Cancer

Transcriptomic Profiling of Mouse Mammary Tumors Enables Prognostic and Predictive Biomarker Discovery for Human Breast Cancer
The development and validation of prognostic and predictive biomarkers in breast cancer is limited by the availability of …
Matthew D. Sutcliffe, Kevin R. Mott, Tulay Yilmaz-Swenson, Brooke M. Felsheim, Alexander V. Lobanov, Anna R. Michmerhuizen, Patrick D. Rädler, Denis O. Okumu, Xiaping He, Adam D. Pfefferle, Stephanie Dance-Barnes, Christian Brueffer, Lao H. Saal, Michael P. East, Daniel P. Hollern, Timothy C. Elston, Gary L. Johnson, Charles M. Perou
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NeoCircle: pre- and post-operative circulating tumor DNA dynamics predicts survival in neoadjuvant-treated early breast cancer
Persistent circulating tumor DNA (ctDNA) during neoadjuvant treatment (NAT) of early breast cancer (EBC) indicates high-risk disease. …
Anthony M. George, Yilun Chen, Sergii Gladchuk, Miguel Alcaide, Hina Dalal, Pei Meng, Christian Brueffer, Hani Saghir, Siker Kimbung, Kristina Aaltonen, Lucia Oton, Christopher Rushton, Sofia Birkeälv, Mats Jönsson, Sophia Zackrisson, Ida Skarping, Daniel Förnvik, Lina Zander, Gabriella Honeth, Samuel Woodhouse, Karen Howarth, Åke Borg, Anna Ehinger, Martin Malmberg, Lisa Rydén, Niklas Loman, Lao H. Saal
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A complete human pancreatic cancer genome
In cancer genome sequencing, reference gaps and germline variants obscure detection of small and large somatic variants and methylation …
Justin Wagner, Ayse G. Keskus, Keisuke K. Oshima, T. Rhyker Ranallo-Benavidez, Jennifer McDaniel, Mile Sikic, Dehui Lin, Luis F. Paulin, Adam C. English, Fritz J. Sedlazeck, Elizabeth M. Munding, J. Zachary Sanborn, Andrew Carroll, Pi-Chuan Chang, Daniel E. Cook, Kishwar Shafin, Joep de Ligt, Rayan Hassaine, Daniel Cameron, Severine Catreux, Yeonghun Lee, Lisa Murray, Sean Truong, Christian Brueffer, Aleksey V. Zimin, Erin Cross, Matthew McGowan, Michael Vernich, Andrew S. Liss, Jean-Pierre Kocher, Zachary Stephens, Tanveer Ahmad, Asher Bryant, Nathan Dwarshuis, Hua-Jun He, Zhiyong He, Nathan D. Olson, Francoise Thibaud-Nissen, Dmitry Antipov, Sergey Koren, Adam Phillippy, Rajeeva Lochan Musunuri, Giuseppe Narzisi, Miten Jain, Aaron M. Wenger, Stephen Eacker, Sayed Mohammad Ebrahim Sahraeian, Paul C. Boutros, Yash Patel, Takafumi N. Yamaguchi, Joseph McConnell, Matthew Borchers, Jennifer L. Gerton, Paxton Kostos, Andrea Guarracino, Maryam Jehangir, Hila Benjamin, Mohammed Faizal Eeman Mootor, Yuan Xu, Mobin Asri, Karen H. Miga, Jimin Park, Benedict Paten, Ruibang Luo, Zhenxian Zheng, Jae Young Choi, Linh Nguyen, Dan R. Robinson, Josh N. Vo, Shenghan Gao, Ghulam Murtaza, Christopher E. Mason, Haoyu Cheng, Floris P. Barthel, Chunlin Xiao, Glennis A. Logsdon, Mikhail Kolmogorov, Justin M. Zook
DOI bioRxiv Preprint
Abstract PS1-05: Genomic characteristics related to histology-based immune features in breast cancer
Background: The immune cell component of the tumor microenvironment is an important modulator of tumor progression and suppression. In …
Yoon Jin Cha, Constandina E. O’Connell, Benjamin C. Calhoun, Christian Brueffer, Christer Larsson, Åke Borg, Lao H. Saal, Charles M. Perou
DOI
Abstract PS1-05: Genomic characteristics related to histology-based immune features in breast cancer
NeoCircle: Investigating circulating tumor DNA dynamics as a predictor of survival in primary breast cancer
Background
Persistent circulating tumor DNA (ctDNA) detection during neoadjuvant treatment (NAT) of early-breast cancer (EBC) indicates …
Anthony M. George, Yilun Chen, Sergii Gladchuk, Miguel Alcaide, Hina Dalal, Pei Meng, Christian Brueffer, Hani Saghir, Siker Kimbung, Lucia Oton, Ida Skarping, Daniel Förnvik, Gabriella Honeth, Karen Howarth, Åke Borg, Anna Ehinger, Martin Malmberg, Lisa Rydén, Niklas Loman, Lao H. Saal
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NeoCircle: Investigating circulating tumor DNA dynamics as a predictor of survival in primary breast cancer
ctDNA as an Objective Marker for Postoperative Residual Disease in Primary Advanced High-Grade Serous Ovarian Cancer
Background/Objectives: The surgeon’s subjective intraoperative evaluation is the standard of care to assess postoperative residual …
Valentina Glueck, Christoph Grimm, Magdalena Postl, Christian Brueffer, Nuria Segui, Miguel Alcaide, Lucia Oton, Yilun Chen, Lao H. Saal, Gerda Hofstetter, Stephan Polterauer, Leonhard Muellauer
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Genomic Characteristics Related to Histology-based Immune Features in Breast Cancer
The immune cell component of the tumor microenvironment is an important modulator of tumor progression. In patients with breast cancer, …
Yoon Jin Cha, Constandina E. O’Connell, Benjamin C. Calhoun, Brooke M. Felsheim, Aranzazu Fernandez-Martinez, Cheng Fan, Christian Brueffer, Christer Larsson, Åke Borg, Lao H. Saal, Charles M. Perou
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Monitoring ctDNA dynamics in early breast cancer using a novel ultra-sensitive tumor-informed structural variant approach combining whole-genome sequencing and multiplex dPCR
Background
Persistent circulating cell-free tumor DNA (ctDNA) detection during neoadjuvant treatment of early-breast cancer (EBC) …
Lao H. Saal, Niklas Loman, Yilun Chen, Miguel Alcaide, Christian Brueffer, Sergii Gladchuk, Hina Dalal, Pei Meng, Anthony M. George, Sofia Birkeälv, Hani Saghir, Siker Kimbung, Daniel Förnvik, Lina Zander, Gabriella Honeth, Karen Howarth, Åke Borg, Anna Ehinger, Martin Malmberg, Lisa Rydén
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Monitoring ctDNA dynamics in early breast cancer using a novel ultra-sensitive tumor-informed structural variant approach combining whole-genome sequencing and multiplex dPCR
Tumor-informed ctDNA as an objective marker for postoperative residual disease in epithelial ovarian cancer
Background
The most important predictor of prognosis in patients with high-grade serous ovarian cancer (HGSOC) is complete tumor …
Valentina Paspalj, Christoph Grimm, Magdalena Postl, Christina Viktoria Tauber, Nuria Segui, Christian Brueffer, Miguel Alcaide, Lucia Oton, Yilun Chen, Lao H. Saal, Gerda Hofstetter, Leonhard Muellauer, Mirjana Kessler, Fabian Trillsch
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Tumor-informed ctDNA as an objective marker for postoperative residual disease in epithelial ovarian cancer
Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling
Three quarters of all breast cancers express the estrogen receptor (ER, ESR1 gene), which promotes tumor growth and constitutes a …
Tommaso De Marchi, Chun-Fui Lai, Georgia M. Simmons, Isabella Goldsbrough, Alison Harrod, Thai Lam, Lakjaya Buluwela, Sven Kjellström, Christian Brueffer, Lao H. Saal, Johan Malmström, Simak Ali, Emma Niméus
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Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling