last changed
2022-09-02 18:18:27
@article{53bd93b6-f816-4be8-818f-47aaab60690c,
  abstract     = {{Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. We describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population‐based cohort and relate it to patient survival. We demonstrate that RNA‐seq can be used to call mutations in genes such as PIK3CA, TP53, and ERBB2, as well as the status of molecular pathways and mutational burden, and identify potentially druggable mutations in 86.8% of tumors. To make this rich dataset available for the research community, we developed an open source web application, the SCAN‐B MutationExplorer (http://oncogenomics.bmc.lu.se/MutationExplorer). These results add another dimension to the use of RNA‐seq as a clinical tool, where both gene expression‐ and mutation‐based biomarkers can be interrogated in real‐time within 1 week of tumor sampling.}},
  author       = {{Brueffer, Christian and Gladchuk, Sergii and Winter, Christof and Vallon-Christersson, Johan and Hegardt, Cecilia and Häkkinen, Jari and George, Anthony and Chen, Yilun and Ehinger, Anna and Larsson, Christer and Loman, Niklas and Malmberg, Martin and Ryden, Lisa and Borg, Åke and Saal, Lao}},
  issn         = {{1757-4684}},
  keywords     = {{cancer; breast cancer; mutation; RNA-seq; survival; transcriptome}},
  language     = {{eng}},
  month        = {{09}},
  number       = {{10}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{EMBO Molecular Medicine}},
  title        = {{The mutational landscape of the SCAN‐B real‐world primary breast cancer transcriptome}},
  url          = {{http://dx.doi.org/10.15252/emmm.202012118}},
  doi          = {{10.15252/emmm.202012118}},
  volume       = {{12}},
  year         = {{2020}},
}