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Chapman OS, Luebeck J, Sridhar S, Wong ITL, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JEA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet 2023; 55:2189-2199. [PMID: 37945900 PMCID: PMC10703696 DOI: 10.1038/s41588-023-01551-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.
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Affiliation(s)
- Owen S Chapman
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Sunita Sridhar
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Deobrat Dixit
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Shanqing Wang
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Gino Prasad
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Meghana S Pagadala
- Medical Scientist Training Program, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | - Jon D Larson
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Joshua T Lange
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | | | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ling Morgan
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Sameena Wani
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Ashutosh Tiwari
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Caitlin Guccione
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yingxi Lin
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Aditi Dutta
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Yan Yuen Lo
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Edwin Juarez
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - James T Robinson
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - John-Edward A Michaels
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Yoon-Jae Cho
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Denise M Malicki
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Michael L Levy
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - John R Crawford
- Department of Pediatrics, University of California Irvine and Children's Hospital Orange County, Irvine, CA, USA
| | - Scott L Pomeroy
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeremy N Rich
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anindya Bagchi
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | | | - Hannah Carter
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA.
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Haas BJ, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson JT, Gillani R, Kasif S, Regev A. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Rep Methods 2023; 3:100467. [PMID: 37323575 PMCID: PMC10261907 DOI: 10.1016/j.crmeth.2023.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 06/17/2023]
Abstract
Here, we present FusionInspector for in silico characterization and interpretation of candidate fusion transcripts from RNA sequencing (RNA-seq) and exploration of their sequence and expression characteristics. We applied FusionInspector to thousands of tumor and normal transcriptomes and identified statistical and experimental features enriched among biologically impactful fusions. Through clustering and machine learning, we identified large collections of fusions potentially relevant to tumor and normal biological processes. We show that biologically relevant fusions are enriched for relatively high expression of the fusion transcript, imbalanced fusion allelic ratios, and canonical splicing patterns, and are deficient in sequence microhomologies between partner genes. We demonstrate that FusionInspector accurately validates fusion transcripts in silico and helps characterize numerous understudied fusions in tumor and normal tissue samples. FusionInspector is freely available as open source for screening, characterization, and visualization of candidate fusions via RNA-seq, and facilitates transparent explanation and interpretation of machine-learning predictions and their experimental sources.
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Affiliation(s)
- Brian J. Haas
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | | | | | - Anne Van Arsdale
- Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein Montefiore Medical Center, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Timothy Tickle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James T. Robinson
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
- Boston Children’s Hospital, Boston, MA 02115, USA
| | - Simon Kasif
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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3
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Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun 2023; 14:2300. [PMID: 37085539 PMCID: PMC10121654 DOI: 10.1038/s41467-023-38044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Owen Chapman
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sameena Wani
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abhijit Chakraborty
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Meghana Pagadala
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Rosalind Bump
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sahaana Chandran
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Derek Reid
- Arima Genomics, Inc, San Diego, CA, 92121, USA
| | | | - Monika Mauermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Edwin F Juarez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Anne Jenseit
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - James T Robinson
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Petra Fiesel
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ling Morgan
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sunita Sridhar
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Michael Levy
- Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Denise Malicki
- Pathology, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Stephen Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Robert J Wechsler-Reya
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jennifer Cotter
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - George Michaiel
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Hannah Carter
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kulandaimanuvel Antony Michealraj
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany
| | - Jill P Mesirov
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Jesse R Dixon
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Lukas Chavez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA.
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA.
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Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics 2022; 39:6958554. [PMID: 36562559 PMCID: PMC9825295 DOI: 10.1093/bioinformatics/btac830] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/29/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required. AVAILABILITY AND IMPLEMENTATION The igv.js JavaScript component can be installed from NPM at https://www.npmjs.com/package/igv. The source code is available at https://github.com/igvteam/igv.js under the MIT open-source license. IGV-Web, the end-user application built around igv.js, is available at https://igv.org/app. The source code is available at https://github.com/igvteam/igv-webapp under the MIT open-source license. SUPPLEMENTARY INFORMATION Supplementary information is available at Bioinformatics online.
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Affiliation(s)
| | | | - Douglass Turner
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA,Moores Cancer Center, University of California San Diego La Jolla, CA 92037, USA
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5
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Okonechnikov K, Camgöz A, Park DE, Chapman O, Hübner JM, Jenseit A, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Hidalgo RA, Reid D, Juarez EF, Robinson JT, Pajtler KW, Milde T, Coufal N, Levy M, Malicki D, Nahas S, Snuderl M, Crawford J, Wechsler-Reya R, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Mesirov J, Pfister SP, Ay F, Dixon J, Kool M, Chavez L. EPEN-18. Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma. Neuro Oncol 2022. [PMCID: PMC9165136 DOI: 10.1093/neuonc/noac079.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ependymoma (EPN) is an aggressive pediatric tumor that occurs throughout the central nervous system. The two most aggressive molecular subgroups of EPN are the supratentorial ZFTA-fusion associated group (ST-EPN-ZFTA) and the posterior fossa group A (PF-EPN-A). Although the molecular characteristics underlying the tumorigenesis of these subgroups have been extensively studied, these tumors remain difficult to treat. Hence, innovative therapeutic approaches are urgently needed. Here, we used genome-wide chromosome conformation capture (Hi-C), complemented with CTCF (insulators) and H3K27ac (active enhancers) ChIP-seq, as well as gene expression and whole-genome DNA methylation profiling in primary and relapsed EPN tumors and cell lines, to identify chromosomal rearrangements and regulatory mechanisms underlying aberrant expression of genes that are essential for EPN tumorigenesis. By integrating these heterogenous data types, we have observed the formation of new topologically associated domains (‘neo-TADs’) caused by intra- and inter-chromosomal structural variants in both tumors. In addition, we observed 3D chromatin complexes of regulatory elements, and the replacement of CTCF insulators by DNA hyper-methylation in PF-EPN-A tumors. These tumor-specific 3D genome conformations can be associated with the transcriptional upregulation of nearby genes. Through inhibition experiments we validated that these newly identified genes, including RCOR2, ITGA6, LAMC1, and ARL4C, are highly essential for the survival of patient-derived EPN cell lines in a disease subgroup-specific manner. Thus, our study identifies novel potential therapeutic vulnerabilities in EPN and extends our ability to reveal tumor-dependency genes and pathways by oncogenic 3D genome conformations even in tumors that lack known genetic alterations.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Aylin Camgöz
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego , La Jolla , USA
| | - Owen Chapman
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | | | - Anne Jenseit
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology , La Jolla , USA
| | - Meghana Pagadala
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - Rosalind Bump
- Salk Institute for Biological Studies , La Jolla , USA
| | | | - Katherina Kraft
- Center for Personal Dynamic Regulomes, Stanford University , Stanford , USA
| | | | | | - Edwin F Juarez
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - James T Robinson
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital , Heidelberg , Germany
| | - Till Milde
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital , Heidelberg , Germany
| | - Nicole Coufal
- Department of Pediatrics, University of California San Diego , San Diego , USA
| | - Michael Levy
- Neurosurgery, University of California San Diego – Rady Children's Hospital , San Diego , USA
| | - Denise Malicki
- Pathology, University of California San Diego – Rady Children's Hospital , San Diego , USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine , San Diego , USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine , New York , USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health , New York , USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego – Rady Children's Hospital , San Diego , USA
| | - Robert Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Research Discovery Institute , La Jolla , USA
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics , Berlin , Germany
| | | | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - Kulandaimanuvel Antony Michealraj
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto , Toronto , Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto , Toronto , Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto , Toronto , Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego , La Jolla , USA
| | - Jill Mesirov
- Moores Cancer Center, University of California San Diego (UCSD) , La Jolla , USA
| | - Stefan P Pfister
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital , Heidelberg , Germany
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology , La Jolla , USA
| | - Jesse Dixon
- Salk Institute for Biological Studies , La Jolla , USA
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Princess Máxima Center for Pediatric Oncology , Utrecth , Netherlands
| | - Lukas Chavez
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
- Moores Cancer Center, University of California San Diego (UCSD) , La Jolla , USA
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6
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Muscatello CM, Anderson JP, Boivin RL, Finkenthal DK, Gattuso A, Kramer GJ, LeSher M, Mrazkova TJ, Neilson GH, Peebles WA, Rhodes TL, Robinson JT, Torreblanca H, Zeller K, Zeng L, Zolfaghari A. Performance demonstration of vacuum microwave components critical for the operation of the ITER low-field side reflectometer. Rev Sci Instrum 2021; 92:033524. [PMID: 33820017 DOI: 10.1063/5.0040255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Final design studies in preparation for manufacturing have been performed for functional components of the vacuum portion of the ITER Low-Field Side Reflectometer (LFSR). These components consist of an antenna array, electron cyclotron heating (ECH) protection mirrors, phase calibration mirrors, and vacuum windows. Evaluation of these components was conducted at the LFSR test facility and DIII-D. The antenna array consists of six corrugated-waveguide antennas for simultaneous profile, fluctuation, and Doppler measurements. A diffraction grating, incorporated into the plasma-facing miter bend, provides protection of sensitive components from stray ECH at 170 GHz. For in situ phase calibration of the LFSR profile reflectometer, an embossed mirror is incorporated into the adjacent miter bend. Measurements of the radiated beam profile indicate that these components have a small, acceptable effect on mode conversion and beam quality. Baseline transmission characteristics of the dual-disk vacuum window are obtained and are used to guide ongoing developments. Preliminary simulations indicate that a surface-relief structure on the window surfaces can greatly improve transmission. The workability of real-time phase measurements was demonstrated on the DIII-D profile reflectometer. The new automated real-time analysis agrees well with the standard post-processing routine.
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Affiliation(s)
- C M Muscatello
- General Atomics, 3550 General Atomics Court, San Diego, California 92121-1122, USA
| | - J P Anderson
- General Atomics, 3550 General Atomics Court, San Diego, California 92121-1122, USA
| | - R L Boivin
- General Atomics, 3550 General Atomics Court, San Diego, California 92121-1122, USA
| | - D K Finkenthal
- Palomar Scientific Instruments, San Marcos, California 92069, USA
| | - A Gattuso
- General Atomics, 3550 General Atomics Court, San Diego, California 92121-1122, USA
| | - G J Kramer
- Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543-0451, USA
| | - M LeSher
- General Atomics, 3550 General Atomics Court, San Diego, California 92121-1122, USA
| | - T J Mrazkova
- Palomar Scientific Instruments, San Marcos, California 92069, USA
| | - G H Neilson
- Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543-0451, USA
| | - W A Peebles
- University of California, Los Angeles, 475 Portola Plaza, Los Angeles, California 90095-1547, USA
| | - T L Rhodes
- University of California, Los Angeles, 475 Portola Plaza, Los Angeles, California 90095-1547, USA
| | - J T Robinson
- Virginia Commonwealth University, 907 Floyd Ave., Richmond, Virginia 23284, USA
| | - H Torreblanca
- CompX, P.O. Box 2672, Del Mar, California 92014-5672, USA
| | - K Zeller
- General Atomics, 3550 General Atomics Court, San Diego, California 92121-1122, USA
| | - L Zeng
- University of California, Los Angeles, 475 Portola Plaza, Los Angeles, California 90095-1547, USA
| | - A Zolfaghari
- Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543-0451, USA
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7
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Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst 2019; 3:99-101. [PMID: 27467250 DOI: 10.1016/j.cels.2015.07.012] [Citation(s) in RCA: 874] [Impact Index Per Article: 174.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/23/2015] [Accepted: 07/29/2015] [Indexed: 10/21/2022]
Abstract
Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.
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Affiliation(s)
- Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - James T Robinson
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA
| | - Ido Machol
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA
| | - Jill P Mesirov
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Eric S Lander
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
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8
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Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst 2018; 6:256-258.e1. [PMID: 29428417 PMCID: PMC6047755 DOI: 10.1016/j.cels.2018.01.001] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/22/2017] [Accepted: 12/30/2017] [Indexed: 11/22/2022]
Abstract
Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code.
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Affiliation(s)
- James T Robinson
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Douglass Turner
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA
| | | | - Jill P Mesirov
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92037, USA
| | - Erez Lieberman Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA.
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9
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Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant Review with the Integrative Genomics Viewer. Cancer Res 2017; 77:e31-e34. [PMID: 29092934 DOI: 10.1158/0008-5472.can-17-0337] [Citation(s) in RCA: 600] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/17/2017] [Accepted: 06/29/2017] [Indexed: 11/16/2022]
Abstract
Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Here, we present a short overview of IGV's variant review features for both single-nucleotide variants and structural variants, with examples from both cancer and germline datasets. IGV is freely available at https://www.igv.org Cancer Res; 77(21); e31-34. ©2017 AACR.
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Affiliation(s)
- James T Robinson
- School of Medicine, University of California San Diego, La Jolla, California.
| | | | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jill P Mesirov
- School of Medicine, University of California San Diego, La Jolla, California.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Moores Cancer Center, University of California San Diego, La Jolla, California
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10
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Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL. Cohesin Loss Eliminates All Loop Domains. Cell 2017; 171:305-320.e24. [PMID: 28985562 PMCID: PMC5846482 DOI: 10.1016/j.cell.2017.09.026] [Citation(s) in RCA: 1040] [Impact Index Per Article: 148.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/02/2017] [Accepted: 09/18/2017] [Indexed: 01/12/2023]
Abstract
The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound by CTCF and cohesin-lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.
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Affiliation(s)
- Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | | | | | | | - Adrian L Sanborn
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Sarah E Johnstone
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Gavin D Bascom
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ivan D Bochkov
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xingfan Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaeweon Shin
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Douglass Turner
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ziyi Ye
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James T Robinson
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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11
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C Yuen RK, Merico D, Bookman M, L Howe J, Thiruvahindrapuram B, Patel RV, Whitney J, Deflaux N, Bingham J, Wang Z, Pellecchia G, Buchanan JA, Walker S, Marshall CR, Uddin M, Zarrei M, Deneault E, D'Abate L, Chan AJS, Koyanagi S, Paton T, Pereira SL, Hoang N, Engchuan W, Higginbotham EJ, Ho K, Lamoureux S, Li W, MacDonald JR, Nalpathamkalam T, Sung WWL, Tsoi FJ, Wei J, Xu L, Tasse AM, Kirby E, Van Etten W, Twigger S, Roberts W, Drmic I, Jilderda S, Modi BM, Kellam B, Szego M, Cytrynbaum C, Weksberg R, Zwaigenbaum L, Woodbury-Smith M, Brian J, Senman L, Iaboni A, Doyle-Thomas K, Thompson A, Chrysler C, Leef J, Savion-Lemieux T, Smith IM, Liu X, Nicolson R, Seifer V, Fedele A, Cook EH, Dager S, Estes A, Gallagher L, Malow BA, Parr JR, Spence SJ, Vorstman J, Frey BJ, Robinson JT, Strug LJ, Fernandez BA, Elsabbagh M, Carter MT, Hallmayer J, Knoppers BM, Anagnostou E, Szatmari P, Ring RH, Glazer D, Pletcher MT, Scherer SW. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat Neurosci 2017; 20:602-611. [PMID: 28263302 DOI: 10.1038/nn.4524] [Citation(s) in RCA: 505] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/01/2017] [Indexed: 12/13/2022]
Abstract
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.
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Affiliation(s)
- Ryan K C Yuen
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Deep Genomics Inc., Toronto, Canada
| | - Matt Bookman
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | - Jennifer L Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Rohan V Patel
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Nicole Deflaux
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | - Jonathan Bingham
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | - Zhuozhi Wang
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Janet A Buchanan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Susan Walker
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Mohammed Uddin
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Eric Deneault
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ada J S Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Stephanie Koyanagi
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Tara Paton
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ny Hoang
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Karen Ho
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Weili Li
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Fiona J Tsoi
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - John Wei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Lizhen Xu
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University, Montreal, Canada
| | - Emily Kirby
- Public Population Project in Genomics and Society, McGill University, Montreal, Canada
| | | | | | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Irene Drmic
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Sanne Jilderda
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Bonnie MacKinnon Modi
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Barbara Kellam
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michael Szego
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl Cytrynbaum
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
| | - Rosanna Weksberg
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
| | | | - Marc Woodbury-Smith
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Jessica Brian
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | - Lili Senman
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | - Alana Iaboni
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | | | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Christina Chrysler
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Jonathan Leef
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | | | - Isabel M Smith
- Departments of Pediatrics and of Psychology &Neuroscience, Dalhousie University and Autism Research Centre, IWK Health Centre, Halifax, Canada
| | - Xudong Liu
- Department of Psychiatry, Queen's University, Kinston, Canada
| | - Rob Nicolson
- Children's Health Research Institute, London, Ontario, Canada.,Western University, London, Ontario, Canada
| | | | | | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephen Dager
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - Annette Estes
- Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington, USA
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Beth A Malow
- Sleep Disorders Division, Department of Neurology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK
| | - Sarah J Spence
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Brendan J Frey
- Deep Genomics Inc., Toronto, Canada.,Department of Electrical and Computer Engineering and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - James T Robinson
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lisa J Strug
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Canada
| | - Bridget A Fernandez
- Disciplines of Genetics and Medicine, Memorial University of Newfoundland and Provincial Medical Genetic Program, Eastern Health, St. John's, Canada
| | | | - Melissa T Carter
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada.,Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA
| | | | | | - Peter Szatmari
- Child Youth and Family Services, Centre for Addiction and Mental Health, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Canada.,Department of Psychiatry, The Hospital for Sick Children, Toronto, Canada
| | - Robert H Ring
- Department of Pharmacology &Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - David Glazer
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,McLaughlin Centre, University of Toronto, Toronto, Canada
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Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB. Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics 2015; 31:2400-2. [PMID: 25617416 DOI: 10.1093/bioinformatics/btv034] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/15/2015] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. RESULTS To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program. AVAILABILITY AND IMPLEMENTATION Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html
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Affiliation(s)
- Yarden Katz
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, Department of Biology, MIT, Cambridge, MA
| | | | | | | | - Bang Wong
- The Broad Institute of Harvard, MIT, Cambridge, MA, USA
| | | | | | | | - Edoardo M Airoldi
- The Broad Institute of Harvard, MIT, Cambridge, MA, USA, Department of Statistics, Harvard University, Cambridge, MA, USA and
| | - Christopher B Burge
- Department of Biology, MIT, Cambridge, MA, Department of Biological Engineering, MIT, Cambridge, MA
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Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 2014; 159:1665-80. [PMID: 25497547 PMCID: PMC5635824 DOI: 10.1016/j.cell.2014.11.021] [Citation(s) in RCA: 4664] [Impact Index Per Article: 466.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 12/13/2022]
Abstract
We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.
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Affiliation(s)
- Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Miriam H Huntley
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elena K Stamenova
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Ivan D Bochkov
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA
| | - James T Robinson
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Adrian L Sanborn
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ido Machol
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
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14
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Li CH, van 't Erve OMJ, Robinson JT, Liu Y, Li L, Jonker BT. Electrical detection of charge-current-induced spin polarization due to spin-momentum locking in Bi2Se3. Nat Nanotechnol 2014; 9:218-224. [PMID: 24561354 DOI: 10.1038/nnano.2014.16] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/17/2014] [Indexed: 06/03/2023]
Abstract
Topological insulators exhibit metallic surface states populated by massless Dirac fermions with spin-momentum locking, where the carrier spin lies in-plane, locked at right angles to the carrier momentum. Here, we show that a charge current produces a net spin polarization via spin-momentum locking in Bi2Se3 films, and this polarization is directly manifested as a voltage on a ferromagnetic contact. This voltage is proportional to the projection of the spin polarization onto the contact magnetization, is determined by the direction and magnitude of the charge current, scales inversely with Bi2Se3 film thickness, and its sign is that expected from spin-momentum locking rather than Rashba effects. Similar data are obtained for two different ferromagnetic contacts, demonstrating that these behaviours are independent of the details of the ferromagnetic contact. These results demonstrate direct electrical access to the topological insulators' surface-state spin system and enable utilization of its remarkable properties for future technological applications.
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Affiliation(s)
- C H Li
- Materials Science and Technology Division, Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - O M J van 't Erve
- Materials Science and Technology Division, Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - J T Robinson
- Electronics Science and Technology Division, Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Y Liu
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin 53211, USA
| | - L Li
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin 53211, USA
| | - B T Jonker
- Materials Science and Technology Division, Naval Research Laboratory, Washington, District of Columbia 20375, USA
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Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014; 505:495-501. [PMID: 24390350 PMCID: PMC4048962 DOI: 10.1038/nature12912] [Citation(s) in RCA: 2177] [Impact Index Per Article: 217.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/27/2013] [Indexed: 12/13/2022]
Abstract
Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2-20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600-5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.
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Affiliation(s)
- Michael S Lawrence
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Petar Stojanov
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Craig H Mermel
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital, Cancer Center and Department of Pathology, 55 Fruit Street, Boston, Massachusetts 02114, USA
| | - James T Robinson
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Levi A Garraway
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
| | - Todd R Golub
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [4] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815, USA
| | - Matthew Meyerson
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
| | - Stacey B Gabriel
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Eric S Lander
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [3] Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4]
| | - Gad Getz
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital, Cancer Center and Department of Pathology, 55 Fruit Street, Boston, Massachusetts 02114, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [4]
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16
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van 't Erve OMJ, Friedman AL, Cobas E, Li CH, Robinson JT, Jonker BT. Low-resistance spin injection into silicon using graphene tunnel barriers. Nat Nanotechnol 2012; 7:737-42. [PMID: 23023645 DOI: 10.1038/nnano.2012.161] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/17/2012] [Indexed: 05/14/2023]
Abstract
Spin manipulation in a semiconductor offers a new paradigm for device operation beyond Moore's law. Ferromagnetic metals are ideal contacts for spin injection and detection, but the intervening tunnel barrier required to accommodate the large difference in conductivity introduces defects, trapped charge and material interdiffusion, which severely compromise performance. Here, we show that single-layer graphene successfully circumvents the classic issue of conductivity mismatch between a metal and a semiconductor for electrical spin injection and detection, providing a highly uniform, chemically inert and thermally robust tunnel barrier. We demonstrate electrical generation and detection of spin accumulation in silicon above room temperature, and show that the contact resistance-area products are two to three orders of magnitude lower than those achieved with oxide tunnel barriers on silicon substrates with identical doping levels. Our results identify a new route to low resistance-area product spin-polarized contacts, a key requirement for semiconductor spintronic devices that rely on two-terminal magnetoresistance, including spin-based transistors, logic and memory.
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Abstract
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today’s sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.
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Abstract
Abstract
Cancer genome characterization studies, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), are producing a flood of diverse data including whole-genome sequencing scans, expression profiles, high-resolution SNP and copy number data, and epigenetic profiles. These diverse datasets are enabling researchers to study the cancer genome in unprecedented detail. However, their sheer size and diversity presents significant challenges to downstream interpretation. While much progress has been made in automated analysis, human review enabled by intuitive and responsive visualizations remains an essential component of data analysis. The Integrative Genomics Viewer (IGV) was developed to address this need by providing researchers with an intuitive, user-friendly, interactive visualization tool for exploration of diverse genomic datasets. IGV has extensive support for both next-generation and micro-array based platforms, and for integration of these data types with clinical and phenotypic data. It provides an intuitive interface similar to online mapping tools such as Google Maps, enabling smooth zooming and panning at all resolution scales, from whole genome to base pairs. Data can be annotated, filtered, grouped, and sorted in a variety of ways. This ability to dynamically and flexibly integrate multiple different datasets, and view them at any scale, allows investigators to elucidate complex biological relationships that are not otherwise readily apparent. In this presentation we describe the IGV, with emphasis on recent features focused on data integration and interpretation, developed in close collaboration with cancer researchers. Specifically (1) a multi-locus pathway view which supports simultaneous viewing of data in multiple genomic regions defined by pathways or gene sets, (2) integration with external tools such as Mutation Assessor and PolyPhen, to provide views and data to asses the functional significance of somatic events, and (3) a flexible, interactive charting capability to enable detailed exploration of inter-dependencies between data types at a specific locus or set of loci. These features will be illustrated in the context of use cases drawn from the TCGA glioblastoma multiforme and ovarian datasets.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3968. doi:1538-7445.AM2012-3968
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Abstract
The interaction of small molecules (CCl(4), CS(2), H(2)O, and acetone) with single-layer graphene (SLG) has been studied under steady-state conditions using infrared multiple-internal-reflection spectroscopy. Adsorption results in a broad and intense absorption band, spanning the ∼200 to 500 meV range, which is attributed to electronic excitation. This effect, which has not previously been reported for SLG, has been further investigated using dispersion-corrected density functional theory to model the adsorption of H(2)O on SLG supported on an SiO(2) substrate. However, the ideal and defect-free model does not reproduce the observed adsorption-induced electronic transition. This and other observations suggest that the effect is extrinsic, possibly the result of an adsorption-induced change in the in-plane strain, with important differences arising between species that form liquid-like layers under steady-state conditions and those that do not. Furthermore, the C-H stretching modes of CH(2) groups, incorporated in the SLG as defects, undergo nonadiabatic coupling to the electronic transition. This leads to pronounced antiresonance effects in the line shapes, which are analyzed quantitatively. These results are useful in understanding environmental effects on graphene electronic structure and in demonstrating the use of the vibrational spectroscopy of H-containing defects in characterizing SLG structure.
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Affiliation(s)
- V M Bermudez
- Electronics Science and Technology Division, Naval Research Laboratory, Washington, DC 20375-5347, USA.
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Affiliation(s)
- James T. Robinson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Helga Thorvaldsdóttir
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Wendy Winckler
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Mitchell Guttman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric S. Lander
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jill P. Mesirov
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
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Abstract
The organization of semiconductor nanostructures into functional macroassemblies remains a fundamental challenge in nanoscience and nanotechnology. In the context of semiconductor epitaxial growth, efforts have focused on the application of advanced substrate patterning strategies for the directed assembly quantum-dot islands. We present a comprehensive investigation on the use of simple metal patterns to control the nucleation and growth of heteroepitaxial islands. In the Ge on Si model system, a square array of metal dots induces the assembly of Ge islands into an extensive two-dimensional lattice. The islands grow at sites between the metal dots and are characterized by unique shapes including truncated pyramids and nanorods, which are programmed prior to growth by the choices of metal species and substrate orientation. Our results indicate that ordering arises from the metal-induced oxidation of the Si surface; the oxide around each metal dot forms an array of periodic diffusion barriers that induce island ordering. The metals decorate the island surfaces and enhanced the growth of particular facets that are able to grow as a result of significant intermixing between deposited Ge and Si substrate atoms.
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Affiliation(s)
- J T Robinson
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
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Robinson JT, Walko DA, Arms DA, Tinberg DS, Evans PG, Cao Y, Liddle JA, Rastelli A, Schmidt OG, Dubon OD. Sculpting semiconductor heteroepitaxial islands: from dots to rods. Phys Rev Lett 2007; 98:106102. [PMID: 17358549 DOI: 10.1103/physrevlett.98.106102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Indexed: 05/14/2023]
Abstract
In the Ge on Si model heteroepitaxial system, metal patterns on the silicon surface provide unprecedented control over the morphology of highly ordered Ge islands. Island shape including nanorods and truncated pyramids is set by the metal species and substrate orientation. Analysis of island faceting elucidates the prominent role of the metal in promoting growth of preferred facet orientations while investigations of island composition and structure reveal the importance of Si-Ge intermixing in island evolution. These effects reflect a remarkable combination of metal-mediated growth phenomena that may be exploited to tailor the functionality of island arrays in heteroepitaxial systems.
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Affiliation(s)
- J T Robinson
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
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Stannard JP, Robinson JT, Anderson ER, McGwin G, Volgas DA, Alonso JE. Negative pressure wound therapy to treat hematomas and surgical incisions following high-energy trauma. ACTA ACUST UNITED AC 2006; 60:1301-6. [PMID: 16766975 DOI: 10.1097/01.ta.0000195996.73186.2e] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE To evaluate the use of negative pressure wound therapy (NPWT) to augment healing of surgical incisions and hematomas after high-energy trauma. MATERIALS This study is a prospective randomized evaluation of NPWT in trauma patients, randomizing patients with draining hematomas to either a pressure dressing (group A) or a VAC (group B). Additionally, patients with calcaneus, pilon, and high-energy tibial plateau fractures were randomized to either a standard postoperative dressing or a VAC over the sutures. RESULTS There were 44 patients randomized into the hematoma study. Group A drained a mean of 3.1 days, compared with only 1.6 days for group B. This difference was significant (p=0.03). The infection rate for group A was 16%, compared with 8% in group B. An additional 44 patients have been randomized into the fracture study. Again, a significant difference (p=0.02) was present when comparing drainage in group A (4.8 days) and group B (1.8 days). No significant difference was present at current enrollment for infection or wound breakdown. DISCUSSION NPWT has been used on many complex traumatic wounds. Potential mechanisms of action include angiogenesis, increased blood flow, and decreased interstitial fluid. This ongoing randomized study has demonstrated decreased drainage and improved wound healing following both hematomas and severe fractures.
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Affiliation(s)
- James P Stannard
- Department of Surgery, Orthopaedic Division, University of Alabama at Birmingham, Birmingham, Alabama 35294-3295, USA.
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Robinson JT, Liddle JA, Minor A, Radmilovic V, Yi DO, Greaney PA, Long KN, Chrzan DC, Dubon OD. Metal-induced assembly of a semiconductor island lattice: Ge truncated pyramids on Au-patterned Si. Nano Lett 2005; 5:2070-3. [PMID: 16218739 DOI: 10.1021/nl051719d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We report the two-dimensional alignment of semiconductor islands using rudimentary metal patterning to control nucleation and growth. In the Ge on Si system, a square array of submicron Au dots on the Si (001) surface induces the assembly of deposited Ge adatoms into an extensive island lattice. Remarkably, these highly ordered Ge islands form between the patterned Au dots and are characterized by a unique truncated pyramidal shape. A model based on patterned diffusion barriers explains the observed ordering and establishes general criteria for the broader applicability of such a directed assembly process to quantum dot ordering.
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Affiliation(s)
- J T Robinson
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
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Abstract
PURPOSE To describe a technique for reconstruction of the posterolateral corner (PLC) of the knee and report the results of a prospective series of patients. TYPE OF STUDY Case series. METHODS Twenty-two patients with PLC injuries underwent reconstruction; 15 patients had multiligamentous knee injuries and 7 had isolated PLC injuries. We used the modified 2-tailed technique that reconstructs the popliteofibular ligament and fibulocollateral ligament. The technique includes use of an allograft tendon placed through transtibial and transfibular bone tunnels and around a screw on the lateral femoral condyle. All patients have been followed-up prospectively with clinical examinations, Lysholm knee scores, KT-2000 ligament arthrometer examinations, and evaluation of work and recreational functional status. RESULTS There were 15 male and 7 female patients (mean age, 32 years; range, 17 to 55 years). Follow-up was a minimum of 24 months (mean, 29.5 months; range, 24 to 38 months). Mean range of motion is extension of 0.2 degrees (range, 0 degrees to 5 degrees) and flexion of 133.4 degrees (80 degrees to 144 degrees). The range of motion for the multiligamentous knees was 0.3 degrees to 129 degrees compared with 0 degrees to 143 degrees for knees with isolated corner injuries. Mean Lysholm knee scores were 90 for the entire group with a score of 92 for the multiligamentous knees and 88 for the isolated corners. Stability was clinically graded on a scale of 0 to 3 for both varus stress and external rotation, with a score of 2 or 3 indicating a failed PLC reconstruction. The mean score for varus stress was 0.2 for the whole group, with 0.3 in the multiligamentous knee and 0.1 for the isolated injuries. Similarly, the mean score for external rotation was 0.4, with a 0.5 for multiligamentous knee and 0.3 for isolated PLC injuries. There were 2 failures in the multiligamentous knee injury group (13%), compared with no failures in the isolated PLC group. The failure rate for the whole study was 9%. CONCLUSIONS Reconstruction of the PLC using an allograft reconstruction of the popliteus, popliteofibular, and fibulocollateral ligaments yielded a stable reconstruction with excellent functional results. Predictably, range of motion and incidence of failure were both better for patients with isolated PLC injuries than for those with multiligamentous knees. Both groups, however, showed excellent overall functional results. LEVEL OF EVIDENCE Level IV, case series.
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Affiliation(s)
- James P Stannard
- Division of Orthopaedic Surgery, The University of Alabama, Birmingham, Alabama 5294-3409, USA.
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Stannard JP, Sheils TM, Lopez-Ben RR, McGwin G, Robinson JT, Volgas DA. Vascular injuries in knee dislocations: the role of physical examination in determining the need for arteriography. J Bone Joint Surg Am 2004; 86:910-5. [PMID: 15118031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Popliteal artery injury is frequently associated with knee dislocation following blunt trauma, an injury that is being seen with increasing frequency. The primary purpose of the present study was to evaluate the use of physical examination to determine the need for arteriography in a large series of patients with knee dislocation. The secondary purpose was to evaluate the correlation between physical examination findings and clinically important vascular injury in the subgroup of patients who underwent arteriography. METHODS One hundred and thirty consecutive patients (138 knees) who had sustained an acute multiligamentous knee injury were evaluated at our level-1 trauma center between August 1996 and May 2002 and were included in a prospective outcome study. Four patients (four knees) were lost to follow-up, leaving 126 patients (134 knees) available for inclusion in the study. The results of the physical examination of the vascular status of the extremities were used to determine the need for arteriography. The mean duration of follow-up was nineteen months (range, eight to forty-eight months). Physical examination findings, magnetic resonance imaging findings, and surgical findings were combined to determine the extent of ligamentous damage. RESULTS Nine patients had flow-limiting popliteal artery damage, for an overall prevalence of 7%. Ten patients had abnormal findings on physical examination, with one patient having a false-positive result and nine having a true-positive result. The knee dislocations in the nine patients with popliteal artery damage were classified, according to the Wascher modification of the Schenck system, as KD-III (one knee), KD-IV (seven knees), and KD-V (one knee). CONCLUSIONS Selective arteriography based on serial physical examinations is a safe and prudent policy following knee dislocation. There is a strong correlation between the results of physical examination and the need for arteriography. Increased vigilance may be justified in the case of a patient with a KD-IV dislocation, for whom serial examinations should continue for at least forty-eight hours.
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Affiliation(s)
- James P Stannard
- Division of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, AL 35294-3409, USA.
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Gallivan GJ, Barker IK, Artsob H, Magnarelli LA, Robinson JT, Voigt DR. Serologic survey for antibodies to Borrelia burgdorferi in white-tailed deer in Ontario. J Wildl Dis 1998; 34:411-4. [PMID: 9577798 DOI: 10.7589/0090-3558-34.2.411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Serum samples collected from 623 white-tailed deer (Odocoileus virginianus) in southern Ontario (Canada) from 1985 to 1989 were tested for antibodies to Borrelia burgdorferi using an indirect fluorescent antibody (IFA) staining method. Samples from 150 of the deer were also tested using an enzyme-linked immunosorbent assay (ELISA). At IFA titers of 1:64 and 1:128 deer with antibodies to B. burgdorferi appeared to be widespread throughout southern Ontario, with an apparent prevalence ranging from 3 to 47%. At IFA titres > or = 1:256 and ELISA titres > or = 1:160 deer with antibodies to B. burgdorferi were only present on Long Point which is the only known endemic focus of Ixodes scapularis, the primary vector for B. burgdorferi, in southern Ontario. At these titres the apparent prevalence of antibodies to B. burgdorferi on Long Point was only 5 to 7%, even though the mean intensity of infestation of adult I. scapularis on deer was > 180, and 60% of the adult ticks are infected with B. burgdorferi. Based on these results, white-tailed deer do not appear to be a good sentinel species for the distribution of B. burgdorferi.
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Affiliation(s)
- G J Gallivan
- Department of Pathology, Ontario Veterinary College, University of Guelph, Canada
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Herman SM, Robinson JT, McCredie RJ, Adams MR, Boyer MJ, Celermajer DS. Androgen deprivation is associated with enhanced endothelium-dependent dilatation in adult men. Arterioscler Thromb Vasc Biol 1997; 17:2004-9. [PMID: 9351365 DOI: 10.1161/01.atv.17.10.2004] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Male gender is an independent risk factor for coronary artery disease, and androgen administration has been associated with increased atherosclerosis in experimental animals. Since endothelial dysfunction is an important event in the atherogenic process, we hypothesized that androgen deprivation in adult men might be associated with enhanced arterial endothelial function. Using external vascular ultrasound, brachial artery diameter was measured at rest, after flow increase (causing endothelium-dependent dilatation) and after nitroglycerin (an endothelium-independent dilator). We studied 30 adult males aged 40 to 70 years: 10 had had bilateral orchidectomy and/or maximal androgen blockade for > or = 6 months for treatment of prostate cancer, and all were in complete remission (group 1). Ten healthy controls (group 2) and 10 controls who had remission from nonprostate cancers (group 3) were matched for age and smoking history. Testosterone levels were lower in men in group 1 versus groups 2 or 3 (0.8 +/- 0.1 versus 19.2 +/- 8.4 or 16.1 +/- 4.9 nmol/L, P < .001). By contrast, endothelium-dependent dilatation was markedly higher in group 1 than in groups 2 or 3 (6.2 +/- 3 versus 2.7 +/- 2 or 2.0 +/- 1.9%, P < .001). The nitroglycerin response was similar in all three groups (P = .92). On multivariate analysis, increased endothelium-dependent dilatation was significantly associated with low serum testosterone levels (P = .001) but not with cholesterol levels or with a past history of malignancy (P > .25). The withdrawal of male sex hormones may be associated with enhanced endothelial function in adult men. This is consistent with a deleterious effect of physiologic levels of male sex steroids on the arterial wall.
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Affiliation(s)
- S M Herman
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
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Woo KS, Robinson JT, Chook P, Adams MR, Yip G, Mai ZJ, Lam CW, Sorensen KE, Deanfield JE, Celermajer DS. Differences in the effect of cigarette smoking on endothelial function in chinese and white adults. Ann Intern Med 1997; 127:372-5. [PMID: 9273828 DOI: 10.7326/0003-4819-127-5-199709010-00006] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The prevalence of coronary artery disease in southern China is approximately one fifth that in "westernized" countries, even though approximately 70% of Chinese men smoke cigarettes and Chinese women have substantial passive exposure to cigarette smoke. OBJECTIVES Endothelial dysfunction is an early event in atherosclerosis and occurs in young white active and passive smokers; we compared endothelial physiology in healthy young Chinese and white smokers and nonsmokers. PATIENTS 144 healthy adults who were 16 to 45 years of age: 72 Chinese persons in a village in southern China and 72 white persons in Australia and England who were matched for exposure to cigarette smoke. Each ethnic group comprised 36 controls (lifelong nonsmokers with no regular exposure to cigarette smoke; 16 men and 20 women) and 36 active or passive smokers (15 men and 21 women). MEASUREMENTS Arterial endothelial function was tested with high-resolution external vascular ultrasonography, and brachial artery diameter was measured at rest, after flow increase (which causes endothelium-dependent dilatation), and after administration of sublingual nitroglycerin (an endothelium-independent dilator). RESULTS Endothelium-dependent dilatation was similar in Chinese (7.9%) and white (8.4%) nonsmokers (P > 0.2). Among white persons, endothelium-dependent dilatation was lower in active or passive smokers (3.9%) than in nonsmokers (8.4%) (P < 0.001). Among Chinese persons, dilatation was not significantly lower in active or passive smokers (7.3%) than in nonsmokers (7.9%) (P > 0.2). Dilatation was higher in Chinese active or passive smokers (7.3%) than in white active or passive smokers (3.9%) (P < 0.001). Dilatation responses to nitroglycerin were similar in all groups (P = 0.17). CONCLUSION Young Chinese adults have less evidence of arterial endothelial dysfunction than young white adults with similar direct or indirect exposure to cigarette smoke.
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Affiliation(s)
- K S Woo
- Chinese University of Hong Kong, Hong Kong
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Woo KS, McCrohon JA, Chook P, Adams MR, Robinson JT, McCredie RJ, Lam CW, Feng JZ, Celermajer DS. Chinese adults are less susceptible than whites to age-related endothelial dysfunction. J Am Coll Cardiol 1997; 30:113-8. [PMID: 9207630 DOI: 10.1016/s0735-1097(97)00111-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES We sought to assess the effects of aging on the endothelial physiology of a group of Chinese adults. BACKGROUND Several studies have documented an association between aging and progressive arterial endothelial dysfunction in white subjects. We hypothesized that age-related endothelial dysfunction, an important event in atherosclerosis, might be less marked in southern Chinese subjects, in whom the prevalence of coronary heart disease is only approximately 20% of that in industrialized countries. METHODS We studied endothelial function in 76 healthy adults aged 16 to 70 years: 38 Chinese from a village of 3,000 people in southern China and 38 white subjects from Sydney, Australia. In each ethnic group, there were 19 younger persons (16 to 40 years) and 19 older adults (55 to 70 years). None had evidence of diabetes, hypertension or clinical vascular disease or had ever been regular cigarette smokers. With the use of high resolution external vascular ultrasound, brachial artery diameter was measured at rest, after flow increase (causing endothelium-dependent dilation) and after sublingual nitroglycerin (an endothelium-independent dilator). RESULTS Endothelium-dependent dilation was similar in young Chinese (mean +/- SD 8.3 +/- 2.5%), young whites (7.9 +/- 2.0%) and older Chinese (6.8 +/- 2.9%), but it was significantly impaired in older whites (1.8 +/- 2.5%, p < 0.001 by analysis of variance). On multivariate analysis, older age was associated with impaired endothelium-dependent dilation (p < 0.001) (independent of the effects of serum cholesterol, gender and vessel size) in the white but not in the Chinese subjects (p = 0.83). Nitroglycerin-induced dilation was not significantly different with aging in either ethnic group. CONCLUSIONS Endothelium-dependent dilation is similar in the arteries of healthy young Chinese and white adults. With older age, however, Chinese subjects are less susceptible to impaired endothelial function.
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Affiliation(s)
- K S Woo
- Department of Medicine, Chinese University of Hong Kong, Hong Kong
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34
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McCrohon JA, Walters WA, Robinson JT, McCredie RJ, Turner L, Adams MR, Handelsman DJ, Celermajer DS. Arterial reactivity is enhanced in genetic males taking high dose estrogens. J Am Coll Cardiol 1997; 29:1432-6. [PMID: 9180100 DOI: 10.1016/s0735-1097(97)00063-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES We sought to assess whether high dose estrogen treatment is associated with enhanced arterial reactivity in genetic males. BACKGROUND Although estrogens have been shown to enhance arterial reactivity in women, and are thereby thought to confer cardiovascular benefit, the vascular effects of long-term estrogen therapy in genetic males is unknown. METHODS We studied the arterial physiology of 30 genetic males--15 male to female transsexuals receiving long-term high dose estrogen therapy and 15 healthy male control subjects matched for age, smoking history and vessel size. Using external vascular ultrasound, brachial artery diameter was measured at rest, after flow increase (causing endothelium-dependent dilation [EDD]) and after nitroglycerin (GTN), an endothelium-independent dilator. Blood pressure, cholesterol and testosterone levels were also measured in each subject. RESULTS Total testosterone and free testosterone index levels were lower in the transsexuals compared with the control subjects (p < 0.001). In contrast, EDD was significantly higher in the transsexuals than in the control males (mean [+/-SD] 7.1 +/- 3.1% vs. 3.2 +/- 2.8%, p = 0.001), as was the GTN response (21.2 +/- 6.7% vs. 14.6 +/- 3.3%, p = 0.002). Total and high density lipoprotein cholesterol, blood pressure levels and baseline vessel size were similar in the two groups. On multivariate analysis, enhanced EDD was associated independently with estrogen therapy (p = 0.02) and with low total cholesterol (p = 0.04). An enhanced GTN response was also significantly associated with estrogen therapy (p = 0.03). CONCLUSIONS Long-term treatment with high dose estrogens is associated with enhanced arterial reactivity in genetic males, which may be due to the effects of estrogen excess or androgen deprivation, or both.
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Affiliation(s)
- J A McCrohon
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
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McCrohon JA, Woo KS, Robinson JT, Celermajer DS. P151 Menopause and impaired endothelial function in caucasian but not in Chinese women. Maturitas 1996. [DOI: 10.1016/s0378-5122(97)81347-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Penrith ML, Robinson JT. Selenium toxicosis with focal symmetrical poliomyelomalacia in postweaning pigs in South Africa. Onderstepoort J Vet Res 1996; 63:171-9. [PMID: 8856766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
An outbreak of paralysis in finisher pigs in South Africa after ingestion of feed containing 54,581 mg/kg of selenium is described. The main and entirely consistent lesion was bilaterally symmetrical focal poliomalacia of the ventral horns of the spinal cord, which was most severe and consistent in the lumbar intumescence. Acute and subacute lesions were characterized by malacia with large numbers of gitter cells. The main features of chronic lesions were loss of neurons and gliosis. Focal degeneration and necrosis of the myocardium and skeletal muscles were also consistent, but there were fewer specific changes. Endothelial swelling, mild fibrinoid degeneration and perivascular leukocytic infiltration were present in the acute stage. Dermatitis, coronitis and hoof sloughing, usually present in more chronic cases of intoxication, were not a feature of the present outbreak, although alopecia and crusting were evident on the backs of a few pigs several weeks after the episode of intoxication. Serum-and tissue-selenium levels were elevated in the early stages after intoxication. Serum levels were nearly normal in chronic cases two months after the episode, while liver and kidney levels were still higher than normal. Higher levels were found in liver, kidney and serum than in muscle, with the highest levels in the kidney. Less than 20% of affected pigs recovered sufficiently to be marketed.
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Affiliation(s)
- M L Penrith
- Section of Pathology, Onderstepoort Veterinary Institute, South Africa
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Potts AD, Lötter C, Robinson JT. Serological prevalence of leptospiral antibodies in pigs in South Africa. Onderstepoort J Vet Res 1995; 62:281-4. [PMID: 8668327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A serological survey for leptospiral antibodies was carried out on 5 041 abattoir pigs from different regions in South Africa. Antibodies to at least one serovar were detected in 22,2% of the animals. The serovars showing the highest prevalence were: icterohaemorrhagiae (12,6%), hardjo (12,1%) and bratislava (7,5%). The serum dilution level at which 90% of the sera reacted was 1/80 or 1,160.
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Affiliation(s)
- A D Potts
- Onderstepoort Veterinary Institute, South Africa
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Lindsay LR, Barker IK, Surgeoner GA, McEwen SA, Gillespie TJ, Robinson JT. Survival and development of Ixodes scapularis (Acari: Ixodidae) under various climatic conditions in Ontario, Canada. J Med Entomol 1995; 32:143-152. [PMID: 7608920 DOI: 10.1093/jmedent/32.2.143] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Distribution of the blacklegged tick, Ixodes scapularis Say, is poorly defined in Ontario. An endemic population is known on Long Point peninsula, Lake Erie, Ontario, but I. scapularis adults have also been collected from other localities within the province. To test the hypothesis that distribution of the blacklegged tick is limited by cold climatic extremes, 35 fed female, 70 unfed adult, and 70 unfed nymphal I. scapularis were held in containers within four natural habitats on Long Point (42 degrees 36' N; 80 degrees 5' W) and at northern localities near Ottawa (45 degrees 27' N; 75 degrees 42' W), Hearst (49 degrees 40' N; 83 degrees 41' W), and Kenora (49 degrees 47' N; 94 degrees 29' W), Ontario, from early December 1991 until May 1993. At the northern localities, 84.8 and 30.5% of fed females and unfed adults survived overwinter, respectively. On Long Point, 56.4% of fed females and 23.6% of unfed adults successfully overwintered. Longevity of fed females and unfed adults was increased by > 2 mo at the northern localities compared with Long Point, although survival rates for unfed nymphs at the northern sites and on Long Point were similar. Females within the four habitats on Long Point, and at Kenora and Ottawa, laid eggs from late April to mid-May, whereas eggs were deposited in late June at Hearst. Emergence of larvae from eggs began in late July or early August on Long Point and at Ottawa. Larvae were first observed in early October at Kenora, and no larvae emerged during 1992 at Hearst. Some eggs that overwintered during 1992-1993 at the northern sites were viable; however, hatching rate was < 10%. The minimum duration of the life cycle of I. scapularis is extended when ticks are introduced into regions of the province with seasonal degree-day accumulations lower than those observed on Long Point. Delays in deposition of eggs and emergence of larvae at Hearst and Kenora were likely a result of insufficient accumulation of degree-days above threshold temperatures for development in 1992. Though some eggs can overwinter successfully, suggesting that latitude-related reduction in seasonal temperature may not limit distribution of this tick in Ontario, hatchability was low. This factor, combined with innate incremental mortality at each instar, difficulty in finding a mate, and low density of medium to large mammal hosts for adults, may mitigate against establishment of I. scapularis by introduction of individual ticks into certain northern regions.
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Affiliation(s)
- L R Lindsay
- Department of Environmental Biology, Ontario Agricultural College, University of Guelph, Canada
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Williams R, Esterhuysen JJ, Robinson JT. Pseudorabies and transmissible gastroenteritis: a serological survey in South Africa. Onderstepoort J Vet Res 1994; 61:67-70. [PMID: 7898899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two specific and sensitive, indirect enzyme-linked immunosorbent assays (ELISAs) utilizing a protein G-peroxidase conjugate were developed to detect antibodies to the pseudorabies virus (PRV) and the transmissible gastroenteritis virus (TGEV) in pig sera. Sera from 5,337 pigs, obtained from various abattoirs in South Africa, were tested with both ELISAs. No serological evidence of infection with either PRV or TGEV was found in any of the pigs tested.
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Affiliation(s)
- R Williams
- Virology Section, Onderstepoort Veterinary Institute, South Africa
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Abstract
BACKGROUND Vascular access for cardiac catheterisation of children and young adults who have had previous catheter procedures is often difficult. OBJECTIVE To assess the influence of age at and type and technique of previous cardiac catheterisation on the ease of vascular access for subsequent study of paediatric and adolescent patients. SETTING Tertiary referral centre for paediatric cardiology. PATIENTS 478 Consecutive patients aged 1 day to 19 years undergoing cardiac catheterisation over a 12 month period, including 131 patients who had had previous catheterisation(s). METHODS Prospective study, recording for each patient the age, weight, diagnosis, vascular access (artery, vein, or both), vessels eventually catheterised, access time, total duration of the procedure, and details of any previous catheter studies. RESULTS Of 131 patients who had had previous catheterisations, 80 (61%) had been studied once previously, 38 (29%) twice, and 13 (10%) on three or more occasions. The right femoral vessels were cannulated without difficulty in 72 cases (55%). Elective cannulation of left femoral vessels (because of scar tissue on the right side) or upper body vessels was undertaken in 18 cases (14%). Problems cannulating the right femoral vessels were encountered in 41 cases (31%); the vein was blocked in 29, the artery in six and the femoral veins were blocked bilaterally in six cases. The mean (SD) access time was significantly prolonged in these 41 children (41(18) v 21(13) minutes, p < 0.001) as was total duration of the procedure (116(31) v 94(34) minutes, p < 0.001). Children who had had a saphenous vein cut down as neonates subsequently had a blocked ipsilateral femoral vein in 10/15 cases (67%). Risk factors for problematic cannulation also included a higher number of previous catheterisation procedures. CONCLUSIONS Difficulties with vascular access are common in children and adolescents who have had previous cardiac catheterisations. In those who have had cut down or multiple previous studies, elective entry to the left femoral vessels should be undertaken and procedure time may be prolonged. Such cases should therefore be performed under general anaesthesia.
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Ebeling-Koning DB, Robinson JT, Todreas NE. Models for the fluid-solid interaction force for multidimensional single phase flow within tube bundles. Nuclear Engineering and Design 1986. [DOI: 10.1016/0029-5493(86)90182-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wells PW, Robinson JT, Gilmour NJ, Donachie W, Sharp JM. Development of a combined clostridial and Pasteurella haemolytica vaccine for sheep. Vet Rec 1984; 114:266-9. [PMID: 6231764 DOI: 10.1136/vr.114.11.266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The efficacy of a multicomponent clostridial vaccine containing Pasteurella haemolytica antigens was tested in specific pathogen free or conventionally reared lambs exposed to experimental infection with P haemolytica serotypes A1, A2 or A6. In four experiments assessment was based upon the findings of clinical, pathological and bacteriological examinations. Three experiments carried out in conventionally reared lambs demonstrated protection against challenge infection with P haemolytica serotypes A1, A2 and A6 in vaccinated lambs. However, the inconsistency of the disease induced in these experiments emphasised the need to perform definitive studies in specific pathogen free conditions. The final experiment was carried out with specific pathogen free lambs and confirmed the efficacy of the multicomponent clostridial vaccine containing P haemolytica antigen in protecting against the effects of infection with P haemolytica serotype A6. In addition, this experiment indicated that the inclusion of several components in a vaccine did not affect the efficacy of an individual antigenic component.
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Robinson JT. Beef carcase icterus: an evaluation of diagnostic methods in terms of visual assessment. J S Afr Vet Assoc 1975; 46:281-3. [PMID: 1219110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Two laboratory tests on beef carcase fat, two on serum and one on urine from suspect icteric carcases were compared. Used singly on serum, the indirect van den Bergh and Fouchet tests were found to be most useful, and either of these two used together with the indirect van den Bergh test on fat gave results which agreed most closely with a subjective assessment of the marketability of suspect jaundice carcases after 24 hours' chilling.
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Abstract
While the beneficial effect of lysergic acid diethylamide (LSD) in the treatment of carefully selected patients as an adjunct to psychotherapy has been amply reported (Robinson et al., 1963), concern has been expressed regarding the damage to chromosomes in those taking the drug.
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Robinson JT. Rehabilitating the emotionally disabled. Nurs Mirror Midwives J 1968; 126:37-9 contd. [PMID: 5185723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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