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Bandres-Ciga S, Faghri F, Majounie E, Koretsky MJ, Kim J, Levine KS, Leonard H, Makarious MB, Iwaki H, Crea PW, Hernandez DG, Arepalli S, Billingsley K, Lohmann K, Klein C, Lubbe SJ, Jabbari E, Saffie-Awad P, Narendra D, Reyes-Palomares A, Quinn JP, Schulte C, Morris HR, Traynor BJ, Scholz SW, Houlden H, Hardy J, Dumanis S, Riley E, Blauwendraat C, Singleton A, Nalls M, Jeff J, Vitale D. NeuroBooster Array: A Genome-Wide Genotyping Platform to Study Neurological Disorders Across Diverse Populations. medRxiv 2023:2023.11.06.23298176. [PMID: 37986980 PMCID: PMC10659467 DOI: 10.1101/2023.11.06.23298176] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Genome-wide genotyping platforms have the capacity to capture genetic variation across different populations, but there have been disparities in the representation of population-dependent genetic diversity. The motivation for pursuing this endeavor was to create a comprehensive genome-wide array capable of encompassing a wide range of neuro-specific content for the Global Parkinson's Genetics Program (GP2) and the Center for Alzheimer's and Related Dementias (CARD). CARD aims to increase diversity in genetic studies, using this array as a tool to foster inclusivity. GP2 is the first supported resource project of the Aligning Science Across Parkinson's (ASAP) initiative that aims to support a collaborative global effort aimed at significantly accelerating the discovery of genetic factors contributing to Parkinson's disease and atypical parkinsonism by generating genome-wide data for over 200,000 individuals in a multi-ancestry context. Here, we present the Illumina NeuroBooster array (NBA), a novel, high-throughput and cost-effective custom-designed content platform to screen for genetic variation in neurological disorders across diverse populations. The NBA contains a backbone of 1,914,934 variants (Infinium Global Diversity Array) complemented with custom content of 95,273 variants implicated in over 70 neurological conditions or traits with potential neurological complications. Furthermore, the platform includes over 10,000 tagging variants to facilitate imputation and analyses of neurodegenerative disease-related GWAS loci across diverse populations. The NBA can identify low frequency variants and accurately impute over 15 million common variants from the latest release of the TOPMed Imputation Server as of August 2023 (reference of over 300 million variants and 90,000 participants). We envisage this valuable tool will standardize genetic studies in neurological disorders across different ancestral groups, allowing researchers to perform genetic research inclusively and at a global scale.
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Affiliation(s)
- Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC 20037, USA
| | | | - Mathew J Koretsky
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Kim
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kristin S Levine
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC 20037, USA
| | - Hampton Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC 20037, USA
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC 20037, USA
| | - Peter Wild Crea
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kimberley Billingsley
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Edwin Jabbari
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Paula Saffie-Awad
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centro de Trastornos del Movimiento (CETRAM), Santiago, Chile
- Clínica Santa María, Santiago, Chile
| | - Derek Narendra
- Inherited Movement Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Armando Reyes-Palomares
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - John P Quinn
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, UK
| | - Claudia Schulte
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen and German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Against Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Bryan J. Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Henry Houlden
- Aligning Science Against Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - John Hardy
- Aligning Science Against Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Sonya Dumanis
- Aligning Science Against Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Ekemini Riley
- Aligning Science Against Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mike Nalls
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC 20037, USA
| | | | - Dan Vitale
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC 20037, USA
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Rodriguez I, Rossi NM, Keskus A, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O’Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley K, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing. medRxiv 2023:2023.08.21.23294276. [PMID: 37662332 PMCID: PMC10473792 DOI: 10.1101/2023.08.21.23294276] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and this is one of the first analyses of these events using long-read sequencing. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes and only one BFB breakpoint showed chromothripsis. Five cell lines have a Chr11q BFB event, with YAP1/BIRC2/BIRC3 gene amplification. Indeed, YAP1 amplification is associated with a 10-year earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that cervical cancer patients with YAP1/BIRC2/BIRC3-amplification, especially those of African American ancestry, might benefit from targeted therapy. In summary, we uncovered new insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F. Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Tim O’Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Laksh Malik
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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3
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Kaivola K, Chia R, Ding J, Rasheed M, Fujita M, Menon V, Walton RL, Collins RL, Billingsley K, Brand H, Talkowski M, Zhao X, Dewan R, Stark A, Ray A, Solaiman S, Alvarez Jerez P, Malik L, Dawson TM, Rosenthal LS, Albert MS, Pletnikova O, Troncoso JC, Masellis M, Keith J, Black SE, Ferrucci L, Resnick SM, Tanaka T, Topol E, Torkamani A, Tienari P, Foroud TM, Ghetti B, Landers JE, Ryten M, Morris HR, Hardy JA, Mazzini L, D'Alfonso S, Moglia C, Calvo A, Serrano GE, Beach TG, Ferman T, Graff-Radford NR, Boeve BF, Wszolek ZK, Dickson DW, Chiò A, Bennett DA, De Jager PL, Ross OA, Dalgard CL, Gibbs JR, Traynor BJ, Scholz SW. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias. Cell Genom 2023; 3:100316. [PMID: 37388914 PMCID: PMC10300553 DOI: 10.1016/j.xgen.2023.100316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 07/01/2023]
Abstract
We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer's dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.
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Affiliation(s)
- Karri Kaivola
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Memoona Rasheed
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Ronald L. Walton
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Ryan L. Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
| | - Ramita Dewan
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Ali Stark
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Anindita Ray
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Sultana Solaiman
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Laksh Malik
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Ted M. Dawson
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Liana S. Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Juan C. Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Mario Masellis
- Cognitive & Movement Disorders Clinic, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
| | - Julia Keith
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
| | - Sandra E. Black
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - PROSPECT Consortium
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
- Cognitive & Movement Disorders Clinic, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute, Department of Neurogenerative Disease and Reta Lila Weston Institute, London, UK
- Institute of Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Maggiore della Carita University Hospital, Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
- Department of Psychiatry and Psychology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Center for Sleep Medicine, Mayo Clinic, Rochester, MN, USA
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Eric Topol
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Ali Torkamani
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Pentti Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Huw R. Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - John A. Hardy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute, Department of Neurogenerative Disease and Reta Lila Weston Institute, London, UK
- Institute of Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Cristina Moglia
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
| | - Andrea Calvo
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
| | - Geidy E. Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G. Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Tanis Ferman
- Department of Psychiatry and Psychology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | | | | | - Zbigniew K. Wszolek
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Bryan J. Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
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4
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Bowman K, Peña Marquez LA, Hawthorne L, Billingsley K, Kelham S, Liang S, Kalvelage M. A comparison of results from antihuman globulin-graded reactions with the monocyte monolayer assay. Immunohematology 2023; 39:77-81. [PMID: 37405849 DOI: 10.21307/immunohematology-2023-013] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Blood transfusions are a common medical treatment. Risks arise when compatible blood is not available. This study assesses the correlation between antibody reaction strength at the antihuman globulin (AHG) phase of testing and the antibody clinical significance as predicted using the monocyte monolayer assay (MMA). Multiple examples of anti-K donor plasma samples were selected to sensitize K+k+ red blood cells (RBCs). Reactivity was confirmed by testing the sensitized K+k+ RBCs at saline-AHG. Antibody titers were determined by serial dilution using neat plasma. Sixteen samples were selected for the study based on comparable graded reactions with neat plasma (1+, 2+, 3+, and 4+) and similar titration endpoints. Each sample was used to sensitize the same Kk donor and then tested by monocytes to evaluate the clinical significance using the MMA, an in vitro procedure that mimics in vivo extravascular hemolysis to predict the survivability of incompatible transfused RBCs. The monocyte index (MI), i.e., the percentage of RBCs adhered, ingested, or both versus free monocytes, was calculated for each sample. Regardless of the reaction strength, all examples of anti-K were predicted to be clinically significant. While anti-K is known to be clinically significant, the immunogenicity rate of K ensures ample supply of antibody samples for inclusion in this project. This study demonstrates that in vitro antibody strength is highly subjective and variable. These results show no correlation between graded reaction strength at AHG and the predicted clinical significance of an antibody as assessed using the MMA.
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Affiliation(s)
- K Bowman
- MLS(ASCP)SBBCM, Immunohematology Technologist III, LifeShare Blood Center, Shreveport, LA, USA
| | | | - L Hawthorne
- MHS, MLS(ASCP)SBB, Immunohematology Technologist II, LifeShare Blood Center, Shreveport, LA, USA
| | - K Billingsley
- MSTM, MLS(ASCP)SBBCM Director, Scientific Services, LifeShare Blood Center, 8910 Linwood Avenue, Shreveport, LA 71106, USA
| | - S Kelham
- MLS(ASCP), Supervisor, Scientific Services, LifeShare Blood Center, Shreveport, LA, USA
| | - S Liang
- MLS(ASCP)SBBCM, Immunohematology Technologist II, LifeShare Blood Center, Shreveport, LA, USA
| | - M Kalvelage
- MSTM, MLS(ASCP)MBCM, SBBCM, Chief Operations Officer, LifeShare Blood Center, Shreveport, LA, USA
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Keskus A, Ahmad T, Donmez A, Xie Y, Rodriguez I, Milano R, Rossi N, Lou H, Malik L, Billingsley K, Blauwendraat C, Dean M, Kolmogorov M. Abstract 4289: Long-read, assembly-based characterization of rearranged cancer karyotypes. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4289] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Recent pan-cancer whole-genome sequencing studies revealed the rich landscape of structural variants (SV), from simpler indels to complex events involving multiple breakpoints and sequence gain/loss. SVs may contribute to tumorigenesis through direct modification of coding sequence or deregulation from copy number alterations, enhancer hijacking, or topological domain modification.
A substantial part of the variation in the human genome is not accessible to short reads due to mapping ambiguities. Recent benchmarking studies reported that the best short-read methods only have 30-70% SV sensitivity. Long-read sequencing (such as PacBio or Oxford Nanopore) can overcome the limitations of short reads, however the current methods were not designed for the analysis of rearranged cancer genomes with complex copy number profiles.
Methods: We developed BGA (Breakpoint Graph Assembler), a method that combines the ideas from long-read assembly and breakpoint graph frameworks. BGA detects abnormally mapped reads and builds a breakpoint graph that characterizes the structure of derived cancer karyotypes. Complex events with multiple breakpoints form connectivity clusters and are classified based on the subgraph properties. BGA also takes advantage of phased haplotypes and can incorporate multiple related datasets (such as in tumor-normal comparison or multi-site tumor sampling). BGA is freely available at: https://github.com/KolmogorovLab/BGA.
Results: We first analyzed three cancer cell lines and corresponding matching normal DNAs (HCC1954, H2009, and COLO829). In each cell line, we identified 8-56 somatic rearrangement clusters involving more than two breakpoints and at least 1kb of sequence. In H2009, we identified a chromoplexy event involving chr13 and chr1, consistent with previous FISH experiments. COLO829 showed the lowest number of somatic rearrangement clusters (n=8), including translocation and inversion events between chr3, chr10, and chr12 within the RARB, BICC1, and TRHDE genes. Homologous recombination deficient HCC1954 has the highest number of complex events including the chr17q arm which hosts ERBB2, chromoplexy between chr8, chr5, and chromothripsis in chr21.
In addition, we analyzed three other HPV-infected cell lines (CaSki, SCC152, SNU1000). In each of them, we observed complex clusters of HPV-HPV and HPV-human breakpoints that formed cycles, suggesting extrachromosomal amplification. The HPV fragments had many interactions with chromosomal DNA in CaSki and SC152, but not in mostly episomal SNU1000 cells. We also observed karyotype-scale changes that did not involve HPV sequences, such as the simultaneous exchange of six chromosome arms of chr2, chr7, and chr17 in CaSki.
Citation Format: Ayse Keskus, Tanveer Ahmad, Ataberk Donmez, Yi Xie, Isabel Rodriguez, Rose Milano, Nicole Rossi, Hong Lou, Laksh Malik, Kimberley Billingsley, Cornelis Blauwendraat, Michael Dean, Mikhail Kolmogorov. Long-read, assembly-based characterization of rearranged cancer karyotypes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4289.
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Affiliation(s)
- Ayse Keskus
- 1National Cancer Institute, NCI, Bethesda, MD
| | | | | | - Yi Xie
- 2National Cancer Institute, NCI, Rockville, MD
| | | | - Rose Milano
- 2National Cancer Institute, NCI, Rockville, MD
| | | | - Hong Lou
- 3National Laboratory for Cancer Research, Frederick, MD
| | - Laksh Malik
- 4National Institutes of Health, Bethesda, MD
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6
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Bustos BI, Billingsley K, Blauwendraat C, Gibbs JR, Gan-Or Z, Krainc D, Singleton AB, Lubbe SJ. Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk. Brain 2023; 146:65-74. [PMID: 36347471 DOI: 10.1093/brain/awac301] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 08/05/2021] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/11/2022] Open
Abstract
Parkinson's disease is a complex neurodegenerative disorder with a strong genetic component, for which most known disease-associated variants are single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). DNA repetitive elements account for >50% of the human genome; however, little is known of their contribution to Parkinson's disease aetiology. While select short tandem repeats (STRs) within candidate genes have been studied in Parkinson's disease, their genome-wide contribution remains unknown. Here we present the first genome-wide association study of STRs in Parkinson's disease. Through a meta-analysis of 16 imputed genome-wide association study cohorts from the International Parkinson's Disease Genomic Consortium (IPDGC), totalling 39 087 individuals (16 642 cases and 22 445 controls of European ancestry), we identified 34 genome-wide significant STR loci (P < 5.34 × 10-6), with the strongest signal located in KANSL1 [chr17:44 205 351:[T]11, P = 3 × 10-39, odds ratio = 1.31 (95% confidence interval = 1.26-1.36)]. Conditional-joint analyses suggested that four significant STRs mapping nearby NDUFAF2, TRIML2, MIRNA-129-1 and NCOR1 were independent from known risk SNPs. Including STRs in heritability estimates increased the variance explained by SNPs alone. Gene expression analysis of STRs (eSTRs) in RNA sequencing data from 13 brain regions identified significant associations of STRs influencing the expression of multiple genes, including known Parkinson's disease genes. Further functional annotation of candidate STRs revealed that significant eSTRs within NUDFAF2 and ZSWIM7 overlap with regulatory features and are associated with change in the expression levels of nearby genes. Here, we show that STRs at known and novel candidate loci contribute to Parkinson's disease risk and have functional effects in disease-relevant tissues and pathways, supporting previously reported disease-associated genes and giving further evidence for their functional prioritization. These data represent a valuable resource for researchers currently dissecting Parkinson's disease risk loci.
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Affiliation(s)
- Bernabe I Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada.,Department of Human Genetics, McGill University, Montréal, QC, Canada.,Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada
| | - Dimitri Krainc
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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Korenblik R, van Zon JFJA, Olij B, Heil J, Dewulf MJL, Neumann UP, Olde Damink SWM, Binkert CA, Schadde E, van der Leij C, van Dam RM, van Baardewijk LJ, Barbier L, Binkert CA, Billingsley K, Björnsson B, Andorrà EC, Arslan B, Baclija I, Bemelmans MHA, Bent C, de Boer MT, Bokkers RPH, de Boo DW, Breen D, Breitenstein S, Bruners P, Cappelli A, Carling U, Robert MCI, Chan B, De Cobelli F, Choi J, Crawford M, Croagh D, van Dam RM, Deprez F, Detry O, Dewulf MJL, Díaz-Nieto R, Dili A, Erdmann JI, Font JC, Davis R, Delle M, Fernando R, Fisher O, Fouraschen SMG, Fretland ÅA, Fundora Y, Gelabert A, Gerard L, Gobardhan P, Gómez F, Guiliante F, Grünberger T, Grochola LF, Grünhagen DJ, Guitart J, Hagendoorn J, Heil J, Heise D, Herrero E, Hess G, Hilal MA, Hoffmann M, Iezzi R, Imani F, Inmutto N, James S, Borobia FJG, Jovine E, Kalil J, Kingham P, Kollmar O, Kleeff J, van der Leij C, Lopez-Ben S, Macdonald A, Meijerink M, Korenblik R, Lapisatepun W, Leclercq WKG, Lindsay R, Lucidi V, Madoff DC, Martel G, Mehrzad H, Menon K, Metrakos P, Modi S, Moelker A, Montanari N, Moragues JS, Navinés-López J, Neumann UP, Nguyen J, Peddu P, Primrose JN, Olde Damink SWM, Qu X, Raptis DA, Ratti F, Ryan S, Ridouani F, Rinkes IHMB, Rogan C, Ronellenfitsch U, Serenari M, Salik A, Sallemi C, Sandström P, Martin ES, Sarría L, Schadde E, Serrablo A, Settmacher U, Smits J, Smits MLJ, Snitzbauer A, Soonawalla Z, Sparrelid E, Spuentrup E, Stavrou GA, Sutcliffe R, Tancredi I, Tasse JC, Teichgräber U, Udupa V, Valenti DA, Vass D, Vogl TJ, Wang X, White S, De Wispelaere JF, Wohlgemuth WA, Yu D, Zijlstra IJAJ. Resectability of bilobar liver tumours after simultaneous portal and hepatic vein embolization versus portal vein embolization alone: meta-analysis. BJS Open 2022; 6:6844022. [PMID: 36437731 PMCID: PMC9702575 DOI: 10.1093/bjsopen/zrac141] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Many patients with bi-lobar liver tumours are not eligible for liver resection due to an insufficient future liver remnant (FLR). To reduce the risk of posthepatectomy liver failure and the primary cause of death, regenerative procedures intent to increase the FLR before surgery. The aim of this systematic review is to provide an overview of the available literature and outcomes on the effectiveness of simultaneous portal and hepatic vein embolization (PVE/HVE) versus portal vein embolization (PVE) alone. METHODS A systematic literature search was conducted in PubMed, Web of Science, and Embase up to September 2022. The primary outcome was resectability and the secondary outcome was the FLR volume increase. RESULTS Eight studies comparing PVE/HVE with PVE and six retrospective PVE/HVE case series were included. Pooled resectability within the comparative studies was 75 per cent in the PVE group (n = 252) versus 87 per cent in the PVE/HVE group (n = 166, OR 1.92 (95% c.i., 1.13-3.25)) favouring PVE/HVE (P = 0.015). After PVE, FLR hypertrophy between 12 per cent and 48 per cent (after a median of 21-30 days) was observed, whereas growth between 36 per cent and 67 per cent was reported after PVE/HVE (after a median of 17-31 days). In the comparative studies, 90-day primary cause of death was similar between groups (2.5 per cent after PVE versus 2.2 per cent after PVE/HVE), but a higher 90-day primary cause of death was reported in single-arm PVE/HVE cohort studies (6.9 per cent, 12 of 175 patients). CONCLUSION Based on moderate/weak evidence, PVE/HVE seems to increase resectability of bi-lobar liver tumours with a comparable safety profile. Additionally, PVE/HVE resulted in faster and more pronounced hypertrophy compared with PVE alone.
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Affiliation(s)
- Remon Korenblik
- Correspondence to: R. K., Universiteigssingel 50 (room 5.452) 6229 ER Maastricht, The Netherlands (e-mail: ); R. M. v. D., Maastricht UMC+, Dept. of Surgery, Level 4, PO Box 5800, 6202 AZ Maastricht, The Netherlands (e-mail: )
| | - Jasper F J A van Zon
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Bram Olij
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands,GROW—Department of Surgery, School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands,Department of General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Jan Heil
- Department of General, Visceral and Transplant Surgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maxime J L Dewulf
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ulf P Neumann
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands,Department of General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Steven W M Olde Damink
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands,Department of General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany,NUTRIM—Department of Surgery, School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Christoph A Binkert
- Department of Radiology, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Erik Schadde
- Department of General, Visceral and Transplant Surgery, Klinik Hirslanden, Zurich, Switzerland,Department of General, Visceral and Transplant Surgery, Hirslanden Klink St. Anna Luzern, Luzern, Switzerland
| | | | - Ronald M van Dam
- Correspondence to: R. K., Universiteigssingel 50 (room 5.452) 6229 ER Maastricht, The Netherlands (e-mail: ); R. M. v. D., Maastricht UMC+, Dept. of Surgery, Level 4, PO Box 5800, 6202 AZ Maastricht, The Netherlands (e-mail: )
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8
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Dolzhenko E, Weisburd B, Ibañez K, Rajan-Babu IS, Anyansi C, Bennett MF, Billingsley K, Carroll A, Clamons S, Danzi MC, Deshpande V, Ding J, Fazal S, Halman A, Jadhav B, Qiu Y, Richmond PA, Saunders CT, Scheffler K, van Vugt JJFA, Zwamborn RRAJ, Chong SS, Friedman JM, Tucci A, Rehm HL, Eberle MA. REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats. Genome Med 2022; 14:84. [PMID: 35948990 PMCID: PMC9367089 DOI: 10.1186/s13073-022-01085-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/11/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads. RESULTS We implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions and FlipBook, a companion image viewer designed for manual curation of large collections of REViewer images. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in short tandem repeat research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR. CONCLUSIONS Read pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer and FlipBook to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions. REViewer and FlipBook are available under open-source licenses at https://github.com/illumina/REViewer and https://github.com/broadinstitute/flipbook respectively.
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Affiliation(s)
- Egor Dolzhenko
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Ben Weisburd
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Kristina Ibañez
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Indhu-Shree Rajan-Babu
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and Children’s & Women’s Hospital, Vancouver, BC V6H3N1 Canada ,grid.13097.3c0000 0001 2322 6764Department of Medical and Molecular Genetics, King’s College London, Strand, London, WC2R 2LS UK
| | - Christine Anyansi
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Mark F. Bennett
- grid.1042.70000 0004 0432 4889Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia ,grid.410678.c0000 0000 9374 3516Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC 3084 Australia
| | - Kimberley Billingsley
- grid.419475.a0000 0000 9372 4913Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD USA ,grid.419475.a0000 0000 9372 4913Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Ashley Carroll
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Samuel Clamons
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Matt C. Danzi
- grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Viraj Deshpande
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Jinhui Ding
- grid.419475.a0000 0000 9372 4913Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892 USA
| | - Sarah Fazal
- grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Andreas Halman
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Bharati Jadhav
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Yunjiang Qiu
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Phillip A. Richmond
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4 Canada
| | | | - Konrad Scheffler
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Joke J. F. A. van Vugt
- grid.5477.10000000120346234Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ramona R. A. J. Zwamborn
- grid.5477.10000000120346234Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Samuel S. Chong
- grid.4280.e0000 0001 2180 6431Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.4280.e0000 0001 2180 6431Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.412106.00000 0004 0621 9599Department of Laboratory Medicine, National University Hospital, Singapore, 119074 Singapore
| | - Jan M. Friedman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and Children’s & Women’s Hospital, Vancouver, BC V6H3N1 Canada
| | - Arianna Tucci
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Michael A. Eberle
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
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9
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Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LC, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DM, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, Lötter A, Majidian S, Mendem SK, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon CL, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res 2022; 11:530. [PMID: 36262335 PMCID: PMC9557141 DOI: 10.12688/f1000research.110194.1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 01/25/2023] Open
Abstract
In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.
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Affiliation(s)
- Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
| | | | - Guangyi Chen
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany,Center for Bioinformatics, Saarland University, Saarbrücken, Germany,
| | - David Molik
- Tropical Crop and Commodity Protection Research Unit, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Daniela C. Soto
- Biochemistry & Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, Davis, CA, 95616, USA
| | - Fawaz Dabbaghie
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany,Institute for Medical Biometry and Bioinformatics, University hospital Düsseldorf, Düsseldorf, Germany
| | - Ahmad Al Khleifat
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Muhammad Sohail Raza
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Daniel Paiva Agustinho
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Elbay Aliyev
- Research Department, Sidra Medicine, Doha, Qatar
| | - Pavel Avdeyev
- Computational Biology Institute, The George Washington University, Washington, DC, 20052, USA
| | - Enrico R. Barrozo
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Turkey
| | - Deepak Choubey
- Department of Technology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Alejandro R. Gener
- Association of Public Health Labs, Centers for Disease Control and Prevention, Downey, CA, USA
| | - Timothy Hefferon
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Morgan Henke
- Department Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wolfram Höps
- EMBL Heidelberg, Genome Biology Unit, Heidelberg, Germany
| | | | - Michael D. Jochum
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Jose
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | - Rupesh K. Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | - Priya Lakra
- Department of Zoology, University of Delhi, Delhi, India
| | - Damaris Lattimer
- University of Applied Sciences Upper Austria - FH Hagenberg, Mühlkreis, Austria
| | - Chia-Sin Liew
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Bai-Wei Lo
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Chunhsuan Lo
- Human Genetics Laboratory, National Institute of Genetics, Japan, Mishima City, Japan
| | - Anneri Lötter
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Rajarshi Mondal
- Department of Biotechnology, The University of Burdwan, West Bengal, India
| | - Hiroko Ohmiya
- Genetic Reagent Development Unit, Medical & Biological Laboratories Co., Ltd., Tokoyo, Japan
| | - Nasrin Parvin
- Department of Biotechnology, The University of Burdwan, West Bengal, India
| | | | | | | | - Marie Saitou
- Center of Integrative Genetics (CIGENE),Faculty of Biosciences, Norwegian University of Life Sciences, As, Norway
| | - Aditi Sammi
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Philippe Sanio
- University of Applied Sciences Upper Austria - FH Hagenberg, Hagenberg im Mühlkreis, Austria
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Najeeb Syed
- Research Department, Sidra Medicine, Doha, Qatar
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Tiancheng Xu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Jianzhi Yang
- Department of Quantitative and Computational Biology,, University of Southern California, Los Angeles, CA, USA
| | - Shangzhe Zhang
- School of Biology, University of St Andrews, St Andrews, UK
| | - Weiyu Zhou
- Department of Statistical Science, George Mason University, Fairfax, Virginia, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
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Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T. Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C. Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J. Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res 2021; 10:246. [PMID: 34621504 PMCID: PMC8479851 DOI: 10.12688/f1000research.51477.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
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Affiliation(s)
| | | | | | | | | | | | - Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | | | | | | | | | | | | | - Ahmed Arslan
- Stanford University School of Medicine, California, USA
| | | | | | | | - Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Haowei Du
- Baylor College of Medicine, Houston, USA
| | | | | | | | | | | | | | | | | | | | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | | | | | | | | | | | | | | | - Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
| | | | | | | | | | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | | | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
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11
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Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T. Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C. Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J. Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res 2021; 10:246. [PMID: 34621504 PMCID: PMC8479851 DOI: 10.12688/f1000research.51477.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2021] [Indexed: 11/08/2023] Open
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
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Affiliation(s)
| | | | | | | | | | | | - Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | | | | | | | | | | | | | - Ahmed Arslan
- Stanford University School of Medicine, California, USA
| | | | | | | | - Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Haowei Du
- Baylor College of Medicine, Houston, USA
| | | | | | | | | | | | | | | | | | | | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | | | | | | | | | | | | | | | - Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
| | | | | | | | | | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | | | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
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12
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Grenn FP, Kim JJ, Makarious MB, Iwaki H, Illarionova A, Brolin K, Kluss JH, Schumacher‐Schuh AF, Leonard H, Faghri F, Billingsley K, Krohn L, Hall A, Diez‐Fairen M, Periñán MT, Foo JN, Sandor C, Webber C, Fiske BK, Gibbs JR, Nalls MA, Singleton AB, Bandres‐Ciga S, Reed X, Blauwendraat C. The Parkinson's Disease Genome-Wide Association Study Locus Browser. Mov Disord 2020; 35:2056-2067. [PMID: 32864809 PMCID: PMC7754106 DOI: 10.1002/mds.28197] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 04/03/2020] [Revised: 05/27/2020] [Accepted: 06/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a neurodegenerative disease with an often complex component identifiable by genome-wide association studies. The most recent large-scale PD genome-wide association studies have identified more than 90 independent risk variants for PD risk and progression across more than 80 genomic regions. One major challenge in current genomics is the identification of the causal gene(s) and variant(s) at each genome-wide association study locus. The objective of the current study was to create a tool that would display data for relevant PD risk loci and provide guidance with the prioritization of causal genes and potential mechanisms at each locus. METHODS We included all significant genome-wide signals from multiple recent PD genome-wide association studies including themost recent PD risk genome-wide association study, age-at-onset genome-wide association study, progression genome-wide association study, and Asian population PD risk genome-wide association study. We gathered data for all genes 1 Mb up and downstream of each variant to allow users to assess which gene(s) are most associated with the variant of interest based on a set of self-ranked criteria. Multiple databases were queried for each gene to collect additional causal data. RESULTS We created a PD genome-wide association study browser tool (https://pdgenetics.shinyapps.io/GWASBrowser/) to assist the PD research community with the prioritization of genes for follow-up functional studies to identify potential therapeutic targets. CONCLUSIONS Our PD genome-wide association study browser tool provides users with a useful method of identifying potential causal genes at all known PD risk loci from large-scale PD genome-wide association studies. We plan to update this tool with new relevant data as sample sizes increase and new PD risk loci are discovered. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Francis P. Grenn
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Jonggeol J. Kim
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Mary B. Makarious
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Hirotaka Iwaki
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | | | - Kajsa Brolin
- Lund UniversityTranslational Neurogenetics Unit, Department of Experimental Medical ScienceLundSweden
| | - Jillian H. Kluss
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | | | - Hampton Leonard
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | - Faraz Faghri
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | - Kimberley Billingsley
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Lynne Krohn
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
| | - Ashley Hall
- Department of Molecular and Clinical PharmacologyInstitute of Translational Medicine, University of LiverpoolLiverpoolUK
| | - Monica Diez‐Fairen
- Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of NeurologyUniversity Hospital Mútua TerrassaBarcelonaSpain
| | - Maria Teresa Periñán
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de SevillaHospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Jia Nee Foo
- Lee Kong Chian School of MedicineNanyang Technological University SingaporeSingaporeSingapore
- Human GeneticsGenome Institute of Singapore, A*STARSingaporeSingapore
| | - Cynthia Sandor
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Caleb Webber
- UK Dementia Research Institute, Cardiff UniversityCardiffUK
| | - Brian K. Fiske
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central StationNew YorkNYUSA
| | - J. Raphael Gibbs
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Mike A. Nalls
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
- Data Tecnica InternationalGlen EchoMarylandUSA
| | - Andrew B. Singleton
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Sara Bandres‐Ciga
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Xylena Reed
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
| | - Cornelis Blauwendraat
- Laboratory of NeurogeneticsNational Institute on Aging, National Institutes of HealthBethesdaMarylandUSA
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13
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Bandres-Ciga S, Saez-Atienzar S, Bonet-Ponce L, Billingsley K, Vitale D, Blauwendraat C, Gibbs JR, Pihlstrøm L, Gan-Or Z, Cookson MR, Nalls MA, Singleton AB. The endocytic membrane trafficking pathway plays a major role in the risk of Parkinson's disease. Mov Disord 2019; 34:460-468. [PMID: 30675927 DOI: 10.1002/mds.27614] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 10/03/2018] [Revised: 12/05/2018] [Accepted: 12/23/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND PD is a complex polygenic disorder. In recent years, several genes from the endocytic membrane-trafficking pathway have been suggested to contribute to disease etiology. However, a systematic analysis of pathway-specific genetic risk factors is yet to be performed. OBJECTIVES To comprehensively study the role of the endocytic membrane-trafficking pathway in the risk of PD. METHODS Linkage disequilibrium score regression was used to estimate PD heritability explained by 252 genes involved in the endocytic membrane-trafficking pathway including genome-wide association studies data from 18,869 cases and 22,452 controls. We used pathway-specific single-nucleotide polymorphisms to construct a polygenic risk score reflecting the cumulative risk of common variants. To prioritize genes for follow-up functional studies, summary-data based Mendelian randomization analyses were applied to explore possible functional genomic associations with expression or methylation quantitative trait loci. RESULTS The heritability estimate attributed to endocytic membrane-trafficking pathway was 3.58% (standard error = 1.17). Excluding previously nominated PD endocytic membrane-trafficking pathway genes, the missing heritability was 2.21% (standard error = 0.42). Random heritability simulations were estimated to be 1.44% (standard deviation = 0.54), indicating that the unbiased total heritability explained by the endocytic membrane-trafficking pathway was 2.14%. Polygenic risk score based on endocytic membrane-trafficking pathway showed a 1.25 times increase of PD risk per standard deviation of genetic risk. Finally, Mendelian randomization identified 11 endocytic membrane-trafficking pathway genes showing functional consequence associated to PD risk. CONCLUSIONS We provide compelling genetic evidence that the endocytic membrane-trafficking pathway plays a relevant role in disease etiology. Further research on this pathway is warranted given that critical effort should be made to identify potential avenues within this biological process suitable for therapeutic interventions. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Sara Saez-Atienzar
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Luis Bonet-Ponce
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.,Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Dan Vitale
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Jesse Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Ziv Gan-Or
- Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | | | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Mike A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Data Tecnica International, Glen Echo, Maryland, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
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14
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Fuss M, Waller J, Naugler S, Zaman A, Kolbeck K, Orloff S, Billingsley K, Chang M, Sasaki A, Kaufman J. Outcomes of Hypofractionated Radiation Therapy (HFxRT) for Hepatocellular Carcinoma (HCC). Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.865] [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: 11/24/2022]
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15
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Bicquart C, El Youssef R, Sheppard B, Corless C, Billingsley K, Thomas C. Effect of Chemoradiation on Survival of Resected Pancreatic Ductal Adenocarcinoma with Close or Positive Margins. Int J Radiat Oncol Biol Phys 2009. [DOI: 10.1016/j.ijrobp.2009.07.671] [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: 11/25/2022]
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16
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Smith S, Wallner K, Dominitz JA, Han B, True L, Sutlief S, Billingsley K. Argon plasma coagulation for rectal bleeding after prostate brachytherapy. Int J Radiat Oncol Biol Phys 2001; 51:636-42. [PMID: 11597803 DOI: 10.1016/s0360-3016(01)01704-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [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: 12/14/2022]
Abstract
PURPOSE To better define the efficacy and safety of argon plasma coagulation (APC), specifically for brachytherapy-related proctitis, we reviewed the clinical course of 7 patients treated for persistent rectal bleeding. Approximately 2-10% of prostate cancer patients treated with 125I or 103Pd brachytherapy will develop radiation proctitis. The optimum treatment for patients with persistent bleeding is unclear from the paucity of available data. Prior reports lack specific dosimetric information, and patients with widely divergent forms of radiation were grouped together in the analyses. METHODS AND MATERIALS Seven patients were treated with APC at the Veterans Affairs Puget Sound Health Care System and the University of Washington from 1997 to 1999 for persistent rectal bleeding due to prostate brachytherapy-related proctitis. Four patients received supplemental external beam radiation, delivered by a four-field technique. A single gastroenterologist at the Veterans Affairs Puget Sound Health Care System treated 6 of the 7 patients. If the degree of proctitis was limited, all sites of active bleeding were coagulated in symptomatic patients. An argon plasma coagulator electrosurgical system was used to administer treatments every 4-8 weeks as needed. The argon gas flow was set at 1.6 L/min, with an electrical power setting of 40-45 W. RESULTS The rectal V100 (the total rectal volume, including the lumen, receiving the prescription dose or greater) for the 7 patients ranged from 0.13 to 4.61 cc. Rectal bleeding was first noticed 3-18 months after implantation. APC (range 1-3 sessions) was performed 9-22 months after implantation. Five patients had complete resolution of their bleeding, usually within days of completing APC. Two patients had only partial relief from bleeding, but declined additional APC therapy. No patient developed clinically evident progressive rectal wall abnormalities after APC, (post-APC follow-up range 4-13 months). CONCLUSIONS Most patients benefited from APC, and no cases of clinically evident progressive tissue destruction were noted. Although APC appears to be efficacious and safe in the setting of the rectal doses described here, caution is in order when contemplating APC for brachytherapy patients.
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Affiliation(s)
- S Smith
- Department of Radiation Oncology, University of Washington, Seattle, WA, USA
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Schwartz D, Billingsley K, Wallner K. Follow-up care for cancer: making the benefits equal the cost. Oncology (Williston Park) 2000; 14:1493-8, 1501; discussion 1502-5. [PMID: 11098513] [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] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Posttreatment follow-up is a staple of oncologic practice. Clinicians have traditionally presumed that close surveillance improves clinical outcome. However, new evidence reveals that frequent, procedure-intensive follow-up may provide no more significant benefit to patients than simpler approaches. Several recent consensus recommendations from major oncology organizations support this theory. Published surveys of clinician and institutional follow-up policies reveal significant variations in practice, with many providers continuing to use costly, unproven regimens. This review highlights current data on follow-up care for three common cancers--breast, colorectal, and prostate. These data suggest an acute need for changes leading to more rational, consistent, and efficient follow-up practices.
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Affiliation(s)
- D Schwartz
- Department of Radiation Oncology, Seattle VA Hospital-Puget Sound Health Care System, Washington, USA
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