Structural Variants

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
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, Febian Trillsch
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Tumor-informed ctDNA as an objective marker for postoperative residual disease in epithelial ovarian cancer
805P Tumor-informed ctDNA detection as a predictive marker for postoperative residual disease in epithelial ovarian cancer: A feasibility study
Background
Complete tumor resection is the most relevant prognostic factor for overall survival in high grade serous ovarian cancer …
Christoph Grimm, Valentina Paspalj, Magdalena Postl, Lao H. Saal, Christian Brueffer, Nuria Segui Gracia, Miguel Alcaide, Stephan Polterauer, Lucia Oton, Yilun Chen, Gerda Hofstetter, Leonhard Müllauer
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805P Tumor-informed ctDNA detection as a predictive marker for postoperative residual disease in epithelial ovarian cancer: A feasibility study
#898 Tumor-informed ctDNA detection as a marker for postoperative residual disease in epithelial ovarian cancer – results of a feasibility study
Introduction/Background
Complete tumor resection is the most relevant prognostic factor for overall survival in high grade serous …
Magdalena Postl, Valentina Paspalj, Christian Brueffer, Nuria Segui Gracia, Miguel Alcaide, Lucia Oton, Yilun Chen, Lao H. Saal, Gerda Hofstetter, Leonhard Müllauer, Stephan Polterauer, Christoph Grimm
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#898 Tumor-informed ctDNA detection as a marker for postoperative residual disease in epithelial ovarian cancer – results of a feasibility study
Abstract 5710: Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens
Venetoclax (Ven) is a selective B-cell lymphoma 2 inhibitor being studied in t(11;14)+ relapsed/refractory multiple myeloma (MM). …
Xiaotong Li, Lao H. Saal, Christian Brueffer, Yilun Chen, Johanna Asklin, Saman Alvi, Srinivas Venkatram, Jeremy A. Ross
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Abstract 5710: Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens
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
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A crowdsourced set of curated structural variants for the human genome
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
Abstract 4805: Whole genome sequencing of primary breast cancers and matched distant metastases
Metastatic disease is the main cause of death for breast cancer patients, but it is still unclear whether primary tumor characteristics …
Man-Hung Eric Tang, Malin Dahlgren, Christian Brueffer, Christof Winter, Yilun Chen, Eleonor Olsson, Martin Sjöström, Pär-Ola Bendahl, Emma Niméus-Malmström, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal
DOI
Abstract 4805: Whole genome sequencing of primary breast cancers and matched distant metastases