Bioinformatics

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
Sixth Annual BCM Hackathon on Structural Variation and Pangenomics
Background
Structural variants (SVs) and metagenomics remain challenging areas in genomics, requiring new tools and collaborative …
Farhang Jaryani, Bishnu Adhikar, Shaghayegh Beheshti, Sarah Fross, Jędrzej Kubica, Jen-Yu Wang, Aanuoluwa Adekoya, Daniel P. Agustinho, Oluwaseun Akinsulire, Francesco Andreace, Abolhassan Bahari, Christian Brueffer, Siyuan Cheng, Jonah Cullen, Kristen Curry, Ryan Doughty, Adam English, Neda Ghohabi Esfahani, Natali Gulbahce, Tina Han, Nha Van Huynh, Michal Izydorczyk, Minal Jamsandekar, Emrah Kacar, Arthur Shem Kasambula, Rupesh K. Kesharwani, Divya Kalra, Shwetha V Kumar, Iva Kotásková, Callum MacPhillamy, Sina Majidian, Mauricio Moldes, Abraham (Jon) Moller, Rajarshi Mondal, Eleni Mourouzidou, Michael Nute, Dmitrii Olisov, Anika Pallapothu, Meghana Ram, Marcus Chan Hua Rui, Philippe Sanio, Russel T. Santos, Michael Olufemi, Narges SangaraniPour, Moustafa Shokrof, Sam Stroupe, Gobikrishnan Subramaniam, Todd J. Treangen, Pankhuri Wanjari, Umran Yaman, Farha Zain, Xinchang Zheng, Fritz J Sedlazeck, Ben Busby
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Sixth Annual BCM Hackathon on Structural Variation and Pangenomics
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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The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
Background
The goal of the Fifth Annual Baylor College of Medicine & DNAnexus Structural Variation Hackathon was to push forward …
Sontosh K Deb, Divya Kalra, Jędrzej Kubica, Erik Stricker, Van Q. Truong, Qiandong Zeng, Christopher J. Fiscus, Daniel Paiva Agustinho, Adam Alexander, Marlon Arciniega-Sanchez, Lorianne Bosseau, Christian Brueffer, Astrid Canal, Joyjit Daw, David Enoma, Alison Diaz-Cuevas, Colin Diesh, Janet M. Doolittle-Hall, Luis Fernandez-Luna, Tina Han, Wolfram Höps, Peiming Peter Huang, Tony Huang, Michal Bogumil Izydorczyk, Farhang Jaryani, Rupesh K. Kesharwani, Shaheerah Khan, Sina Majidian, Ayan Malakar, Tania Girão Mangolini, Sejal Modha, Mauricio Moldes, Rajarshi Mondal, Abdullah Al Nahid, Chi-Lam Poon, Sagayamary Sagayaradj, Philippe Sanio, Tania Sepulveda-Morales, Muhammad Shahzaib, Muhammad Sohail Raza, Trinh Tat, Ishaan Thota, Umran Yaman, Jason Yeung, Qiyi Yu, Xinchang Zheng, Medhat Mahmoud, Fritz J. Sedlazeck, Ben Busby
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The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
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