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Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

Nature Communications 2025年第1期16卷 1-18页

作者： Maria Zanti Denise G. O’Mahony Kristia Yiangou Kyriaki Michailidou Michael T. Parsons Amanda B. Spurdle Leila Dorling Joe Dennis Marc Naven Antonis C. Antoniou Manjeet K. Bolla Qin Wang Douglas F. Easton Nicholas J. Boddicker Wenan Chen Chunling Hu Steven N. Hart Fergus J. Couch Thomas U. Ahearn Jonine D. Figueroa Montserrat García-Closas Christine B. Ambrosone Song Yao Irene L. Andrulis Gord Glendon Paul L. Auer Caroline Baynes Don M. Conroy Alison M. Dunning Craig Luccarini Clara Bodelon James M. Hodge Alpa V. Patel Lauren R. Teras Natalia V. Bogdanova Stig E. Bojesen Kristen D. Brantley Nicola J. Camp Archie Campbell Jose E. Castelao Melissa H. Cessna Jenny Chang-Claude Fei Chen Christopher A. Haiman Georgia Chenevix-Trench Kamila Czene Arcangela De Nicolo Susan M. Domchek Katherine L. Nathanson Thilo Dörk A. Heather Eliassen D. Gareth Evans Peter A. Fasching Henrik Flyger Manuela Gago-Dominguez Anna González-Neira Rocio Nuñez-Torres Felix Grassmann Andreas Hadjisavvas Mihalis I. Panayiotidis Ute Hamann Muhammad U. Rashid Diana Torres Mikael B. A. Hartman Weang-Kee Ho Reiner Hoppe Sacha J. Howell Anna Jakubowska Elza K. Khusnutdinova Yon-Dschun Ko Peter Kraft Vessela N. Kristensen James V. Lacey Jingmei Li Geok Hoon Lim Veronique Kiak-Mien Tan Sara Lindström Artitaya Lophatananon Kenneth Muir Arto Mannermaa Maria Elena Martinez Dimitrios Mavroudis Roger L. Milne Melissa C. Southey Nadia Obi Janet E. Olson Celine M. Vachon Julie R. Palmer Gary R. Zirpoli Paul D. P. Pharoah Eric C. Polley Kathryn J. Ruddy Siddhartha Yadav Emmanouil Saloustros Elinor J. Sawyer Marjanka K. Schmidt Soo Hwang Teo Amy Trentham-Dietz Thérèse Truong Jeffrey N. Weitzel Melissa S. Cline Peter Devilee Sean V. Tavtigian David E. Goldgar Biostatistics Unit The Cyprus Institute of Neurology & Genetics Nicosia Cyprus Department of Medical Genetics Oslo University Hospital Oslo Norway Population Health Program QIMR Berghofer Medical Research Institute Brisbane Queensland Australia Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Cambridge UK Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge UK Department of Quantitative Health Sciences Division of Computational Biology Mayo Clinic Rochester MN USA Department of Laboratory Medicine and Pathology Mayo Clinic Rochester MN USA Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA Usher Institute of Population Health Sciences and Informatics The University of Edinburgh Edinburgh UK Cancer Research UK Edinburgh Centre The University of Edinburgh Edinburgh UK Department of Cancer Prevention and Control Roswell Park Comprehensive Cancer Institute Buffalo NY USA Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto Ontario Canada Department of Molecular Genetics University of Toronto Toronto Ontario Canada Division of Biostatistics Data Science Institute and Cancer Center Medical College of Wisconsin Milwaukee WI USA Department of Population Science American Cancer Society Atlanta GA USA Radiation Oncology Research Unit Hannover Medical School Hannover Germany Copenhagen General Population Study Herlev and Gentofte Hospital Copenhagen University Hospital Herlev Denmark Department of Clinical Biochemistry Herlev and Gentofte Hospital Copenhagen University Hospital Herlev Denmark Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Internal Medicine and Hu

Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyze germline sequencing data ofBRCA1andBRCA2from 96,691 female breast cancer cases and 302,116 controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observe 11,207BRCA1andBRCA2variants, with 6909 being coding, covering 23.4% ofBRCA1andBRCA2VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control likelihood ratio (ccLR) evidence is highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.3% specificity forBRCA1and 93.3% sensitivity and 86.6% specificity forBRCA2. This approach provides case-control evidence for 787 unclassified variants; these include 579 with strong or moderate benign evidence and 10 with strong pathogenic evidence for which ccLR evidence is sufficient to alter clinical classification.

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The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

arXiv

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arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

关键词： Image segmentation

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Diabetic foot ulcers segmentation challenge report: Benchmark and analysis

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Medical image analysis 2024年 94卷 103153页

作者： Moi Hoon Yap Bill Cassidy Michal Byra Ting-Yu Liao Huahui Yi Adrian Galdran Yung-Han Chen Raphael Brüngel Sven Koitka Christoph M Friedrich Yu-Wen Lo Ching-Hui Yang Kang Li Qicheng Lao Miguel A González Ballester Gustavo Carneiro Yi-Jen Ju Juinn-Dar Huang Joseph M Pappachan Neil D Reeves Vishnu Chandrabalan Darren Dancey Connah Kendrick Department of Computing and Mathematics Manchester Metropolitan University John Dalton Building Chester Street Manchester M1 5GD United Kingdom Lancashire Teaching Hospitals NHS Trust Preston PR2 9HT United Kingdom. Electronic address: m.yap@mmu.ac.uk. Department of Computing and Mathematics Manchester Metropolitan University John Dalton Building Chester Street Manchester M1 5GD United Kingdom. Institute of Fundamental Technological Research Polish Academy of Sciences Warsaw Poland RIKEN Center for Brain Science Wako Japan. Department of Computer Science National Tsing Hua University No. 101 Section 2 Kuang-Fu Road Hsinchu Taiwan. West China Biomedical Big Data Center West China Hospital Sichuan University Chengdu China. BCN Medtech Universitat Pompeu Fabra Barcelona Spain AIML University of Adelaide Australia. Institute of Electronics National Yang Ming Chiao Tung University No. 1001 University Road Hsinchu 300 Taiwan. Department of Computer Science University of Applied Sciences and Arts Dortmund (FH Dortmund) Emil-Figge-Str. 42 44227 Dortmund Germany Institute for Medical Informatics Biometry and Epidemiology (IMIBE) University Hospital Essen Zweigertstr. 37 45130 Essen Germany Institute for Artificial Intelligence in Medicine (IKIM) University Hospital Essen Girardetstr. 2 45131 Essen Germany. Institute for Artificial Intelligence in Medicine (IKIM) University Hospital Essen Girardetstr. 2 45131 Essen Germany Institute of Diagnostic and Interventional Radiology and Neuroradiology University Hospital Essen Hufelandstr. 55 45147 Essen Germany. Institute for Medical Informatics Biometry and Epidemiology (IMIBE) University Hospital Essen Zweigertstr. 37 45130 Essen Germany. West China Biomedical Big Data Center West China Hospital Sichuan University Chengdu China Shanghai Artificial Intelligence Laboratory Shanghai China. School of Artificial Intelligence Beijing University of Posts and Telecommunications Beijing China BCN Medtech Universit

Monitoring the healing progress of diabetic foot ulcers is a challenging process. Accurate segmentation of foot ulcers can help podiatrists to quantitatively measure the size of wound regions to assist prediction of healing status. The main challenge in this field is the lack of publicly available manual delineation, which can be time consuming and laborious. Recently, methods based on deep learning have shown excellent results in automatic segmentation of medical images, however, they require large-scale datasets for training, and there is limited consensus on which methods perform the best. The 2022 Diabetic Foot Ulcers segmentation challenge was held in conjunction with the 2022 International Conference on Medical Image Computing and Computer Assisted Intervention, which sought to address these issues and stimulate progress in this research domain. A training set of 2000 images exhibiting diabetic foot ulcers was released with corresponding segmentation ground truth masks. Of the 72 (approved) requests from 47 countries, 26 teams used this data to develop fully automated systems to predict the true segmentation masks on a test set of 2000 images, with the corresponding ground truth segmentation masks kept private. Predictions from participating teams were scored and ranked according to their average Dice similarity coefficient of the ground truth masks and prediction masks. The winning team achieved a Dice of 0.7287 for diabetic foot ulcer segmentation. This challenge has now entered a live leaderboard stage where it serves as a challenging benchmark for diabetic foot ulcer segmentation.

关键词： Convolutional neural networks Deep learning Diabetic foot ulcers Metrics Segmentation

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Allogeneic Hematopoietic Cell Transplantation (HCT) Vs. Non-HCT Consolidation Therapies in Acute Myeloid Leukemia (AML) Patients 60-75 Years of Age in First Complete Remission (CR1): An Alliance (A151509), SWOG, ECOG-ACRIN and CIBMTR Study

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Blood 2018年 132卷 2170-2170页

作者： Celalettin Ustun Jennifer Le-Rademacher Hai-Lin Wang Megan Othus Zhuoxin Sun Brittny Major Mei-Jie Zhang Elizabeth Storrick Jacqueline M Lafky Selina Chow Krzysztof Mrózek Eyal C. Attar Clara D. Bloomfield Larry D Cripe Richard A. Larson Guido Marcucci Gail J. Roboz Geoffrey L. Uy Richard M. Stone Aminah Jatoi Andrew S Artz Blood and Marrow Transplant Program University of Minnesota Minneapolis MN Dept of Biomedical Statistics and Informatics Mayo Clinic Rochester MN CIBMTR (Center for International Blood and Marrow Transplant Research) Department of Medicine Medical College of Wisconsin Milwaukee WI Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle Harvard T.H. Chan School of Public Health Boston Department of Health Sciences Research Mayo Clinic Rochester Alliance Statistics and Data Center Mayo Clinic Rochester MN Mayo Clinic Rochester University of Chicago Comprehensive Cancer Center Chicago The Ohio State University Comprehensive Cancer Center Columbus OH Massachusetts General Hospital Boston Agios Pharmaceuticals Inc. Cambridge MA Comprehensive Cancer Center The Ohio State University Columbus OH Indiana University Simon Cancer Center Indianapolis Department of Medicine and Comprehensive Cancer Center University of Chicago Chicago IL Department of Hematological Malignancies Translational Science Gehr Family Center for Leukemia Research Hematologic Malignancies and Stem Cell Transplantation Institute Beckman Research Institute City of Hope Medical Center Duarte CA Weill Cornell Medicine and The Weill Medical College of Cornell University New York NY Washington University School of Medicine Saint Louis MO Dana-Farber Cancer Institute Boston MA Department of Medicine Section of Hematology/Oncology University of Chicago Chicago IL

Introduction: The preferred post-remission therapy for older patients (pts) with AML remains uncertain. We compared outcomes for older AML pts in CR1 receiving HCT reported to the CIBMTR to older AML pts achieving CR1 on National Clinical Trials Network induction and non-HCT consolidation therapy (CT) trials. Methods: This study focused on pts 60-75 years of age treated between 2004 to 2013. CT pts (n=211) underwent induction and consolidation on Alliance for Clinical Trials in Oncology, ECOG-ACRIN or SWOG clinical trials for initial therapy for newly diagnosed AML; the CIBMTR provided data for HCT pts (n=431). CT patients received at least one cycle of CT on study and were excluded if HCT occurred at any time. Time to event started at CR1 and pts entered at CT or HCT, respectively, using left-truncation to account for differential entry times. Results: For the CT cohort, first consolidation included standard therapy (e.g., cytarabine or a hypomethylating agent) and additional study drug (e.g., bortezomib, dasatinib, sorafenib, and Zosuquidar, gemtuzumab) or tipifarnib alone. Among HCT pts, the donor was a HLA-matched sibling or unrelated donor (URD) in 66% and the others were partially HLA-matched/mismatched URD (10%) or cord blood (24%). HCT pts were younger and more frequently had high-risk AML (high WBC, secondary AML and unfavorable cytogenetics) (Table). The median time from CR1 to HCT and CT was 3.2 and 0.5 months, respectively. Allogeneic HCT showed worse overall survival (OS) (HR=1.52, p=0.02) prior to 9 months and better OS thereafter (HR= 0.53, p <0.0001) relative to CT (figure 1A). Treatment-related mortality (TRM) was worse after HCT in the first 9 months (HR=2.8, CI: 1.5 -5.2, p =.0009), while relapse was less frequent beyond 9 months after treatment (HR = 0.42, CI: 0.29 to 0.61, p <.0001). Despite higher early TRM, HCT recipients went on to manifest superior OS [5 year OS: HCT 29% (24-34%), CT 13.8% (9 -22%)] (Figure 1A). The benefit of HCT for surviv

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Brain Tumor Segmentation (BraTS) Challenge 2024: Meningioma Radiotherapy Planning Automated Segmentation

arXiv

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arXiv 2024年

作者： LaBella, Dominic Schumacher, Katherine Mix, Michael Leu, Kevin McBurney-Lin, Shan Nedelec, Pierre Villanueva-Meyer, Javier Shapey, Jonathan Vercauteren, Tom Chia, Kazumi Ivory, Marina Barfoot, Theodore Al-Salihi, Omar Leu, Justin Halasz, Lia Velichko, Yury Wang, Chunhao Kirkpatrick, John Floyd, Scott Reitman, Zachary J. Mullikin, Trey Bagci, Ulas Sachdev, Sean Hattangadi-Gluth, Jona A. Seibert, Tyler M. Farid, Nikdokht Puett, Connor Pease, Matthew W. Shiue, Kevin Anwar, Syed Muhammad Faghani, Shahriar Taylor, Peter Haider, Muhammad Ammar Warman, Pranav Albrecht, Jake Jakab, András Moassefi, Mana Chung, Verena Aristizabal, Alejandro Karargyris, Alexandros Kassem, Hasan Pati, Sarthak Sheller, Micah Coley, Aaron Huang, Christina Ghanta, Siddharth Schneider, Alex Sharp, Conrad Saluja, Rachit Kofler, Florian Lohmann, Philipp Vollmuth, Phillipp Gagnon, Louis Adewole, Maruf Li, Hongwei Bran Kazerooni, Anahita Fathi Tahon, Nourel Hoda Anazodo, Udunna Moawad, Ahmed W. Menze, Bjoern Linguraru, Marius George Aboian, Mariam Wiestler, Benedikt Baid, Ujjwal Conte, Gian-Marco Rauschecker, Andreas M. Nada, Ayman Abayazeed, Aly H. Huang, Raymond de Verdier, Maria Correia Rudie, Jeffrey D. Bakas, Spyridon Calabrese, Evan Department of Radiation Oncology Duke University Medical Center DurhamNC United States Department of Radiation Oncology SUNY Upstate Medical University SyracuseNY United States San FranciscoCA United States Department of Neurosurgery King’s College Hospital London United Kingdom School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Guy’s and St Thomas’ NHS Foundation Trust United Kingdom Department of Radiation Oncology University of Washington SeattleWA United States Department of Radiology Northwestern University EvanstonIL United States Department of Radiation Oncology Northwestern University EvanstonIL United States Department of Radiation Medicine and Applied Sciences University of California San Diego La Jolla CA United States Department of Radiology University of California San Diego La Jolla CA United States Department of Bioengineering University of California San Diego La Jolla CA United States Department of Neurological Surgery Indiana University School of Medicine IndianapolisIN United States Department of Radiation Oncology Indiana University IndianapolisIN United States Children’s National Hospital WashingtonDC United States George Washington University WashingtonDC United States Mayo Clinic RochesterMN United States CMH Lahore Medical College Lahore Pakistan Duke University Medical Center School of Medicine DurhamNC United States Sage Bionetworks United States University of Zürich Zürich Switzerland Artificial Intelligence Lab Department of Radiology Mayo Clinic RochesterMN United States MLCommons United States Factored AI United States Center For Federated Learning in Medicine Indiana University IndianapolisIN United States Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Medical Working Group MLCommons San FranciscoCA United States Intel United States Duke Universi

The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aims to advance automated segmentation algorithms using the largest known multi-institutional dataset of 750 radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or postoperative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery. Each case includes a defaced 3D post-contrast T1-weighted radiotherapy planning MRI in its native acquisition space, accompanied by a single-label "target volume" representing the gross tumor volume (GTV) and any at-risk postoperative site. Target volume annotations adhere to established radiotherapy planning protocols, ensuring consistency across cases and institutions. For preoperative meningiomas, the target volume encompasses the entire GTV and associated nodular dural tail, while for postoperative cases, it includes at-risk resection cavity margins as determined by the treating institution. Case annotations were reviewed and approved by expert neuroradiologists and radiation oncologists. Participating teams will develop, containerize, and evaluate automated segmentation models using this comprehensive dataset. Model performance will be assessed using an adapted lesion-wise Dice Similarity Coefficient and the 95% Hausdorff distance. The top-performing teams will be recognized at the Medical Image Computing and Computer Assisted Intervention Conference in October 2024. BraTS-MEN-RT is expected to significantly advance automated radiotherapy planning by enabling precise tumor segmentation and facilitating tailored treatment, ultimately improving patient outcomes. © 2024, CC BY.

关键词： Radiotherapy

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology (vol 13, 634, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-13页

作者： Bjornsdottir, Gyda Stefansdottir, Lilja Thorleifsson, Gudmar Sulem, Patrick Norland, Kristjan Ferkingstad, Egil Oddsson, Asmundur Zink, Florian Lund, Sigrun H. Nawaz, Muhammad S. Walters, G. Bragi Skuladottir, Astros Th. Gudjonsson, Sigurjon A. Einarsson, Gudmundur Halldorsson, Gisli H. Bjarnadottir, Valgerdur Sveinbjornsson, Gardar Helgadottir, Anna Styrkarsdottir, Unnur Gudmundsson, Larus J. Pedersen, Ole B. Hansen, Thomas Folkmann Werge, Thomas Banasik, Karina Troelsen, Anders Skou, Soren T. Thorner, Lise Wegner Erikstrup, Christian Nielsen, Kaspar Rene Mikkelsen, Susan Jonsdottir, Ingileif Bjornsson, Aron Olafsson, Ingvar H. Ulfarsson, Elfar Blondal, Josep Vikingsson, Arnor Brunak, Soren Ostrowski, Sisse R. Ullum, Henrik Thorsteinsdottir, Unnur Stefansson, Hreinn Gudbjartsson, Daniel F. Thorgeirsson, Thorgeir E. Stefansson, Kari deCODE Genetics/Amgen Inc. Reykjavik Iceland (GRID:grid.421812.c) (ISNI:0000 0004 0618 6889) deCODE Genetics/Amgen Inc. Reykjavik Iceland (GRID:grid.421812.c) (ISNI:0000 0004 0618 6889) University of Iceland Faculty of Medicine School of Health Sciences Reykjavik Iceland (GRID:grid.14013.37) (ISNI:0000 0004 0640 0021) deCODE Genetics/Amgen Inc. Reykjavik Iceland (GRID:grid.421812.c) (ISNI:0000 0004 0618 6889) University of Iceland School of Engineering and Natural Sciences Reykjavik Iceland (GRID:grid.14013.37) (ISNI:0000 0004 0640 0021) Landspitali University Hospital Reykjavik Iceland (GRID:grid.410540.4) (ISNI:0000 0000 9894 0842) Zealand University Hospital Department of Clinical Immunology Køge Denmark (GRID:grid.512923.e) (ISNI:0000 0004 7402 8188) University of Copenhagen Department of Clinical Medicine Faculty of Health and Medical Sciences Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) Rigshospitalet-Glostrup Danish Headache Center Dept. Neurology Glostrup Denmark (GRID:grid.475435.4) University of Copenhagen Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) University of Copenhagen Department of Clinical Medicine Faculty of Health and Medical Sciences Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) Copenhagen University Hospital Institute of Biological Psychiatry Mental Health Services Copenhagen Denmark (GRID:grid.4973.9) (ISNI:0000 0004 0646 7373) University of Copenhagen Lundbeck Foundation for GeoGenetics GLOBE Institute Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) University of Copenhagen Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X) University of Copenhagen Department of Clinical Medicine Faculty of Health and Medical Sciences Copenhagen Denmark (GRID:grid.5254.6) (ISNI:0000 0001

Back pain is a common and debilitating disorder with largely unknown underlying biology. Here we report a genome-wide association study of back pain using diagnoses assigned in clinical practice; dorsalgia (119,100 cases, 909,847 controls) and intervertebral disc disorder (IDD) (58,854 cases, 922,958 controls). We identify 41 variants at 33 loci. The most significant association (ORIDD = 0.92, P = 1.6 × 10−39; ORdorsalgia = 0.92, P = 7.2 × 10−15) is with a 3’UTR variant (rs1871452-T) in CHST3, encoding a sulfotransferase enzyme expressed in intervertebral discs. The largest effects on IDD are conferred by rare (MAF = 0.07 − 0.32%) loss-of-function (LoF) variants in SLC13A1, encoding a sodium-sulfate co-transporter (LoF burden OR = 1.44, P = 3.1 × 10−11); variants that also associate with reduced serum sulfate. Genes implicated by this study are involved in cartilage and bone biology, as well as neurological and inflammatory *** is known about the biology of back pain, a leading cause of disability. Here the authors report 30 new back pain loci, implicating genes involved in cartilage/bone biology, as well as neurological and inflammatory processes.

关键词： Bone Genome-wide association studies Pain

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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