Bioinformatics

RNA Sequencing for Molecular Diagnostics in Breast Cancer
Breast cancer is the most common type of cancer in women and, in Sweden, is the most deadly second only to lung cancer. While treatment …
Christian Brueffer
PDF Code PhD Project LUCRIS Project
RNA Sequencing for Molecular Diagnostics in Breast Cancer
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and …
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
DOI PDF bioRxiv Preprint Code Dataset Press Release PhD Project
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome
Features of increased malignancy in eosinophilic clear cell renal cell carcinoma
Clear cell renal cell carcinoma (ccRCC) is the most common form of renal cancer. Due to inactivation of the von Hippel–Lindau tumour …
Helén Nilsson, David Lindgren, Håkan Axelson, Christian Brueffer, Lao H. Saal, Jaana Lundgren, Martin Johansson
DOI PDF
Features of increased malignancy in eosinophilic clear cell renal cell carcinoma
Abstract CT074: Pre-existing ESR1 mutations in early-stage primary breast cancer predict failure of endocrine therapy and poor survival
Background
More than three-quarters of primary breast cancers are positive for estrogen receptor alpha (ER; encoded by the gene ESR1), …
Malin Dahlgren, Anthony M. George, Christian Brueffer, Sergii Gladchuk, Yilun Chen, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Lisa Rydén, Martin Malmberg, Christer Larsson, Sofia K. Gruvberger-Saal, Anna Ehinger, Niklas Loman, Åke Borg, Lao H. Saal
DOI
Abstract CT074: Pre-existing ESR1 mutations in early-stage primary breast cancer predict failure of endocrine therapy and poor survival
A crowdsourced set of curated structural variants for the human genome
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a …
Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook
DOI PDF bioRxiv Preprint Code
A crowdsourced set of curated structural variants for the human genome
Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492)
Background
Breast cancer is a disease of genomic alterations, of which the complete panorama of somatic mutations and how these relate …
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
DOI
Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492)
Plasma circulating tumor DNA as a genomic biomarker for ovarian cancer
Introduction
Ovarian cancer (OC) remains the most lethal disease among gynecological malignancies as most patients are diagnosed in an …
Yoshiko Nanki, Anthony M. George, Yilun Chen, Christian Brueffer, Akira Hirasawa, Tatsuyuki Chiyoda, Tomoko Akahane, Daisuke Aoki, Lao H. Saal
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
Purpose
It is not known if mammographic breast compression of a primary tumor causes shedding of tumor cells into the circulatory …
Daniel Förnvik, Kristina E. Aaltonen, Yilun Chen, Anthony M. George, Christian Brueffer, Robert Rigo, Niklas Loman, Lao H. Saal, Lisa Rydén
DOI PDF
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
Bioconda: sustainable and comprehensive software distribution for the life sciences
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multiplatform and …
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Devon Ryan, Anthony Bretaudeau, Gildas Le Corguillé, Christian Brueffer, et al
DOI bioRxiv Preprint Project Code
Bioconda: sustainable and comprehensive software distribution for the life sciences
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
Purpose
In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal …
Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H. Saal
DOI PDF Dataset PhD Project
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