Bioinformatics

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting …
Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz Barrera, Luis A. Rubio-Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, ChouXian Ma, LinQi Tang, YuanPing Du, ShaoWei Zhang, Jordi Morata, Raúl Tonda, Genís Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Gungor Budak, Kübra Narcı, Elif Arslan, Richard Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook
DOI PDF bioRxiv Preprint Project
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
Clinical associations of ESR2 (estrogen receptor beta; ERβ) expression across thousands of primary breast tumors
Estrogen receptor alpha (ERα, encoded by ESR1) is a well-characterized transcription factor expressed in more than 75% of breast tumors …
Hina Dalal, Malin Dahlgren, Sergii Gladchuk, Christian Brueffer, Sofia K. Gruvberger-Saal, Lao H. Saal
DOI PDF Dataset
Clinical associations of ESR2 (estrogen receptor beta; ERβ) expression across thousands of primary breast tumors
Preexisting Somatic Mutations of Estrogen Receptor Alpha (ESR1) in Early-Stage Primary Breast Cancer
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 PDF Dataset Press Release
Preexisting Somatic Mutations of Estrogen Receptor Alpha (ESR1) in Early-Stage Primary Breast Cancer
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