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Lemire G, Sanchis-Juan A, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O'Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argilli E, Le C, Sherr EH, Gleeson JG, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan TY, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H, O'Donnell-Luria A. Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease. Am J Hum Genet 2024; 111:863-876. [PMID: 38565148 PMCID: PMC11080278 DOI: 10.1016/j.ajhg.2024.03.008] [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: 10/05/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
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Affiliation(s)
- Gabrielle Lemire
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Alba Sanchis-Juan
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn Russell
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha Baxter
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine R Chao
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Groopman
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Isaac Wong
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina England
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Julia Goodrich
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lynn Pais
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christina Austin-Tse
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie DiTroia
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily O'Heir
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijay S Ganesh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Monica H Wojcik
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Emily Evangelista
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hana Snow
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mugdha Singh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yulia Mostovoy
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Huang
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran Garimella
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha L Kirkham
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Diane D Shao
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Le
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shirlee Shril
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ronen Schneider
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Alan H Beggs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Kinga M Bujakowska
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Emily Place
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Eric A Pierce
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Tiong Yang Tan
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark D Fleming
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Martin R Pollak
- Harvard Medical School, Boston, MA, USA; Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Zandre Bruwer
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Gianina Ravenscroft
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Daniel G MacArthur
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Heidi L Rehm
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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Lemire G, Sanchis-Juan A, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O’Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argili E, Le C, Sherr EH, Gleeson J, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan T, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H, O’Donnell-Luria A. Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease. medRxiv 2023:2023.10.05.23296595. [PMID: 37873196 PMCID: PMC10593084 DOI: 10.1101/2023.10.05.23296595] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and with new innovative methods can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the GREGoR consortium. Each family's CNV data was analyzed using the seqr platform and candidate CNVs classified using the 2020 ACMG/ClinGen CNV interpretation standards. We developed additional evidence criteria to address situations not covered by the current standards. The addition of CNV calling to exome analysis identified causal CNVs for 173 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb with estimates that 44% would not have been detected by standard chromosomal microarrays. The causal CNVs consisted of 141 deletions, 15 duplications, 4 suspected complex structural variants (SVs), 3 insertions and 10 complex SVs, the latter two groups being identified by orthogonal validation methods. We interpreted 153 CNVs as likely pathogenic/pathogenic and 20 CNVs as high interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
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Affiliation(s)
- Gabrielle Lemire
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- These authors contributed equally
| | - Alba Sanchis-Juan
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- These authors contributed equally
| | - Kathryn Russell
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha Baxter
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine R. Chao
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Groopman
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina England
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Goodrich
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lynn Pais
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christina Austin-Tse
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie DiTroia
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily O’Heir
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijay S. Ganesh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Monica H. Wojcik
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hana Snow
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mugdha Singh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yulia Mostovoy
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Huang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran Garimella
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha L. Kirkham
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
| | - Diane D. Shao
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Christopher A. Walsh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
| | - Emanuela Argili
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Le
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H. Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | - Shirlee Shril
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Ronen Schneider
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Vijay G. Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jill A. Madden
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Alan H. Beggs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Pankaj B. Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Kinga M. Bujakowska
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Emily Place
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Eric A. Pierce
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Tiong Tan
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Susan M. White
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark D. Fleming
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA, USA
| | - Martin R. Pollak
- Harvard Medical School, Boston, MA, USA
- Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- University of Cape Town, Cape Town, South Africa
| | - Zandre Bruwer
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- University of Cape Town, Cape Town, South Africa
| | - Gianina Ravenscroft
- University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Nigel G. Laing
- University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Daniel G. MacArthur
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute, Sydney, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Heidi L. Rehm
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E. Talkowski
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Senior authors
| | - Anne O’Donnell-Luria
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Senior authors
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3
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Wojcik MH, Lemire G, Zaki MS, Wissman M, Win W, White S, Weisburd B, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Okur V, Oja KT, O'Leary M, O'Heir E, Morel C, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gazda HT, Ganesh VS, Ganapathy M, Gallacher L, Fu J, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bonnemann C, Beggs AH, Baxter SM, Agrawal PB, Talkowski M, Austin-Tse C, Rehm HL, O'Donnell-Luria A. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis. medRxiv 2023:2023.08.08.23293829. [PMID: 38328047 PMCID: PMC10849673 DOI: 10.1101/2023.08.08.23293829] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Background Causal variants underlying rare disorders may remain elusive even after expansive gene panels or exome sequencing (ES). Clinicians and researchers may then turn to genome sequencing (GS), though the added value of this technique and its optimal use remain poorly defined. We therefore investigated the advantages of GS within a phenotypically diverse cohort. Methods GS was performed for 744 individuals with rare disease who were genetically undiagnosed. Analysis included review of single nucleotide, indel, structural, and mitochondrial variants. Results We successfully solved 218/744 (29.3%) cases using GS, with most solves involving established disease genes (157/218, 72.0%). Of all solved cases, 148 (67.9%) had previously had non-diagnostic ES. We systematically evaluated the 218 causal variants for features requiring GS to identify and 61/218 (28.0%) met these criteria, representing 8.2% of the entire cohort. These included small structural variants (13), copy neutral inversions and complex rearrangements (8), tandem repeat expansions (6), deep intronic variants (15), and coding variants that may be more easily found using GS related to uniformity of coverage (19). Conclusion We describe the diagnostic yield of GS in a large and diverse cohort, illustrating several types of pathogenic variation eluding ES or other techniques. Our results reveal a higher diagnostic yield of GS, supporting the utility of a genome-first approach, with consideration of GS as a secondary or tertiary test when higher-resolution structural variant analysis is needed or there is a strong clinical suspicion for a condition and prior targeted genetic testing has been negative.
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4
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Bruessel P, Concannon E, Snow H, Zinn R. Islanded SCIP flap after sarcoma resection: a novel approach for Mons pubis defects. ANZ J Surg 2023. [PMID: 37218038 DOI: 10.1111/ans.18462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/17/2023] [Accepted: 04/05/2023] [Indexed: 05/24/2023]
Affiliation(s)
- P Bruessel
- Department of Surgery, University College London Hospital, London, UK
| | - E Concannon
- Department of Plastic and Reconstructive Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - H Snow
- Department of Plastic and Reconstructive Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - R Zinn
- Department of Plastic and Reconstructive Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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5
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Pais LS, Snow H, Weisburd B, Zhang S, Baxter SM, DiTroia S, O’Heir E, England E, Chao KR, Lemire G, Osei-Owusu I, VanNoy GE, Wilson M, Nguyen K, Arachchi H, Phu W, Solomonson M, Mano S, O’Leary M, Lovgren A, Babb L, Austin-Tse CA, Rehm HL, MacArthur DG, O’Donnell-Luria A. seqr: A web-based analysis and collaboration tool for rare disease genomics. Hum Mutat 2022; 43:698-707. [PMID: 35266241 PMCID: PMC9903206 DOI: 10.1002/humu.24366] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023]
Abstract
Exome and genome sequencing have become the tools of choice for rare disease diagnosis, leading to large amounts of data available for analyses. To identify causal variants in these datasets, powerful filtering and decision support tools that can be efficiently used by clinicians and researchers are required. To address this need, we developed seqr - an open-source, web-based tool for family-based monogenic disease analysis that allows researchers to work collaboratively to search and annotate genomic callsets. To date, seqr is being used in several research pipelines and one clinical diagnostic lab. In our own experience through the Broad Institute Center for Mendelian Genomics, seqr has enabled analyses of over 10,000 families, supporting the diagnosis of more than 3,800 individuals with rare disease and discovery of over 300 novel disease genes. Here, we describe a framework for genomic analysis in rare disease that leverages seqr's capabilities for variant filtration, annotation, and causal variant identification, as well as support for research collaboration and data sharing. The seqr platform is available as open source software, allowing low-cost participation in rare disease research, and a community effort to support diagnosis and gene discovery in rare disease.
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Affiliation(s)
- Lynn S. Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hana Snow
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shifa Zhang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samantha M. Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily O’Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eleina England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Grace E. VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Harindra Arachchi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - William Phu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stacy Mano
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Melanie O’Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alysia Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lawrence Babb
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christina A. Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, Australia,Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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6
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Wilkinson MJ, Snow H, Downey K, Thomas K, Riddell A, Francis N, Strauss DC, Hayes AJ, Smith MJF, Messiou C. CT diagnosis of ilioinguinal lymph node metastases in melanoma using radiological characteristics beyond size and asymmetry. BJS Open 2021; 5:6104886. [PMID: 33609385 PMCID: PMC7893466 DOI: 10.1093/bjsopen/zraa005] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Diagnosis of lymph node (LN) metastasis in melanoma with non-invasive methods is challenging. The aim of this study was to evaluate the diagnostic accuracy of six LN characteristics on CT in detecting melanoma-positive ilioinguinal LN metastases, and to determine whether inguinal LN characteristics can predict pelvic LN involvement. Methods This was a single-centre retrospective study of patients with melanoma LN metastases at a tertiary cancer centre between 2008 and 2016. Patients who had preoperative contrast-enhanced CT assessment and ilioinguinal LN dissection were included. CT scans containing significant artefacts obscuring the pelvis were excluded. CT scans were reanalysed for six LN characteristics (extracapsular spread (ECS), minimum axis (MA), absence of fatty hilum (FH), asymmetrical cortical nodule (CAN), abnormal contrast enhancement (ACE) and rounded morphology (RM)) and compared with postoperative histopathological findings. Results A total of 90 patients were included. Median age was 58 (range 23–85) years. Eighty-eight patients (98 per cent) had pathology-positive inguinal disease and, of these, 45 (51 per cent) had concurrent pelvic disease. The most common CT characteristics found in pathology-positive inguinal LNs were MA greater than 10 mm (97 per cent), ACE (80 per cent), ECS (38 per cent) and absence of RM (38 per cent). In multivariable analysis, inguinal LN characteristics on CT indicative of pelvic disease were RM (odds ratio (OR) 3.3, 95 per cent c.i. 1.2 to 8.7) and ECS (OR 4.2, 1.6 to 11.3). Cloquet’s node is known to be a poor predictor of pelvic spread. Pelvic LN disease was present in 50 per cent patients, but only 7 per cent had a pathology-positive Cloquet’s node. Conclusion Additional CT radiological characteristics, especially ECS and RM, may improve diagnostic accuracy and aid clinical decisions regarding the need for inguinal or ilioinguinal dissection.
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Affiliation(s)
- M J Wilkinson
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - H Snow
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - K Downey
- Department of Radiology, The Royal Marsden Hospital, London, UK
| | - K Thomas
- Statistics Department, The Royal Marsden Hospital, London, UK
| | - A Riddell
- Department of Radiology, The Royal Marsden Hospital, London, UK
| | - N Francis
- Department of Pathology, The Royal Marsden Hospital (Honorary) and Charing Cross Hospital, London, UK
| | - D C Strauss
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - A J Hayes
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK.,Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - M J F Smith
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - C Messiou
- Department of Radiology, The Royal Marsden Hospital, London, UK.,Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
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7
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Halse H, Colebatch AJ, Petrone P, Henderson MA, Mills JK, Snow H, Westwood JA, Sandhu S, Raleigh JM, Behren A, Cebon J, Darcy PK, Kershaw MH, McArthur GA, Gyorki DE, Neeson PJ. Multiplex immunohistochemistry accurately defines the immune context of metastatic melanoma. Sci Rep 2018; 8:11158. [PMID: 30042403 PMCID: PMC6057961 DOI: 10.1038/s41598-018-28944-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [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: 02/15/2018] [Accepted: 07/02/2018] [Indexed: 01/01/2023] Open
Abstract
A prospective study explored the heterogeneous nature of metastatic melanoma using Multiplex immunohistochemistry (IHC) and flow cytometry (FACS). Multiplex IHC data quantitated immune subset number present intra-tumoral (IT) vs the tumor stroma, plus distance of immune subsets from the tumor margin (TM). In addition, mIHC showed a close association between the presence of IT CD8+ T cells and PDL1 expression in melanoma, which was more prevalent on macrophages than on melanoma cells. In contrast, FACS provided more detailed information regarding the T cell subset differentiation, their activation status and expression of immune checkpoint molecules. Interestingly, mIHC detected significantly higher Treg numbers than FACS and showed preferential CD4+ T cell distribution in the tumor stroma. Based on the mIHC and FACS data, we provide a model which defines metastatic melanoma immune context into four categories using the presence or absence of PDL1+ melanoma cells and/or macrophages, and their location within the tumor or on the periphery, combined with the presence or absence of IT CD8+ T cells. This model interprets melanoma immune context as a spectrum of tumor escape from immune control, and provides a snapshot upon which interpretation of checkpoint blockade inhibitor (CBI) therapy responses can be built.
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Affiliation(s)
- H Halse
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - A J Colebatch
- Division of Cancer Medicine Melanoma Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - P Petrone
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - M A Henderson
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - J K Mills
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - H Snow
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - J A Westwood
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - S Sandhu
- Division of Cancer Medicine Melanoma Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - J M Raleigh
- Division of Cancer Medicine Melanoma Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - A Behren
- Olivia Newton John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, 3086, Australia
| | - J Cebon
- Olivia Newton John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, 3086, Australia
| | - P K Darcy
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - M H Kershaw
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - G A McArthur
- Division of Cancer Medicine Melanoma Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia
| | - D E Gyorki
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia.,Department of Surgery, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - P J Neeson
- Cancer Immunology Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia.
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8
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Aamodt K, Abel N, Abeysekara U, Abrahantes Quintana A, Abramyan A, Adamová D, Aggarwal MM, Aglieri Rinella G, Agocs AG, Aguilar Salazar S, Ahammed Z, Ahmad A, Ahmad N, Ahn SU, Akimoto R, Akindinov A, Aleksandrov D, Alessandro B, Alfaro Molina R, Alici A, Almaráz Aviña E, Alme J, Alt T, Altini V, Altinpinar S, Andrei C, Andronic A, Anelli G, Angelov V, Anson C, Anticić T, Antinori F, Antinori S, Antipin K, Antończyk D, Antonioli P, Anzo A, Aphecetche L, Appelshäuser H, Arcelli S, Arceo R, Arend A, Armesto N, Arnaldi R, Aronsson T, Arsene IC, Asryan A, Augustinus A, Averbeck R, Awes TC, Aystö J, Azmi MD, Bablok S, Bach M, Badalà A, Baek YW, Bagnasco S, Bailhache R, Bala R, Baldisseri A, Baldit A, Bán J, Barbera R, Barnaföldi GG, Barnby LS, Barret V, Bartke J, Barile F, Basile M, Basmanov V, Bastid N, Bathen B, Batigne G, Batyunya B, Baumann C, Bearden IG, Becker B, Belikov I, Bellwied R, Belmont-Moreno E, Belogianni A, Benhabib L, Beole S, Berceanu I, Bercuci A, Berdermann E, Berdnikov Y, Betev L, Bhasin A, Bhati AK, Bianchi L, Bianchi N, Bianchin C, Bielcík J, Bielcíková J, Bilandzic A, Bimbot L, Biolcati E, Blanc A, Blanco F, Blanco F, Blau D, Blume C, Boccioli M, Bock N, Bogdanov A, Bøggild H, Bogolyubsky M, Bohm J, Boldizsár L, Bombara M, Bombonati C, Bondila M, Borel H, Borisov A, Bortolin C, Bose S, Bosisio L, Bossú F, Botje M, Böttger S, Bourdaud G, Boyer B, Braun M, Braun-Munzinger P, Bravina L, Bregant M, Breitner T, Bruckner G, Brun R, Bruna E, Bruno GE, Budnikov D, Buesching H, Buncic P, Busch O, Buthelezi Z, Caffarri D, Cai X, Caines H, Calvo E, Camacho E, Camerini P, Campbell M, Canoa Roman V, Capitani GP, Cara Romeo G, Carena F, Carena W, Carminati F, Casanova Díaz A, Caselle M, Castillo Castellanos J, Castillo Hernandez JF, Catanescu V, Cattaruzza E, Cavicchioli C, Cerello P, Chambert V, Chang B, Chapeland S, Charpy A, Charvet JL, Chattopadhyay S, Chattopadhyay S, Cherney M, Cheshkov C, Cheynis B, Chiavassa E, Chibante Barroso V, Chinellato DD, Chochula P, Choi K, Chojnacki M, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Chuman F, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Cobanoglu O, Coffin JP, Coli S, Colla A, Conesa Balbastre G, Conesa Del Valle Z, Conner ES, Constantin P, Contin G, Contreras JG, Corrales Morales Y, Cormier TM, Cortese P, Cortés Maldonado I, Cosentino MR, Costa F, Cotallo ME, Crescio E, Crochet P, Cuautle E, Cunqueiro L, Cussonneau J, Dainese A, Dalsgaard HH, Danu A, Das I, Dash A, Dash S, de Barros GOV, De Caro A, de Cataldo G, de Cuveland J, De Falco A, De Gaspari M, de Groot J, De Gruttola D, De Marco N, De Pasquale S, De Remigis R, de Rooij R, de Vaux G, Delagrange H, Delgado Y, Dellacasa G, Deloff A, Demanov V, Dénes E, Deppman A, D'Erasmo G, Derkach D, Devaux A, Di Bari D, Di Giglio C, Di Liberto S, Di Mauro A, Di Nezza P, Dialinas M, Díaz L, Díaz R, Dietel T, Divià R, Djuvsland O, Dobretsov V, Dobrin A, Dobrowolski T, Dönigus B, Domínguez I, Don DMM, Dordic O, Dubey AK, Dubuisson J, Ducroux L, Dupieux P, Dutta Majumdar AK, Dutta Majumdar MR, Elia D, Emschermann D, Enokizono A, Espagnon B, Estienne M, Esumi S, Evans D, Evrard S, Eyyubova G, Fabjan CW, Fabris D, Faivre J, Falchieri D, Fantoni A, Fasel M, Fateev O, Fearick R, Fedunov A, Fehlker D, Fekete V, Felea D, Fenton-Olsen B, Feofilov G, Fernández Téllez A, Ferreiro EG, Ferretti A, Ferretti R, Figueredo MAS, Filchagin S, Fini R, Fionda FM, Fiore EM, Floris M, Fodor Z, Foertsch S, Foka P, Fokin S, Formenti F, Fragiacomo E, Fragkiadakis M, Frankenfeld U, Frolov A, Fuchs U, Furano F, Furget C, Fusco Girard M, Gaardhøje JJ, Gadrat S, Gagliardi M, Gago A, Gallio M, Ganoti P, Ganti MS, Garabatos C, García Trapaga C, Gebelein J, Gemme R, Germain M, Gheata A, Gheata M, Ghidini B, Ghosh P, Giraudo G, Giubellino P, Gladysz-Dziadus E, Glasow R, Glässel P, Glenn A, Gómez Jiménez R, González Santos H, González-Trueba LH, González-Zamora P, Gorbunov S, Gorbunov Y, Gotovac S, Gottschlag H, Grabski V, Grajcarek R, Grelli A, Grigoras A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Grinyov B, Grion N, Gros P, Grosse-Oetringhaus JF, Grossiord JY, Grosso R, Guber F, Guernane R, Guerra C, Guerzoni B, Gulbrandsen K, Gulkanyan H, Gunji T, Gupta A, Gupta R, Gustafsson HA, Gutbrod H, Haaland O, Hadjidakis C, Haiduc M, Hamagaki H, Hamar G, Hamblen J, Han BH, Harris JW, Hartig M, Harutyunyan A, Hasch D, Hasegan D, Hatzifotiadou D, Hayrapetyan A, Heide M, Heinz M, Helstrup H, Herghelegiu A, Hernández C, Herrera Corral G, Herrmann N, Hetland KF, Hicks B, Hiei A, Hille PT, Hippolyte B, Horaguchi T, Hori Y, Hristov P, Hrivnácová I, Hu S, Huang M, Huber S, Humanic TJ, Hutter D, Hwang DS, Ichou R, Ilkaev R, Ilkiv I, Inaba M, Innocenti PG, Ippolitov M, Irfan M, Ivan C, Ivanov A, Ivanov M, Ivanov V, Iwasaki T, Jachołkowski A, Jacobs P, Jancurová L, Jangal S, Janik R, Jena C, Jena S, Jirden L, Jones GT, Jones PG, Jovanović P, Jung H, Jung W, Jusko A, Kaidalov AB, Kalcher S, Kalinák P, Kalisky M, Kalliokoski T, Kalweit A, Kamal A, Kamermans R, Kanaki K, Kang E, Kang JH, Kapitan J, Kaplin V, Kapusta S, Karavichev O, Karavicheva T, Karpechev E, Kazantsev A, Kebschull U, Keidel R, Khan MM, Khan SA, Khanzadeev A, Kharlov Y, Kikola D, Kileng B, Kim DJ, Kim DS, Kim DW, Kim HN, Kim J, Kim JH, Kim JS, Kim M, Kim M, Kim SH, Kim S, Kim Y, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein J, Klein-Bösing C, Kliemant M, Klovning A, Kluge A, Knichel ML, Kniege S, Koch K, Kolevatov R, Kolojvari A, Kondratiev V, Kondratyeva N, Konevskih A, Kornaś E, Kour R, Kowalski M, Kox S, Kozlov K, Kral J, Králik I, Kramer F, Kraus I, Kravcáková A, Krawutschke T, Krivda M, Krumbhorn D, Krus M, Kryshen E, Krzewicki M, Kucheriaev Y, Kuhn C, Kuijer PG, Kumar L, Kumar N, Kupczak R, Kurashvili P, Kurepin A, Kurepin AN, Kuryakin A, Kushpil S, Kushpil V, Kutouski M, Kvaerno H, Kweon MJ, Kwon Y, La Rocca P, Lackner F, Ladrón de Guevara P, Lafage V, Lal C, Lara C, Larsen DT, Laurenti G, Lazzeroni C, Le Bornec Y, Le Bris N, Lee H, Lee KS, Lee SC, Lefèvre F, Lenhardt M, Leistam L, Lehnert J, Lenti V, León H, León Monzón I, León Vargas H, Lévai P, Li X, Li Y, Lietava R, Lindal S, Lindenstruth V, Lippmann C, Lisa MA, Liu L, Loginov V, Lohn S, Lopez X, López Noriega M, López-Ramírez R, López Torres E, Løvhøiden G, Lozea Feijo Soares A, Lu S, Lunardon M, Luparello G, Luquin L, Lutz JR, Ma K, Ma R, Madagodahettige-Don DM, Maevskaya A, Mager M, Mahapatra DP, Maire A, Makhlyueva I, Mal'kevich D, Malaev M, Malagalage KJ, Maldonado Cervantes I, Malek M, Malkiewicz T, Malzacher P, Mamonov A, Manceau L, Mangotra L, Manko V, Manso F, Manzari V, Mao Y, Mares J, Margagliotti GV, Margotti A, Marín A, Martashvili I, Martinengo P, Martínez Hernández MI, Martínez Davalos A, Martínez García G, Maruyama Y, Marzari Chiesa A, Masciocchi S, Masera M, Masetti M, Masoni A, Massacrier L, Mastromarco M, Mastroserio A, Matthews ZL, Matyja A, Mayani D, Mazza G, Mazzoni MA, Meddi F, Menchaca-Rocha A, Mendez Lorenzo P, Meoni M, Mercado Pérez J, Mereu P, Miake Y, Michalon A, Miftakhov N, Milano L, Milosevic J, Minafra F, Mischke A, Miśkowiec D, Mitu C, Mizoguchi K, Mlynarz J, Mohanty B, Molnar L, Mondal MM, Montaño Zetina L, Monteno M, Montes E, Morando M, Moretto S, Morsch A, Moukhanova T, Muccifora V, Mudnic E, Muhuri S, Müller H, Munhoz MG, Munoz J, Musa L, Musso A, Nandi BK, Nania R, Nappi E, Navach F, Navin S, Nayak TK, Nazarenko S, Nazarov G, Nedosekin A, Nendaz F, Newby J, Nianine A, Nicassio M, Nielsen BS, Nikolaev S, Nikolic V, Nikulin S, Nikulin V, Nilsen BS, Nilsson MS, Noferini F, Nomokonov P, Nooren G, Novitzky N, Nyatha A, Nygaard C, Nyiri A, Nystrand J, Ochirov A, Odyniec G, Oeschler H, Oinonen M, Okada K, Okada Y, Oldenburg M, Oleniacz J, Oppedisano C, Orsini F, Ortiz Velasquez A, Ortona G, Oskarsson A, Osmic F, Osterman L, Ostrowski P, Otterlund I, Otwinowski J, Ovrebekk G, Oyama K, Ozawa K, Pachmayer Y, Pachr M, Padilla F, Pagano P, Paić G, Painke F, Pajares C, Pal S, Pal SK, Palaha A, Palmeri A, Panse R, Papikyan V, Pappalardo GS, Park WJ, Pastircák B, Pastore C, Paticchio V, Pavlinov A, Pawlak T, Peitzmann T, Pepato A, Pereira H, Peressounko D, Pérez C, Perini D, Perrino D, Peryt W, Peschek J, Pesci A, Peskov V, Pestov Y, Peters AJ, Petrácek V, Petridis A, Petris M, Petrov P, Petrovici M, Petta C, Peyré J, Piano S, Piccotti A, Pikna M, Pillot P, Pinazza O, Pinsky L, Pitz N, Piuz F, Platt R, Płoskoń M, Pluta J, Pocheptsov T, Pochybova S, Podesta Lerma PLM, Poggio F, Poghosyan MG, Polák K, Polichtchouk B, Polozov P, Polyakov V, Pommeresch B, Pop A, Posa F, Pospísil V, Potukuchi B, Pouthas J, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puddu G, Pujahari P, Pulvirenti A, Punin A, Punin V, Putis M, Putschke J, Quercigh E, Rachevski A, Rademakers A, Radomski S, Räihä TS, Rak J, Rakotozafindrabe A, Ramello L, Ramírez Reyes A, Rammler M, Raniwala R, Raniwala S, Räsänen SS, Rashevskaya I, Rath S, Read KF, Real JS, Redlich K, Renfordt R, Reolon AR, Reshetin A, Rettig F, Revol JP, Reygers K, Ricaud H, Riccati L, Ricci RA, Richter M, Riedler P, Riegler W, Riggi F, Rivetti A, Rodriguez Cahuantzi M, Røed K, Röhrich D, Román López S, Romita R, Ronchetti F, Rosinský P, Rosnet P, Rossegger S, Rossi A, Roukoutakis F, Rousseau S, Roy C, Roy P, Rubio-Montero AJ, Rui R, Rusanov I, Russo G, Ryabinkin E, Rybicki A, Sadovsky S, Safarík K, Sahoo R, Saini J, Saiz P, Sakata D, Salgado CA, Salgueiro Domingues da Silva R, Salur S, Samanta T, Sambyal S, Samsonov V, Sándor L, Sandoval A, Sano M, Sano S, Santo R, Santoro R, Sarkamo J, Saturnini P, Scapparone E, Scarlassara F, Scharenberg RP, Schiaua C, Schicker R, Schindler H, Schmidt C, Schmidt HR, Schossmaier K, Schreiner S, Schuchmann S, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Scott PA, Segato G, Semenov D, Senyukov S, Seo J, Serci S, Serkin L, Serradilla E, Sevcenco A, Sgura I, Shabratova G, Shahoyan R, Sharkov G, Sharma N, Sharma S, Shigaki K, Shimomura M, Shtejer K, Sibiriak Y, Siciliano M, Sicking E, Siddi E, Siemiarczuk T, Silenzi A, Silvermyr D, Simili E, Simonetti G, Singaraju R, Singh R, Singhal V, Sinha BC, Sinha T, Sitar B, Sitta M, Skaali TB, Skjerdal K, Smakal R, Smirnov N, Snellings R, Snow H, Søgaard C, Soloviev A, Soltveit HK, Soltz R, Sommer W, Son CW, Son H, Song M, Soos C, Soramel F, Soyk D, Spyropoulou-Stassinaki M, Srivastava BK, Stachel J, Staley F, Stan E, Stefanek G, Stefanini G, Steinbeck T, Stenlund E, Steyn G, Stocco D, Stock R, Stolpovsky P, Strmen P, Suaide AAP, Subieta Vásquez MA, Sugitate T, Suire C, Sumbera M, Susa T, Swoboda D, Symons J, Szanto de Toledo A, Szarka I, Szostak A, Szuba M, Tadel M, Tagridis C, Takahara A, Takahashi J, Tanabe R, Tapia Takaki JD, Taureg H, Tauro A, Tavlet M, Tejeda Muñoz G, Telesca A, Terrevoli C, Thäder J, Tieulent R, Tlusty D, Toia A, Tolyhy T, Torcato de Matos C, Torii H, Torralba G, Toscano L, Tosello F, Tournaire A, Traczyk T, Tribedy P, Tröger G, Truesdale D, Trzaska WH, Tsiledakis G, Tsilis E, Tsuji T, Tumkin A, Turrisi R, Turvey A, Tveter TS, Tydesjö H, Tywoniuk K, Ulery J, Ullaland K, Uras A, Urbán J, Urciuoli GM, Usai GL, Vacchi A, Vala M, Valencia Palomo L, Vallero S, van der Kolk N, Vande Vyvre P, van Leeuwen M, Vannucci L, Vargas A, Varma R, Vasiliev A, Vassiliev I, Vasileiou M, Vechernin V, Venaruzzo M, Vercellin E, Vergara S, Vernet R, Verweij M, Vetlitskiy I, Vickovic L, Viesti G, Vikhlyantsev O, Vilakazi Z, Villalobos Baillie O, Vinogradov A, Vinogradov L, Vinogradov Y, Virgili T, Viyogi YP, Vodopianov A, Voloshin K, Voloshin S, Volpe G, von Haller B, Vranic D, Vrláková J, Vulpescu B, Wagner B, Wagner V, Wallet L, Wan R, Wang D, Wang Y, Wang Y, Watanabe K, Wen Q, Wessels J, Westerhoff U, Wiechula J, Wikne J, Wilk A, Wilk G, Williams MCS, Willis N, Windelband B, Xu C, Yang C, Yang H, Yasnopolskiy S, Yermia F, Yi J, Yin Z, Yokoyama H, Yoo IK, Yuan X, Yurevich V, Yushmanov I, Zabrodin E, Zagreev B, Zalite A, Zampolli C, Zanevsky Y, Zaporozhets S, Zarochentsev A, Závada P, Zbroszczyk H, Zelnicek P, Zenin A, Zepeda A, Zgura I, Zhalov M, Zhang X, Zhou D, Zhou S, Zhu J, Zichichi A, Zinchenko A, Zinovjev G, Zoccarato Y, Zychácek V, Zynovyev M. Midrapidity antiproton-to-proton ratio in pp collisons at sqrt[s]=0.9 and 7 TeV measured by the ALICE experiment. Phys Rev Lett 2010; 105:072002. [PMID: 20868032 DOI: 10.1103/physrevlett.105.072002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Indexed: 05/29/2023]
Abstract
The ratio of the yields of antiprotons to protons in pp collisions has been measured by the ALICE experiment at sqrt[s]=0.9 and 7 TeV during the initial running periods of the Large Hadron Collider. The measurement covers the transverse momentum interval 0.45<p_{t}<1.05 GeV/c and rapidity |y|<0.5. The ratio is measured to be R_{|y|<0.5}=0.957±0.006(stat)±0.014(syst) at 0.9 TeV and R_{|y|<0.5}=0.991±0.005(stat)±0.014(syst) at 7 TeV and it is independent of both rapidity and transverse momentum. The results are consistent with the conventional model of baryon-number transport and set stringent limits on any additional contributions to baryon-number transfer over very large rapidity intervals in pp collisions.
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Affiliation(s)
- K Aamodt
- Department of Physics, University of Oslo, Oslo, Norway
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Abstract
The plasma membrane uptake system for gamma-amino butyric acid (GABA) is conventionally assumed to be presynaptic, so that after release GABA could be taken up and incorporated into synaptic vesicles for re-use. Using in situ hybridization histochemistry we find that rat spinal motor neurones express GAT-1, a transporter protein for GABA, but that they do not express glutamic acid decarboxylase, the synthetic enzyme for GABA. We conclude that the uptake system is located postsynaptically in these cells. Our observation may explain previous reports where GABA has been detected immunocytochemically in motor neurones.
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Affiliation(s)
- H Snow
- Department of Anatomy and Cell Biology, St Mary's Hospital Medical School, Imperial College, London, UK
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Abstract
Discontinuity defects were created in the mandibles of dogs and then reconstructed immediately with fresh autogenic cancellous bone grafts and Dacron-urethane prostheses. The grafts were irradiated to a total dose of 5000 rads after waiting intervals of between 3 and 12 weeks. Nonirradiated grafts served as controls. The grafts were evaluated clinically, radiographically, and histologically. There was complete incorporation of all grafts, regardless of the interval between surgery and radiotherapy. There were no soft-tissue complications. The controls were distinguishable from the irradiated grafts only by the presence of hematopoietic bone marrow. Fibrofatty marrow was observed in the irradiated grafts. Theoretical support for this technique is found in the biology of cancellous bone grafting and the pathology of radiation injury. In view of the difficulties associated with mandibular bone grafting in preoperatively irradiated patients, a new method of reconstructing selected cancer patients who require both mandibular resection and radiotherapy is suggested.
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Juillard G, Tesler A, Steckel R, Christie B, Snow H, Kolin A. Vasopressin radioprotection of the gastro-intestinal tract. Int J Radiat Oncol Biol Phys 1977. [DOI: 10.1016/0360-3016(77)90623-x] [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: 10/19/2022]
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Lasser KH, Kolin A, Lenz M, Steckel RJ, Snow H. Observation of bronchial dynamics by means of an intraluminal induction gauge. Radiology 1974; 112:448-50. [PMID: 4835046 DOI: 10.1148/112.2.448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Snow H, Tyner JG. Chronic arterial and venous catheterization in sheep. Am J Vet Res 1969; 30:2241-3. [PMID: 5389429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Snow H. PAIN IN CANCER OF THE CERVIX UTERI. West J Med 1903. [DOI: 10.1136/bmj.2.2235.1184] [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: 11/04/2022]
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18
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19
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20
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Snow H. The Treatment of Backward Dislocation of the Thumb. West J Med 1898. [DOI: 10.1136/bmj.1.1934.246-a] [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: 11/03/2022]
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21
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22
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Snow H. Operations for Epithelioma of the Penis. West J Med 1896. [DOI: 10.1136/bmj.1.1830.246-b] [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: 11/04/2022]
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23
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24
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Snow H. Loretin: A New Antiseptic. West J Med 1895; 2:1549-54. [DOI: 10.1136/bmj.2.1825.1549] [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: 11/04/2022]
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25
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26
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Snow H. The Insidious Marrow Lesions of Mammary Carcinoma. West J Med 1892. [DOI: 10.1136/bmj.1.1631.737-d] [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: 11/04/2022]
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27
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28
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Snow H. The Lymph Glands in Tongue Surgery. West J Med 1891. [DOI: 10.1136/bmj.2.1617.1372-d] [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: 11/03/2022]
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29
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Snow H. "The Working of the New Lunacy Act: A Warning". West J Med 1890. [DOI: 10.1136/bmj.1.1535.1278-d] [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: 11/03/2022]
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30
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Snow H. Scirrhus of the Breast: Recurrence Long after Removal. West J Med 1886. [DOI: 10.1136/bmj.1.1325.999-c] [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: 11/03/2022]
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31
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