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33P Immune analysis of lymph nodes in relation to the presence or absence of tumour infiltrating lymphocytes in triple negative breast cancers

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Annals of Oncology 2020年 31卷 S27-S27页

作者： A. Quintana V. Peg T. Moline A. Prat L. Paré P. Galván G. Villacampa R. Dientsmann J. Perez E. Muñoz M. Martí J. Blanco-Heredia C. Dos Anjos M. Vazquez L. de Mattos J. Cortés Breast Cancer Unit Vall d'Hebron University Hospital Barcelona Spain Pathology Department Vall d'Hebron University Hospital Universidad Autónoma de Barcelona Spanish Biomedical Research Network Centre in Oncology (CIBERONC) (Madrid) Barcelona Spain Pathology Department Vall d'Hebron University Hospital Barcelona Spain Medical Oncology Department Hospital Clinic y Provincial de Barcelona Translational Genomics and Targeted Therapeutics Group (IDIBAPS) Barcelona Spain Translational Genomics and Targeted Therapeutics Group Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Barcelona Spain Oncology Data Science (ODysSey Group) Vall d'Hebron University Hospital Barcelona Spain Medical Oncology Department IOB Institute of Oncology Quironsalud Group Barcelona Spain Medical Oncology Department Vall d'Hebron University Hospital Barcelona Spain Cell Immunology Laboratory Universidad Autónoma de Barcelona Bellaterra Spain IrsiCaixa Hospital Universitari Trias i Pujol Badalona Spain Genome Bioinformatics Barcelona Supercomputing Center Barcelona Spain Vall d'Hebron Institute of Oncology (VHIO) IOB Institute of Oncology Madrid & Barcelona Quironsalud Group Barcelona Spain

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Dynamic prediction of mortality in COVID-19 patients in the intensive care unit: A retrospective multi-center cohort study

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Intelligence-Based Medicine 2022年 6卷 100071-100071页

作者： Smit, J.M. Krijthe, J.H. Endeman, H. Tintu, A.N. de Rijke, Y.B. Gommers, D.A.M.P.J. Cremer, O.L. Bosman, R.J. Rigter, S. Wils, E.-J. Frenzel, T. Dongelmans, D.A. De Jong, R. Peters, M.A.A. Kamps, M.J.A. Ramnarain, D. Nowitzky, R. Nooteboom, F.G.C.A. De Ruijter, W. Urlings-Strop, L.C. Smit, E.G.M. Mehagnoul-Schipper, D.J. Dormans, T. De Jager, C.P.C. Hendriks, S.H.A. Achterberg, S. Oostdijk, E. Reidinga, A.C. Festen-Spanjer, B. Brunnekreef, G.B. Cornet, A.D. Van den Tempel, W. Boelens, A.D. Koetsier, P. Lens, J.A. Faber, H.J. karakus, A. Entjes, R. De Jong, P. Rettig, T.C.D. Arbous, M.S. Lalisang, R.C.A. Tonutti, M. De Bruin, D.P. Elbers, P.W.G. Van Bommel, J. Reinders, M.J.T. Intensive Care Erasmus University Medical Center Rotterdam Netherlands Pattern Recognition & Bioinformatics Group EEMCS Delft University of Technology Delft Netherlands Clinical Chemistry Erasmus University Medical Center Rotterdam Netherlands Intensive Care UMC Utrecht Utrecht Netherlands Intensive Care OLVG Amsterdam Netherlands Anesthesiology and Intensive Care St. Antonius Hospital Nieuwegein Netherlands Intensive Care Franciscus Gasthuis Vlietland Rotterdam Netherlands Intensive Care Radboud University Medical Center Nijmegen Netherlands Intensive Care Amsterdam UMC Amsterdam Netherlands Intensive Care Bovenij Ziekenhuis Amsterdam Netherlands Intensive Care Canisius Wilhelmina Ziekenhuis Nijmegen Netherlands Intensive Care Catharina Ziekenhuis Eindhoven Eindhoven Netherlands Intensive Care ETZ Tilburg Tilburg Netherlands Intensive Care HagaZiekenhuis Den Haag Netherlands Intensive Care Laurentius Ziekenhuis Roermond Netherlands Intensive Care Northwest Clinics Alkmaar Netherlands Intensive Care Reinier de Graaf Gasthuis Delft Netherlands Intensive Care Spaarne Gasthuis Haarlem en Hoofddorp Netherlands Intensive Care VieCuri Medisch Centrum Venlo Netherlands Intensive Care Zuyderland MC Heerlen Netherlands Intensive Care Jeroen Bosch Ziekenhuis 's-Hertogenbosch Netherlands Intensive Care Albert Schweitzerziekenhuis Dordrecht Netherlands Intensive Care Haaglanden Medisch Centrum Den Haag Netherlands Intensive Care Maasstad Ziekenhuis Rotterdam Rotterdam Netherlands Intensive Care SEH BWC Martiniziekenhuis Groningen Netherlands Intensive Care Ziekenhuis Gelderse Vallei Ede Netherlands Intensive Care Ziekenhuisgroep Twente Almelo Netherlands Intensive Care Medisch Spectrum Twente Enschede Netherlands Intensive Care Ikazia Ziekenhuis Rotterdam Rotterdam Netherlands Anesthesiology Antonius Ziekenhuis Sneek Sneek Netherlands Intensive Care Medisch Centrum Leeuwarden Leeuwarden Netherlands Intensive Care IJsselland Zieke

Background: The COVID-19 pandemic continues to overwhelm intensive care units (ICUs) worldwide, and improved prediction of mortality among COVID-19 patients could assist decision making in the ICU setting. In this work, we report on the development and validation of a dynamic mortality model specifically for critically ill COVID-19 patients and discuss its potential utility in the ICU. Methods: We collected electronic medical record (EMR) data from 3222 ICU admissions with a COVID-19 infection from 25 different ICUs in the Netherlands. We extracted daily observations of each patient and fitted both a linear (logistic regression) and non-linear (random forest) model to predict mortality within 24 h from the moment of prediction. Isotonic regression was used to re-calibrate the predictions of the fitted models. We evaluated the models in a leave-one-ICU-out (LOIO) cross-validation procedure. Results: The logistic regression and random forest model yielded an area under the receiver operating characteristic curve of 0.87 [0.85;0.88] and 0.86 [0.84;0.88], respectively. The recalibrated model predictions showed a calibration intercept of −0.04 [−0.12;0.04] and slope of 0.90 [0.85;0.95] for logistic regression model and a calibration intercept of −0.19 [−0.27;−0.10] and slope of 0.89 [0.84;0.94] for the random forest model. Discussion: We presented a model for dynamic mortality prediction, specifically for critically ill COVID-19 patients, which predicts near-term mortality rather than in-ICU mortality. The potential clinical utility of dynamic mortality models such as benchmarking, improving resource allocation and informing family members, as well as the development of models with more causal structure, should be topics for future research. © 2022 The Authors

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Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs

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Nature Communications 2025年第1期16卷 1-20页

作者： Thoms, Julie A. I. Yan, Feng Hampton, Henry R. Davidson, Sarah Joshi, Swapna Saw, Jesslyn Sarowar, Chowdhury H. Lim, Xin Ying Nunez, Andrea C. Kakadia, Purvi M. Bhuyan, Golam Sarower Zou, Xiaoheng Nguyen, Mary Ghodousi, Elaheh S. Koch, Forrest C. Vafaee, Fatemeh Thompson, I. Richard Karimi, Mohammad M. Pickford, Russell Raftery, Mark J. Hough, Sally Buckland, Griselda Bailey, Michelle Ghodke, Yuvaraj Absar, Noorul Vaughan, Lachlin Pasalic, Leonardo Fong, Chun Y. Kenealy, Melita Hiwase, Devendra K. Stoddart, Rohanna I. Mohammed, Soma Lee, Linda Passam, Freda H. Larsen, Stephen R. Spring, Kevin J. Skarratt, Kristen K. Rebeiro, Patricia Presgrave, Peter Stevenson, William S. Ling, Silvia Tiley, Campbell Fuller, Stephen J. Roncolato, Fernando Enjeti, Anoop K. Hoenemann, Dirk Lemech, Charlotte Jolly, Christopher J. Bohlander, Stefan K. Curtis, David J. Wong, Jason W. H. Unnikrishnan, Ashwin Hertzberg, Mark Olivier, Jake Polizzotto, Mark N. Pimanda, John E. School of Biomedical Sciences University of New South Wales Sydney NSW Australia Bioinformatics Division Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia ANU Clinical Hub for Interventional Research (CHOIR) John Curtin School of Medical Research Canberra ACT Australia Kirby Institute University of New South Wales Sydney NSW Australia School of Clinical Medicine University of New South Wales Sydney NSW Australia Australian Centre for Blood Diseases Monash University Melbourne VIC Australia Leukaemia & Blood Cancer Research Unit Department of Molecular Medicine and Pathology Faculty of Medical and Health Sciences The University of Auckland Auckland New Zealand School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia UNSW Data Science Hub University of New South Wales Sydney NSW Australia Comprehensive Cancer Centre School of Cancer and Pharmaceutical Sciences King’s College London London United Kingdom Bioanalytical Mass Spectrometry Facility University of New South Wales Sydney NSW Australia Westmead Hospital Sydney NSW Australia ICPMR Department of Haematology Westmead Hospital Sydney NSW Australia Department of Haematology Austin Health Melbourne VIC Australia Cabrini Hospital Melbourne VIC Australia Department of Haematology Royal Adelaide Hospital Adelaide SA Australia University of New South Wales Sydney NSW Australia Royal North Shore Hospital Sydney NSW Australia Haematology Research Group Heart Research Institute Sydney NSW Australia Institute of Haematology Royal Prince Alfred Hospital Sydney NSW Australia Medical Oncology Group Liverpool Clinical School School of Medicine Western Sydney University and Ingham Institute for Applied Medical Research Liverpool NSW Australia South-West Sydney Clinical Campuses UNSW Medicine & Health Sydney NSW Australia Sydney Medical School Nepean Clinical School Faculty of Medicine and Health University of Sydney

Hypomethylating agents are frontline therapies for myelodysplastic neoplasms (MDS), yet clinical responses remain unpredictable. We conducted a phase 2 trial comparing injectable and oral azacitidine (AZA) administered over one or three weeks per four-week cycle, with the primary objective of investigating whether response is linked to in vivo drug incorporation or DNA hypomethylation. Our findings show that injection results in higher drug incorporation, but lower DNA demethylation per cycle, while global DNA methylation levels in mononuclear cells are comparable between responders and non-responders. However, hematopoietic stem and progenitor cells (HSPCs) from responders exhibit distinct baseline and early treatment-induced CpG methylation changes at regulatory regions linked to tissue patterning, cell migration, and myeloid differentiation. By cycle six—when clinical responses typically emerge—further differential hypomethylation in responder HSPCs suggests marrow adaptation as a driver of improved hematopoiesis. These findings indicate that intrinsic baseline and early drug-induced epigenetic differences in HSPCs may underlie the variable clinical response to AZA in MDS. © The Author(s) 2025.

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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain. Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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Erratum for Wang et al., "Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin"

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Microbiology spectrum 2022年第1期10卷 e0261021页

作者： Hsin-Yao Wang Chia-Ru Chung Chao-Jung Chen Ko-Pei Lu Yi-Ju Tseng Tzu-Hao Chang Min-Hsien Wu Wan-Ting Huang Ting-Wei Lin Tsui-Ping Liu Tzong-Yi Lee Jorng-Tzong Horng Jang-Jih Lu Department of Laboratory Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Ph.D. Program in Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Computer Science and Information Engineering National Central Universitygrid.37589.30 Taoyuan City Taiwan. Graduate Institute of Integrated Medicine China Medical Universitygrid.254145.3 Taichung Taiwan. Proteomics Core Laboratory China Medical Universitygrid.254145.3 Hospital Taichung Taiwan. Graduate Program in Biomedical Information Yuan-Ze University Taoyuan City Taiwan. Department of Information Management Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Graduate Institute of Biomedical Informatics Taipei Medical University Taipei City Taiwan. Clinical Big Data Research Center Taipei Medical University Hospital Taipei City Taiwan. Graduate Institute of Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Division of Haematology/Oncology Department of Internal Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Biosensor Group Biomedical Engineering Research Center Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Pathology Kaohsiung Chang Gung Memorial Hospitalgrid.413801.f and Chang Gung University College of Medicine Kaohsiung Taiwan. School of Life and Health Sciences The Chinese University of Hong Kong Shenzhen China. Warshel Institute for Computational Biology The Chinese University of Hong Kong Shenzhen China. Department of Bioinformatics and Medical Engineering Asia University Taichung City Taiwan. School of Medicine Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Medical Biotechnology and Laboratory Science Chang Gung Universitygrid.145695.a Taoyuan City Taiwan.

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Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

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Nature genetics 2023年第3期55卷 519-520页

作者： Ceres Fernandez-Rozadilla Maria Timofeeva Zhishan Chen Philip Law Minta Thomas Stephanie Schmit Virginia Díez-Obrero Li Hsu Juan Fernandez-Tajes Claire Palles Kitty Sherwood Sarah Briggs Victoria Svinti Kevin Donnelly Susan Farrington James Blackmur Peter Vaughan-Shaw Xiao-Ou Shu Jirong Long Qiuyin Cai Xingyi Guo Yingchang Lu Peter Broderick James Studd Jeroen Huyghe Tabitha Harrison David Conti Christopher Dampier Mathew Devall Fredrick Schumacher Marilena Melas Gad Rennert Mireia Obón-Santacana Vicente Martín-Sánchez Ferran Moratalla-Navarro Jae Hwan Oh Jeongseon Kim Sun Ha Jee Keum Ji Jung Sun-Seog Kweon Min-Ho Shin Aesun Shin Yoon-Ok Ahn Dong-Hyun Kim Isao Oze Wanqing Wen Keitaro Matsuo Koichi Matsuda Chizu Tanikawa Zefang Ren Yu-Tang Gao Wei-Hua Jia John Hopper Mark Jenkins Aung Ko Win Rish Pai Jane Figueiredo Robert Haile Steven Gallinger Michael Woods Polly Newcomb David Duggan Jeremy Cheadle Richard Kaplan Timothy Maughan Rachel Kerr David Kerr Iva Kirac Jan Böhm Lukka-Pekka Mecklin Pekka Jousilahti Paul Knekt Lauri Aaltonen Harri Rissanen Eero Pukkala Johan Eriksson Tatiana Cajuso Ulrika Hänninen Johanna Kondelin Kimmo Palin Tomas Tanskanen Laura Renkonen-Sinisalo Brent Zanke Satu Männistö Demetrius Albanes Stephanie Weinstein Edward Ruiz-Narvaez Julie Palmer Daniel Buchanan Elizabeth Platz Kala Visvanathan Cornelia Ulrich Erin Siegel Stefanie Brezina Andrea Gsur Peter Campbell Jenny Chang-Claude Michael Hoffmeister Hermann Brenner Martha Slattery John Potter Konstantinos Tsilidis Matthias Schulze Marc Gunter Neil Murphy Antoni Castells Sergi Castellví-Bel Leticia Moreira Volker Arndt Anna Shcherbina Mariana Stern Bens Pardamean Timothy Bishop Graham Giles Melissa Southey Gregory Idos Kevin McDonnell Zomoroda Abu-Ful Joel Greenson Katerina Shulman Flavio Lejbkowicz Kenneth Offit Yu-Ru Su Robert Steinfelder Temitope Keku Bethany van Guelpen Thomas Hudson Heather Hampel Rachel Pearlman Sonja Berndt Richard Hayes Marie Elena Martinez Sushma Thomas Douglas Corley Paul Pharoah Susanna Larsson Yun Yen Heinz-Jo Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK. Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain. Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark. Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA. Division of Genetics and Epidemiology Institute of Cancer Research London UK. Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA. Genomic Medicine Institute Cleveland Clinic Cleveland OH USA. Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA. Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain. Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain. Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain. Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain. Department of Biostatistics School of Public Health University of Washington Seattle WA USA. Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK. Department of Public Health Richard Doll Building University of Oxford Oxford UK. Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA. Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA. Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA. De

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46. PAN-CANCER ANALYSIS OF ORTHOTOPIC PATIENT DERIVED XENOGRAFTS FROM BRAIN METASTASES

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Neuro-Oncology Advances 2020年第SUPPLEMENT_2期2卷 ii9-ii9页

作者： Zeng, Yu Pelton, Kristine Yerrum, Smitha Kao, Pei-Lun Sinai, Claire Tran, Tony Sinha, Rileen Shetty, Aniket Tolstorukov, Michael Y Jaber, Aliya Freitas, Dylan E Pisano, William Verselis, Sigitas J Herbert, Zach T Lin, Nancy U Zhao, Jean J Weinstock, David M Chukwueke, Ugonma N Aizer, Ayal A Chiocca, E Antonio Bi, Wenya Linda Wen, Patrick Y Lee, Eudocia Q Nayak, Lakshmi Meredith, David M Santagata, Sandro Chow, Kin-Hoe Ligon, Keith L Department of Oncologic Pathology Dana-Farber Cancer Institute Boston MA USA Department of Neurosurgery Xiangya Hospital Central South University Changsha China Center for Patient Derived Models Dana-Farber Cancer Institute Boston MA USA Bioinformatics and Data Science Group Informatics and Analytics Department Dana-Farber Cancer Institute Boston MA USA Molecular Diagnostics Laboratory Dana-Farber Cancer Institute Boston MA USA The Molecular Biology Core Facilities Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Department of Radiation Oncology Dana-Farber/Brigham and Women’s Cancer Center Harvard Medical School Boston MA USA Department of Neurosurgery Brigham and Women’s Hospital Boston MA USA Department of Pathology Brigham and Women’s Hospital Boston MA USA

Brain metastases (BM) are a leading cause of cancer death and prognosis remains poor despite treatment advances at other sites. Models are central to therapeutic development, but few orthotopic patient-derived xenograft (PDX) models of BM exist. To represent diversity across BM types, we established a program to create orthotopic PDX at scale from all BM patients. To date BM were received from 100 patients and PDX attempted by direct brain injection (PDX, n=89) or injection of low passage patient-derived cell lines (PDCLX, n=11). We created 65 successful BM PDX from 13 cancers: 17 lung (55% take), 15 breast (68%), 6 melanoma (75%), 5 CNS lymphoma (83%), 3 gastrointestinal (75%), 2 esophageal (40%), 2 ovarian (67%), 1 sarcoma (100%), 1 laryngeal (100%), 1 prostate (100%), 1 pancreatic (100%), 1 uterine adenosarcoma (100%), and 1 yolk sac tumor (100%). Take rate was similar for models derived from patients with prior chemotherapy-only versus immune/targeted therapy-only (63 vs 58%). Fifteen patients had live tumor and matching PBMCs archived for modeling in vitro immunotherapy responses. Mean time to moribund among different cancer types ranged from 27 days (yolk sac tumor) to 177.5 days (ovarian). BM PDX had a favorable timeline for preclinical study (90% moribund at 180 days). All PDX matched the patient driver SNVs and copy aberrations, even at >P4. No significant differences noted by immunodeficient strain (SCID versus NSG) or injection site (orthotopic versus heterotopic). Explants from BM PDX were able to generate long-term cell lines (60%) or short-term cultures with qualitative concordance of model-to-patient responses to targeted therapy (Osimertinib, EGFRi) and immunotherapy (Pembrolizumab, PD1i). Genomic and clinical data were used to create the DFCI BM PDX cBioPortal for public release and models distribution will be available through the DFCI Center for Patient Derived Models.

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TMOD-03. PAN-CANCER ANALYSIS OF ORTHOTOPIC PATIENT DERIVED XENOGRAFTS FROM BRAIN METASTASES

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Neuro-Oncology 2020年第SUPPLEMENT_2期22卷 ii228–ii228页

作者： Yu Zeng Kristine Pelton Smitha Yerrum Pei-Lun Kao Claire Sinai Tony Tran Rileen Sinha Aniket Shetty Michael Tolstorukov Aliya Jaber Dylan Freitas William Pisano Sigitas J Verselis Zach T Herbert Nancy Lin Jean J Zhao David M Weinstock Ugonma Chukwueke Ayal A Aizer E Antonio Chiocca Wenya Linda Bi Patrick Wen Eudocia Lee Lakshmi Nayak David Meredith Sandro Santagata Kin Hoe Chow Keith Ligon Department of Oncologic Pathology Dana-Farber Cancer Institute Boston MA USA Center for Patient Derived Models Dana-Farber Cancer Institute Boston MA USA Data Science and Bioinformatics Group Dana-Farber Cancer Institute Boston MA USA Molecular Diagnostics Laboratory Dana-Farber Cancer Institute Boston MA USA The Molecular Biology Core Facilities Dana-Farber Cancer Institute Boston MA USA Dana Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Radiation Oncology Dana-Farber/Brigham and Women’s Cancer Center Harvard Medical School Boston MA USA Brigham and Women’s Hospital and Harvard Medical School Boston MA USA Department of Neurosurgery Brigham and Women’s Hospital Boston MA USA Department of Pathology Brigham and Women’s Hospital Boston MA USA

Brain metastases (BM) are a leading cause of cancer death and prognosis remains poor despite treatment advances at other sites. Models are central to therapeutic development, but few orthotopic patient-derived xenograft (PDX) models of BM exist. To represent diversity across BM types, we established a program to create orthotopic PDX at scale from all BM patients. To date BM were received from 100 patients and PDX attempted by direct brain injection (PDX, n=89) or injection of low passage patient-derived cell lines (PDCLX, n=11). We created 65 successful BM PDX from 13 cancers: 17 lung (55% take), 15 breast (68%), 6 melanoma (75%), 5 CNS lymphoma (83%), 3 gastrointestinal (75%), 2 esophageal (40%), 2 ovarian (67%), 1 sarcoma (100%), 1 laryngeal (100%), 1 prostate (100%), 1 pancreatic (100%), 1 uterine adenosarcoma (100%), and 1 yolk sac tumor (100%). Take rate was similar for models derived from patients with prior chemotherapy-only versus immune/targeted therapy-only (63 vs 58%). Fifteen patients had live tumor and matching PBMCs archived for modeling in vitro immunotherapy responses. Mean time to moribund among different cancer types ranged from 27 days (yolk sac tumor) to 177.5 days (ovarian). BM PDX had a favorable timeline for preclinical study (90% moribund at 180 days). All PDX retained high fidelity to the patient driver SNVs and copy aberrations, even at >P4. No significant differences noted by immunodeficient strain (SCID versus NSG) or injection site (orthotopic versus heterotopic). Explants from BM PDX were able to generate long-term cell lines (60%) or short-term cultures with qualitative concordance of model-to-patient responses to targeted therapy (Osimertinib, EGFRi) and immunotherapy (Pembrolizumab, PD1i). Genomic and clinical data were used to create the DFCI BM PDX cBioPortal for public release and models distribution will be available through the DFCI Center for Patient Derived Models.

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Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

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npj Genomic Medicine 2024年第1期9卷 49页

作者： Demidov, German Yaldiz, Burcu Garcia-Pelaez, José de Boer, Elke Schuermans, Nika Van de Vondel, Liedewei Paramonov, Ida Johansson, Lennart F. Musacchia, Francesco Benetti, Elisa Bullich, Gemma Sablauskas, Karolis Beltran, Sergi Gilissen, Christian Hoischen, Alexander Ossowski, Stephan de Voer, Richarda Lohmann, Katja Oliveira, Carla Topf, Ana Vissers, Lisenka E. L. M. Zguro, Kristina Zara, Federico Zaganas, Ioannis Yépez, Vicente A. Wirth, Brunhilde Webb, David Verdin, Hannah Van Nieuwenhove, Erika van Montfrans, Joris van Heurck, Roxane van der Veken, Lars Valle, Laura Uva, Paolo Udd, Bjarne Trimouille, Aurelien Thompson, Rachel Tartaglia, Marco Sznajer, Yves Striano, Pasquale Steinke-Lange, Verena Spilioti, Martha Scudieri, Paolo Schröck, Evelin Schon, Katherine Scala, Marcello Savarese, Marco Santen, Gijs W. E. Rump, Andreas Ruivenkamp, Claudia A. L. Roos, Andreas Rooryck, Caroline Riva, Antonella Renieri, Alessandra Ratnaike, Thiloka Radio, Francesca Clementina Privitera, Flavia De la Paz, Manuel Posada Poppe, Bruce Polavarapu, Kiran Platzer, Konrad Peterlin, Borut Pérez-Dueñas, Belén Pauly, Martje Parrini, Elena Olimpio, Catarina Reghan, Mary O. de Benito, Daniel Natera Osorio, Andrés Nascimento Munell, Francina Münchau, Alexander Moortgat, Stéphanie Monestier, Olivier Molnar, Maria Judit Meunier, Colombine Mertes, Christian Mei, Davide Maystadt, Isabelle May, Patrick Maver, Ales Mathioudakis, Lambros Masclaux, Frédéric Mary, Sandrine Delgado, Beatriz Martínez Marcé-Grau, Anna Malaichamy, Sivasankar Macaya, Alfons Luknárová, Rebeka Martín, Estrella López Lochmüller, Hanns Leitão, Elsa Lederer, Damien Leavis, Helen Laner, Andreas Lacombe, Didier Krass, Leon Korff, Christian Kokosali, Evgenia Karakaya, Mert Karadurmus, Deniz Kapaki, Elisabeth Johari, Mridul Iacomino, Michele Huibers, Manon Horvath, Rita Holinski-Feder, Elke Hoffer, Mariette J. V. Herzog, Rebecca Hemelsoet, Dimitri Bouveret, Eva Hammar Haimel, Matthias Hackman, Peter Guerrini, Renzo Grimbacher, Bodo Greally, Marie Ghani, Hamidah Gagneur, Julien Institute of Medical Genetics and Applied Genomics University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen Tübingen Germany Department of Human Genetics Radboud University Medical Center Nijmegen Netherlands Department of Clinical Genetics Maastricht University Medical Center Maastricht Netherlands i3S - Instituto de Investigação e Inovação em Saúde Rua Alfredo Allen 208 Porto 4200-135 Portugal IPATIMUP - Institute of Molecular Pathology and Immunology University of Porto Porto Portugal Faculty of Medicine University of Porto Porto Portugal Donders Institute for Brain Cognition and Behaviour Radboud University Nijmegen Netherlands Department of Clinical Genetics Erasmus MC University Medical Center Rotterdam Netherlands Center for Medical Genetics Ghent University Hospital Ghent Belgium Translational Neurosciences Faculty of Medicine and Health Sciences University of Antwerp Antwerp Belgium Laboratory of Neuromuscular Pathology Institute Born-Bunge University of Antwerp Antwerp Belgium Centro Nacional de Análisis Genómico (CNAG) C/Baldiri Reixac 4 Barcelona 08028 Spain Universitat de Barcelona (UB) Barcelona Spain University of Groningen University Medical Center Groningen Department of Genetics Groningen Netherlands Center for Human Technologies Italian Institute of Technology (IIT) Genova Italy Telethon Institute for Genetics and Medicine Pozzuoli (Napoli) 80078 Italy Department of Medical Biotechnologies Med Biotech Hub and Competence Center University of Siena Siena 53100 Italy Institute of Data Science and Digital Technologies Vilnius University Vilnius Lithuania Departament de Genètica Microbiologia i Estadística Facultat de Biologia Universitat de Barcelona (UB) Barcelona Spain Radboud Institute for Molecular Life Sciences Nijmegen Netherlands Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI) Radboud University Medical Center Nijmegen N

We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs. © The Author(s) 2024.

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Genomics and epidemiology for gastric adenocarcinomas (GE4GAC): a Brazilian initiative to study gastric cancer

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Applied Cancer Research 2019年第1期39卷 1-4页

作者： Bartelli, Thais F. Senda de Abrantes, Lais L. Freitas, Helano C. Thomas, Andrew M. Silva, Jordana M. Albuquerque, Gabriela E. Araújo, Luiza F. Branco, Gabriela P. de Amorim, Maria G. Serpa, Marianna S. Takenaka, Isabella K. T. M. Souza, Deborah T. Monção, Lucas O. Moda, Bruno S. Valieris, Renan Defelicibus, Alexandre Borges, Rodrigo Drummond, Rodrigo D. Alves, Francisco I. A. Santos, Monize N. P. Bobrovnitchaia, Irina G. Elhaik, Eran Coelho, Luiz G. V. Khayat, André Demachki, Samia Assumpção, Paulo P. Santiago, Karina M. Torrezan, Giovana T. Carraro, Dirce M. Peres, Stela V. Calsavara, Vinícius F. Burbano, Rommel Nóbrega, Calebe R. Baladão, Graziela P. P. Pereira, Ana C. C. Gatti, Camila M. Fagundes, Marcela A. Araújo, Marília S. Miranda, Tayana V. Barbosa, Monica S. Cardoso, Daniela M. M. Carneiro, Lilian C. Brito, Alexandre M. Ramos, Amanda F. P. L. Silva, Lucas L. L. Pontes, Jaqueline C. Tiengo, Tatiane Arantes, Paola E. Santana, Vilma Cordeiro, Milena Sant’Ana, Rosane O. Andrade, Hanna B. Anaissi, Ana K. M. Sampaio, Sara V. Abdallah, Emne A. Chinen, Ludmilla T. D. Braun, Alexcia C. Flores, Bianca C. T. Mello, Celso A. L. Claro, Laura C. L. Sztokfisz, Claudia Z. Altamirano, Carlos C. Carter, David R. F. Jesus, Victor H. F. Riechelmann, Rachel Medina, Tiago Gollob, Kenneth J. Martins, Vilma R. Setúbal, João C. Pelosof, Adriane G. Coimbra, Felipe J. Costa-Jr, Wilson L. Silva, Israel T. Nunes, Diana N. Curado, Maria P. Dias-Neto, Emmanuel Lab of Medical Genomics A.C.Camargo Cancer Center Sao Paulo Brazil International Research Center A.C.Camargo Cancer Center Sao Paulo Brazil Clinical Oncology Department A.C. Camargo Cancer Center São Paulo Brazil Department CIBIO University of Trento Trento Italy Biochemistry Department Chemistry Institute Universidade de São Paulo São Paulo Brazil Lab. of Bioinformatics and Computational Biology A.C.Camargo Cancer Center Sao Paulo Brazil Data Science group International Research Center A.C.Camargo Cancer Center Sao Paulo Brazil Department of Animal & Plant Sciences University of Sheffield Sheffield UK Instituto Alfa de Gastroenterologia Hospital das Clínicas Universidade Federal de Minas Gerais Belo Horizonte Brazil Instituto de Ciências Biológicas Universidade Federal do Pará Belém Brazil Núcleo de Pesquisas em Oncologia Universidade Federal do Pará Belém Brazil Lab. de Genômica e Biologia Molecular A.C.Camargo Cancer Center Sao Paulo Brazil Epidemiology and Statistics Group A.C.Camargo Cancer Center Sao Paulo Brazil Laboratório de Biologia Molecular Hospital Ophir Loyola Belém Brazil Universidade Federal de Goiás IPTESP – Instituto de Patologia Tropical e Saúde Pública Goiânia Brazil Department of Abdominal Surgery Hospital Araujo Jorge Goiânia Brazil Instituto de Saúde Coletiva da Universidade Federal da Bahia Salvador Brazil Instituto do Cancer do Ceará Fortaleza Brazil Department of Pathology A.C.Camargo Cancer Center São Paulo Brazil Endoscopy sector A.C.Camargo Cancer Center São Paulo Brazil Instituto Nacional de Enfermedades Neoplásicas Surquillo Peru Dept. of Biological and Medical Sciences Faculty of Health and Life Sciences Oxford Brookes University Oxford UK Translational Immuno-oncology Group A.C.Camargo Cancer Center Sao Paulo Brazil Tumor Biology and Biomarkers Group A.C.Camargo Cancer Center Sao Paulo Brazil Department of Abdominal Surgery A.C.Camargo Cancer Center São Paulo Brazil

Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epidemiological factors and the rich ancestral admixture found in Brazil, stimulated the implementation of the GE4GAC project. GE4GAC aims to embrace epidemiological, clinical, molecular and microbiological data from Brazilian controls and patients with malignant and pre-malignant gastric disease. In this letter, we summarize the main goals of the project, including subject and sample accrual and current findings.

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