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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
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Features of increased malignancy in eosinophilic clear cell renal cell carcinoma
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
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
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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
TopHat-Recondition: A post-processor for TopHat unmapped reads
Background
TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version …
Christian Brueffer, Lao H. Saal
DOI PDF bioRxiv Preprint Code PhD Project
TopHat-Recondition: A post-processor for TopHat unmapped reads
Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing
To better understand and characterize chromosomal structural variation during breast cancer progression, we enumerated chromosomal …
Man-Hung Eric Tang, Malin Dahlgren, Christian Brueffer, Tamara Tjitrowirjo, Christof Winter, Yilun Chen, Eleonor Olsson, Kun Wang, Therese Törngren, Martin Sjöström, Dorthe Grabau, Pär-Ola Bendahl, Lisa Rydén, Emma Niméus, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal
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Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing
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
Introduction
By convention, a contralateral breast cancer (CBC) is treated as a new primary tumor, independent of the first cancer …
Sara Alkner, Man-Hung Eric Tang, Christian Brueffer, Malin Dahlgren, Yilun Chen, Eleonor Olsson, Christof Winter, Sara Baker, Anna Ehinger, Lisa Rydén, Lao H. Saal, Mårten Fernö, Sofia K. Gruvberger-Saal
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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
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
Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is …
Lao H. Saal, Johan Vallon-Christersson, Jari Häkkinen, Cecilia Hegardt, Dorthe Grabau, Christof Winter, Christian Brueffer, Man-Hung Eric Tang, Christel Reuterswärd, Ralph Schulz, Anna Karlsson, Anna Ehinger, Janne Malina, Jonas Manjer, Martin Malmberg, Christer Larsson, Lisa Rydén, Niklas Loman, Åke Borg
DOI PDF Dataset PhD Project
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