1
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Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BDBD, Abedalthagafi MS, Mutlu O, Mangul S. Packaging and containerization of computational methods. Nat Protoc 2024:10.1038/s41596-024-00986-0. [PMID: 38565959 DOI: 10.1038/s41596-024-00986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.
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Affiliation(s)
- Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Brendan Lawlor
- Department of Computer Science, Munster Technological University, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Richard J Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sharon Waymost
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Neha Rajkumar
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Jaqueline Brito
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Nour Almadhoun
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Varuni Sarwal
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Can Firtina
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Tomasz Osinski
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Qiyang Hu
- Office of Advanced Research Computing, University of California, Los Angeles, CA, USA
| | - Derek Strong
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Byoung-Do B D Kim
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Onur Mutlu
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Serghei Mangul
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
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2
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Aldoukhi AH, Bilalis P, Alhattab DM, Valle-Pérez AU, Susapto HH, Pérez-Pedroza R, Backhoff-García E, Alsawaf SM, Alshehri S, Boshah H, Alrashoudi AA, Aljabr WA, Alaamery M, Alrashed M, Hasanato RM, Farzan RA, Alsubki RA, Moretti M, Abedalthagafi MS, Hauser CAE. Fusing Peptide Epitopes for Advanced Multiplex Serological Testing for SARS-CoV-2 Antibody Detection. ACS Bio Med Chem Au 2024; 4:37-52. [PMID: 38404747 PMCID: PMC10885102 DOI: 10.1021/acsbiomedchemau.3c00010] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 02/27/2024]
Abstract
The tragic COVID-19 pandemic, which has seen a total of 655 million cases worldwide and a death toll of over 6.6 million seems finally tailing off. Even so, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise, the severity of which cannot be predicted in advance. This is concerning for the maintenance and stability of public health, since immune evasion and increased transmissibility may arise. Therefore, it is crucial to continue monitoring antibody responses to SARS-CoV-2 in the general population. As a complement to polymerase chain reaction tests, multiplex immunoassays are elegant tools that use individual protein or peptide antigens simultaneously to provide a high level of sensitivity and specificity. To further improve these aspects of SARS-CoV-2 antibody detection, as well as accuracy, we have developed an advanced serological peptide-based multiplex assay using antigen-fused peptide epitopes derived from both the spike and the nucleocapsid proteins. The significance of the epitopes selected for antibody detection has been verified by in silico molecular docking simulations between the peptide epitopes and reported SARS-CoV-2 antibodies. Peptides can be more easily and quickly modified and synthesized than full length proteins and can, therefore, be used in a more cost-effective manner. Three different fusion-epitope peptides (FEPs) were synthesized and tested by enzyme-linked immunosorbent assay (ELISA). A total of 145 blood serum samples were used, compromising 110 COVID-19 serum samples from COVID-19 patients and 35 negative control serum samples taken from COVID-19-free individuals before the outbreak. Interestingly, our data demonstrate that the sensitivity, specificity, and accuracy of the results for the FEP antigens are higher than for single peptide epitopes or mixtures of single peptide epitopes. Our FEP concept can be applied to different multiplex immunoassays testing not only for SARS-CoV-2 but also for various other pathogens. A significantly improved peptide-based serological assay may support the development of commercial point-of-care tests, such as lateral-flow-assays.
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Affiliation(s)
- Ali H. Aldoukhi
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Panayiotis Bilalis
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Dana M. Alhattab
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Hepi H. Susapto
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Rosario Pérez-Pedroza
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Emiliano Backhoff-García
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sarah M. Alsawaf
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Salwa Alshehri
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Hattan Boshah
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Abdulelah A. Alrashoudi
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Waleed A. Aljabr
- Research
Centre, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Manal Alaamery
- Developmental
Medicine Department, King Abdullah International Medical Research
Center, King Abdulaziz Medical City, Ministry of National Guard-Health
Affairs, King Saud Bin Abdulaziz University
for Health Sciences, Riyadh 11426, Saudi Arabia
- KACST-BWH
Centre of Excellence for Biomedicine, Joint Centers of Excellence
Program, King Abdulaziz City for Science
and Technology (KACST), Riyadh 12371, Saudi Arabia
- Saudi
Human Genome Project (SHGP), Satellite Lab at King Abdulaziz Medical
City (KAMC), Ministry of National Guard Health Affairs (MNG-HA), King Abdulaziz City for Science and Technology (KACST), Riyadh 11426, Saudi Arabia
| | - May Alrashed
- Department
of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Chair
of Medical and Molecular Genetics Research, King Saud University, Riyadh 11433, Saudi Arabia
| | - Rana M. Hasanato
- Department
of Pathology and Laboratory Medicine, King
Saud University, Riyadh 11433, Saudi Arabia
| | - Raed A. Farzan
- Department
of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Chair
of Medical and Molecular Genetics Research, King Saud University, Riyadh 11433, Saudi Arabia
| | - Roua A. Alsubki
- Department
of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Chair
of Medical and Molecular Genetics Research, King Saud University, Riyadh 11433, Saudi Arabia
| | - Manola Moretti
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Malak S. Abedalthagafi
- Pathology and Laboratory Medicine, Emory
School of Medicine, Atlanta, Georgia 30329, United States
| | - Charlotte A. E. Hauser
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
- Red Sea
Research Center, Division of Biological and Environmental
Science and Engineering (BESE), King Abdullah
University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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3
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Sharma NK, Ayyala R, Deshpande D, Patel YM, Munteanu V, Ciorba D, Fiscutean A, Vahed M, Sarkar A, Guo R, Moore A, Darci-Maher N, Nogoy NA, Abedalthagafi MS, Mangul S. Analytical code sharing practices in biomedical research. bioRxiv 2023:2023.07.31.551384. [PMID: 37609176 PMCID: PMC10441317 DOI: 10.1101/2023.07.31.551384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.
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Affiliation(s)
- Nitesh Kumar Sharma
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Ram Ayyala
- Quantitative and Computational Biology Department, USC Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Dhrithi Deshpande
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Yesha M Patel
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Viorel Munteanu
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova
| | - Dumitru Ciorba
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova
| | - Andrada Fiscutean
- Faculty of Journalism and Communication Studies, University of Bucharest, Soseaua Panduri, nr. 90, Sector 5, 050663, Bucharest, Romania
| | - Mohammad Vahed
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Aditya Sarkar
- School of Computing and Electrical Engineering, Indian Institute of Technology Mandi, North Campus, Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Ruiwei Guo
- Department of Pharmacology and Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Andrew Moore
- Daniel J. Epstein Department of Industrial and Systems Engineering, Viterbi School of Engineering, University of Southern California
| | - Nicholas Darci-Maher
- Computational and Systems Biology, University of California, Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Nicole A Nogoy
- GigaScience Press, L26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, N.T., Hong Kong
| | - Malak S. Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Serghei Mangul
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
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4
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Peng K, Nowicki TS, Campbell K, Vahed M, Peng D, Meng Y, Nagareddy A, Huang YN, Karlsberg A, Miller Z, Brito J, Nadel B, Pak VM, Abedalthagafi MS, Burkhardt AM, Alachkar H, Ribas A, Mangul S. Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Brief Bioinform 2023; 24:bbad220. [PMID: 37291798 PMCID: PMC10359085 DOI: 10.1093/bib/bbad220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.
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Affiliation(s)
- Kerui Peng
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Theodore S Nowicki
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Katie Campbell
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, CA, USA
| | - Mohammad Vahed
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Dandan Peng
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yiting Meng
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Anish Nagareddy
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yu-Ning Huang
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Aaron Karlsberg
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zachary Miller
- Department of Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jaqueline Brito
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brian Nadel
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Victoria M Pak
- Emory Nell Hodgson School of Nursing, Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Amanda M Burkhardt
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Houda Alachkar
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Antoni Ribas
- Departments of Medicine (Hematology-Oncology), Surgery (Surgical Oncology) and Molecular & Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
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5
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Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJM, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet 2022; 18:e1010367. [PMID: 36327219 PMCID: PMC9632827 DOI: 10.1371/journal.pgen.1010367] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022] Open
Abstract
Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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Grants
- U24 CA224319 NCI NIH HHS
- RG/13/13/30194 British Heart Foundation
- U01 DK124165 NIDDK NIH HHS
- C18281/A29019 Cancer Research UK
- MC_PC_20004 Medical Research Council
- UL1 TR001873 NCATS NIH HHS
- RG/18/13/33946 British Heart Foundation
- CH/12/2/29428 British Heart Foundation
- CanCOGeN HostSeq
- Fonds de Recherche Québec Santé (FRQS)
- Génome Québec
- Public Health Agency of Canada
- Canadian Institutes of Health Research (CIHR)
- Lady Davis Institute of the Jewish General Hospital
- Canadian Foundation for Innovation
- NIH Foundation
- McGill Interdisciplinary Initiative in Infection and Immunity (MI4)
- Jewish General Hospital Foundation
- McGill University
- Calcul Québec and Compute Canada
- Compute Canada
- Vagelos College of Physicians & Surgeons Office for Research
- Biomedical Informatics Resource of the Columbia University Irving Institute for Clinical and Translational Research (CTSA)
- National Center for Advancing Translational Sciences, National Institutes of Health
- German Research Foundation
- NGS Competence Center Tübingen
- West German Genome Center
- Stiftung Universitätsmedizin Essen
- Technical University of Munich
- BONFOR program of the Medical Faculty, University of Bonn
- Emmy-Noether programm of the German Research Foundation
- State of Saarland
- Dr. Rolf M. Schwiete Foundation
- Munich Clinician Scientist Programm
- Netzwerk-Universitaetsmedizin-COVIM
- Federal Ministry of Education and Research
- Swiss National Science Foundation
- Leenaards Foundation
- Santos-Suarez Foundation
- Carigest
- MIUR project “Dipartimenti di Eccellenza 2018-2020”
- Bando Ricerca COVID-19 Toscana
- charity fund 2020 from Intesa San Paolo
- Italian Ministry of University and Research
- Istituto Buddista Italiano Soka Gakkai
- Instituto de Salud Carlos III
- GePEM
- DIAVIR
- Resvi-Omics
- ReSVinext
- Enterogen
- Agencia Gallega para la Gestión del Conocimiento en Salud
- BI-BACVIR
- CovidPhy
- Agencia Gallega de Innovación (GAIN):
- GEN-COVID
- Framework Partnership Agreement between the Consellería de Sanidad de la XUNTA de Galicia
- GENVIP-IDIS
- consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias
- F. Hoffmann-La Roche Ltd
- U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, and Biomedical Advanced Research and Development Authority
- Nevada Governor's Office of Economic Development
- Renown Health and the Renown Health Foundation
- Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research)
- Grant for Development of New Faculty Staff, Ratchadaphiseksomphot Endowment Fund
- e-ASIA Joint Research Program (National Science and Technology Development Agency)
- Health Systems Research Institute, TSRI Fund
- Thailand Research Fund
- Ratchadapiseksompotch Fund
- Ratchadapiseksompotch Fund, Faculty of Medicine,Chulalongkorn University, Bangkok, Thailand
- Health Systems Research Institute
- Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- NHS Blood and Transplant
- National Institute for Health Research
- UK Medical Research Council
- Japan Agency for Medical Research and Development
- Japan Science and Technology Agency
- National Center for Global Health and Medicine
- Agency for Medical Research and Development
- Polish National Science Centre
- Medical Research Agency
- Perelman School of Medicine at University of Pennsylvania
- Smilow family
- National Center for Advancing Translational Sciences of the National Institutes of Health
- Polish Medical Research Agency
- Qatar Foundation for Education, Science and Community Development
- Saudi Ministry of Health
- King Abdulaziz City for Science and Technology
- European Union’s Horizon 2020 research and innovation program
- Science for Life Laboratory
- Swedish Research Council
- Knut and Alice Wallenberg Foundation
- OCRC
- Microsoft COVID Compute Funding
- Illumina
- UCLA David Geffen School of Medicine - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Award Program
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Jack A. Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States of America
| | | | - Theodore Drivas
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Furini
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Urszula Korotko
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Elifnaz Çelik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amy D. Stockwell
- Genentech Inc, South San Francisco, California, United States of America
| | - Laura G. Sloofman
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Daniel M. Jordan
- Mount Sinai Clnical Intelligence Center, Charles Bronfman Institute for Personalized Medicine, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Ryan C. Thompson
- Icahn Institute of Data Science and Genomics Technology, New York city, New York, United States of America
| | - Diane Del Valle
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Nicole Simons
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Seunghee Kim-Schulze
- Department of Oncological Science, Human Immune Monitoring Center, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Noam D. Beckmann
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | | | - Timothy Chang
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Tess D. Pottinger
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Fabian Brand
- Institute of Genomic Statistics and Bioinformatics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Francesca Fava
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Karolina Chwialkowska
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Centre for Clinical Research, Medical University of Bialystok, Bialystok, Poland
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, United States of America
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kumar Veerapen
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Robert JM Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Langlais
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Robert Frithiof
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Miklos Lipcsey
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - William Lee
- Helix, San Mateo, California, United States of America
| | | | - Simon White
- Helix, San Mateo, California, United States of America
| | | | | | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | - Shaun Dabe
- Renown Health, Reno, Nevada, United States of America
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susanne Motameny
- West German Genome Center, site Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fatima Alqubaishi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sarah Alotaibi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandari Binowayn
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ebtehal A. Alsolm
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammad Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fang Cai
- Genentech Inc, South San Francisco, California, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam Butterworth
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | | | | | | | | | - Daniel H. Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Arteaga
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alexis Stephens
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Manish J. Butte
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul C. Boutros
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Shu Tao
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stefan Eng
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Timothy Sanders
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul J. Tung
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Broudy
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Yu Pan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alfredo Gonzalez
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Nikhil Chavan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Ruth Johnson
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Pathology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Brian Yaspan
- Genentech Inc, South San Francisco, California, United States of America
| | - Sandra Smieszek
- Vanda Pharmaceuticals, Washington, District of Columbia, United States of America
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Maciej Dabrowski
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
| | - Pawel Zawadzki
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | | | - Elżbieta Kaja
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Department of Medical Chemistry and Laboratory Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voraphoj Nilaratanakul
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research) and Division of Infectious Diseases, Department of Medicine,Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Takanori Hasegawa
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | | | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- West German Genome Center, site Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Anurag Verma
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Department of Genetics & Development, Columbia University, New York city, New York, United States of America
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
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6
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Mobark NA, Alharbi M, Alotabi F, Alshoumer A, Al Shakweer W, AlNaqib ZG, AlSaad AN, Balbaid AO, Alsolme E, Abedalthagafi MS. Papillary Tumor of the Pineal Region Rare Pediatric CNS Tumor Case Series Treated in King Fahad Medical City (KFMC). Curr Oncol 2022; 29:7558-7568. [PMID: 36290872 PMCID: PMC9600283 DOI: 10.3390/curroncol29100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/26/2022] [Accepted: 10/09/2022] [Indexed: 11/05/2022] Open
Abstract
The clinical behaviors, prognosis, and appropriate treatments of papillary tumors of the pineal region (PTPR) are not fully defined due to the rarity of these tumors. At diagnosis, PTPR may present with clinical symptoms, including headache with obstructive hydrocephalus, diplopia, vomiting, and lethargy, as well as neurological signs, including Argyll Robertson pupils and Parinaud's syndrome due to compression of the dorsal midbrain, specifically the periaqueductal region with horizontal nystagmus. Radiological assessment of pineal region lesions is challenging, with a wide range of potential differential diagnoses. PTPR typically presents as a heterogeneous, well-circumscribed mass in the pineal region, which might contain cystic areas, calcifications, hemorrhages, or protein accumulations. Here, we report three female pediatric patients with PTPR treated in King Fahad Medical City (KFMC) in Saudi Arabia. Histological and immunohistochemical diagnosis was confirmed by analysis of genome-wide DNA methylation profiles. This case series expands on the available reports on the clinical presentations of PTPR and provides important information on the responses to different treatment modalities.
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Affiliation(s)
- Nahla A. Mobark
- Department of Pediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Musa Alharbi
- Department of Pediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Fahad Alotabi
- Pediatric Neurosurgical Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Azhar Alshoumer
- Department of Pathology & Laboratory Medicine, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Wafa Al Shakweer
- Department of Pathology & Laboratory Medicine, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Zaid G. AlNaqib
- Department of Pediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | | | - Ali O. Balbaid
- Radiation Oncology Department, Comprehensive Cancer Centre, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Ebtehal Alsolme
- Genomics Research Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Malak S. Abedalthagafi
- Genomics Research Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
- Correspondence:
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7
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods 2022; 19:374-380. [PMID: 35396471 PMCID: PMC9467803 DOI: 10.1038/s41592-022-01444-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated development of testing methods, and allowed timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific, and organizational challenges. Here, we discuss the application of genomic and computational methods for the efficient data driven COVID-19 response, advantages of democratization of viral sequencing around the world, and challenges associated with viral genome data collection and processing.
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Affiliation(s)
- Sergey Knyazev
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Translational Biomedical Informatics, University of Southern California, Los Angeles, CA, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Pelin Icer Baykal
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoia Comarova
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Yuri Porozov
- World-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Tetyana I Vasylyeva
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Malak S Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Victoria M Pak
- Emory University, School of Nursing, Atlanta, GA, CA, USA
- Emory University, Rollins School of Public Health, Department of Epidemiology, Atlanta, GA, CA, USA
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrey Komissarov
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Fyodor Kondrashov
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P.R. China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, P.R. China
- Centre for Immunology & Infection Limited, Hong Kong SAR, P.R. China
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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8
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Hajeer A, Jawdat D, Massadeh S, Aljawini N, Abedalthagafi MS, Arabi YM, Alaamery M. Association of KIR gene polymorphisms with COVID-19 disease. Clin Immunol 2022; 234:108911. [PMID: 34929414 PMCID: PMC8683215 DOI: 10.1016/j.clim.2021.108911] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022]
Abstract
Background Methods Results Conclusions
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9
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Povysil G, Butler-Laporte G, Shang N, Wang C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh RJ, Bourgey M, Aziz N, Jones SJ, Knoppers B, Scherer SW, Strug LJ, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albes N, Al-Afghani HM, Alghamdi B, Almutairi MS, Mahmoud ES, Abu-Safieh L, El Bardisy H, Harthi FSA, Alshareef A, Suliman BA, Alqahtani SA, Almalik A, Alrashed MM, Massadeh S, Mooser V, Lathrop M, Fawzy M, Arabi YM, Mbarek H, Saad C, Al-Muftah W, Jung J, Mangul S, Badji R, Thani AA, Ismail SI, Gharavi AG, Abedalthagafi MS, Richards JB, Goldstein DB, Kiryluk K. Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19. J Clin Invest 2021; 131:147834. [PMID: 34043590 PMCID: PMC8279578 DOI: 10.1172/jci147834] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes.
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Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Chen Wang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
| | | | - Robert J.M. Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Naveed Aziz
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | | | | | | | - Lisa J. Strug
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | - Pierre Lepage
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | | | - Nora Aljawini
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nour Albes
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hani M. Al-Afghani
- Laboratory Department, Security Forces Hospital, General Directorate of Medical Services, Ministry of Interior, Makkah, Saudi Arabia
| | - Bader Alghamdi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ebrahim Sabri Mahmoud
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Leen Abu-Safieh
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | | | - Bandar Ali Suliman
- College of Applied Medical Sciences, Taibah University, Madina, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Abdulaziz Almalik
- Life Science and Environmental Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - May M. Alrashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian COVID Genomics Network, HostSeq Project, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Mohamed Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Wadha Al-Muftah
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Radja Badji
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Asma Al Thani
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
- Center for Precision Medicine and Genomics, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - J. Brent Richards
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Twin Research, King’s College London, London, United Kingdom
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
- Department of Genetics & Development, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
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10
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Tsan-Yuk Lam T, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ARXIV 2021. [PMCID: PMC8109901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.
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Affiliation(s)
- Sergey Knyazev
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA,Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, 30333 GA, USA,Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Ram Ayyala
- Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Zoia Comarova
- Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Yuri Porozov
- World-Class Research Center “Digital biodesign and personalized healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow, Russia,Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China,Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia,Translational Research Institute, Brisbane, Australia
| | - Adam L. Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
| | - Jason Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA,Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A. Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
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11
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ArXiv 2021:arXiv:2104.14005v3. [PMID: 33948451 PMCID: PMC8095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 06/04/2021] [Indexed: 12/25/2022]
Abstract
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.
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Affiliation(s)
- Sergey Knyazev
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Ram Ayyala
- Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Zoia Comarova
- Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Yuri Porozov
- World-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Malak S Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, Australia
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
| | - Jason Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
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12
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Rajesh A, Chang Y, Abedalthagafi MS, Wong-Beringer A, Love MI, Mangul S. Improving the completeness of public metadata accompanying omics studies. Genome Biol 2021; 22:106. [PMID: 33858487 PMCID: PMC8048353 DOI: 10.1186/s13059-021-02332-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Anushka Rajesh
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089 USA
| | - Yutong Chang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089 USA
| | - Malak S. Abedalthagafi
- Genomics Research Department, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Annie Wong-Beringer
- Department of Clinical Pharmacy, University of Southern California, Los Angeles, CA 90089 USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516 USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514 USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, University of Southern California, Los Angeles, CA 90089 USA
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13
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Povysil G, Butler-Laporte G, Shang N, Weng C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh R, Bourgey M, Aziz N, Jones S, Knoppers B, Scherer S, Strug L, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albes N, Al-Afghani HM, Alghamdi B, Almutair M, Mahmoud ES, Safie LA, Bardisy HE, Al Harthi FS, Alshareef A, Suliman BA, Alqahtani S, AlMalik A, Alrashed MM, Massadeh S, Mooser V, Lathrop M, Arabi Y, Mbarek H, Saad C, Al-Muftah W, Badji R, Al Thani A, Ismail SI, Gharavi AG, Abedalthagafi MS, Richards JB, Goldstein DB, Kiryluk K. Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19. medRxiv 2020:2020.12.18.20248226. [PMID: 33398295 PMCID: PMC7781338 DOI: 10.1101/2020.12.18.20248226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,934 COVID-19 cases (713 with severe and 1,221 with mild disease) and 15,251 ancestry-matched population controls across four independent COVID-19 biobanks. We then tested if rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only one rare pLOF mutation across these genes amongst 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We find no evidence of association of rare loss-of-function variants in the proposed 13 candidate genes with severe COVID-19 outcomes.
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Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University
| | - Chen Weng
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- KACST-BWH Center of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- King Abdulaziz City for Science and Technology (KACST)-Saudi Human Genome Satellite Lab at Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Japan
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
| | | | - Robert Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montreal, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montreal, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Naveed Aziz
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | - Steven Jones
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | | | | | - Lisa Strug
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | - Pierre Lepage
- Canadian Centre for Computational Genomics, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Centre for Computational Genomics, McGill University, Montreal, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montreal, Canada
| | - Jahad Alghamdi
- Saudi Biobank, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- KACST-BWH Center of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- King Abdulaziz City for Science and Technology (KACST)-Saudi Human Genome Satellite Lab at Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Nour Albes
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- KACST-BWH Center of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Intensive Care Department, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Hani M. Al-Afghani
- Laboratory Department, Security Forces Hospital, General Directorate of Medical Services, Ministry of Interior, Clinical Laboratory Sciences, Taibah University, Madina, Saudi Arabia
| | - Bader Alghamdi
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mansour Almutair
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Ebrahim Sabri Mahmoud
- King Abdulaziz City for Science and Technology (KACST)-Saudi Human Genome Satellite Lab at Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Leen Abu Safie
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Abdulraheem Alshareef
- Laboratory Department, Security Forces Hospital, General Directorate of Medical Services, Ministry of Interior, Clinical Laboratory Sciences, Taibah University, Madina, Saudi Arabia
| | - Bandar Ali Suliman
- The Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saleh Alqahtani
- The Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- The Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, USA
| | - Abdulaziz AlMalik
- Life Science and Environmental Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - May M. Alrashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- KACST-BWH Center of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- King Abdulaziz City for Science and Technology (KACST)-Saudi Human Genome Satellite Lab at Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian COVID Genomics Network, HostSeq Project, Canada
- Canadian Centre for Computational Genomics, McGill University, Montreal, Canada
| | - Yaseen Arabi
- King Abdulaziz City for Science and Technology (KACST)-Saudi Human Genome Satellite Lab at Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Intensive Care Department, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Wadha Al-Muftah
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Radja Badji
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Asma Al Thani
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University
- Center for Precision Medicine and Genomics. Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Life Science and Environmental Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Canada
- Department of Twin Research, King’s College London, London, UK
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics & Development, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University
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14
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Abstract
Congenital and genetic disorders cause many diseases in Arab countries due to large family sizes and high levels of inbreeding. Saudi Arabia (SA) has the highest consanguinity rates among Middle Eastern countries (~60% of all marriages) and is burdened by the highest number of genetic diseases. Genetic diseases can be life-threatening, often manifesting early in life. Approximately 8% of births in SA are affected, and more common genetic diseases, such as metabolic disease and cancer, manifest later in life in up to 20% of the population. This represents a massive healthcare burden to SA hospitals. The number of genetic disorders in the human population ranges from 7000 to 8000, over 3000 of which are caused by unknown mutations. In 2013, SA initiated the Saudi Human Genome Program (SHGP), which aims to sequence over 100,000 human genomes, with the goal of identifying strategies to discover, prevent, diagnose and treat genetic disorders through precision therapy. High-technology genomics and informatic-based centers that exploit next-generation sequencing (NGS) have now identified mutations underlying many unexplained diseases.
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15
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Abedalthagafi MS, Wu MP, Merrill PH, Du Z, Woo T, Sheu SH, Hurwitz S, Ligon KL, Santagata S. Decreased FOXJ1 expression and its ciliogenesis programme in aggressive ependymoma and choroid plexus tumours. J Pathol 2016; 238:584-97. [PMID: 26690880 DOI: 10.1002/path.4682] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 07/13/2015] [Revised: 11/12/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022]
Abstract
Well-differentiated human cancers share transcriptional programmes with the normal tissue counterparts from which they arise. These programmes broadly influence cell behaviour and function and are integral modulators of malignancy. Here, we show that the master regulator of motile ciliogenesis, FOXJ1, is highly expressed in cells along the ventricular surface of the human brain. Strong expression is present in cells of the ependyma and the choroid plexus as well as in a subset of cells residing in the subventricular zone. Expression of FOXJ1 and its transcriptional programme is maintained in many well-differentiated human tumours that arise along the ventricle, including low-grade ependymal tumours and choroid plexus papillomas. Anaplastic ependymomas as well as choroid plexus carcinomas show decreased FOXJ1 expression and its associated ciliogenesis programme genes. In ependymomas and choroid plexus tumours, reduced expression of FOXJ1 and its ciliogenesis programme are markers of poor outcome and are therefore useful biomarkers for assessing these tumours. Transitions in ciliogenesis define distinct differentiation states in ependymal and choroid plexus tumours with important implications for patient care. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Malak S Abedalthagafi
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, King Fahad Medical City, Riyadh, Saudi Arabia.,King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael P Wu
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Parker H Merrill
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ziming Du
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Terri Woo
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shu-Hsien Sheu
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shelley Hurwitz
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sandro Santagata
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
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16
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Abedalthagafi MS, Merrill PH, Bi WL, Jones RT, Listewnik ML, Ramkissoon SH, Thorner AR, Dunn IF, Beroukhim R, Alexander BM, Brastianos PK, Francis JM, Folkerth RD, Ligon KL, Van Hummelen P, Ligon AH, Santagata S. Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5. Oncotarget 2015; 5:10596-606. [PMID: 25347344 PMCID: PMC4279396 DOI: 10.18632/oncotarget.2517] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 09/24/2014] [Indexed: 12/30/2022] Open
Abstract
Meningiomas are a diverse group of tumors with a broad spectrum of histologic features. There are over 12 variants of meningioma, whose genetic features are just beginning to be described. Angiomatous meningioma is a World Health Organization (WHO) meningioma variant with a predominance of blood vessels. They are uncommon and confirming the histopathologic classification can be challenging. Given a lack of biomarkers that define the angiomatous subtype and limited understanding of the genetic changes underlying its tumorigenesis, we compared the genomic characteristics of angiomatous meningioma to more common meningioma subtypes. While typical grade I meningiomas demonstrate monosomy of chromosome 22 or lack copy number aberrations, 13 of 14 cases of angiomatous meningioma demonstrated a distinct copy number profile--polysomies of at least one chromosome, but often of many, especially in chromosomes 5, 13, and 20. WHO grade II atypical meningiomas with angiomatous features have both polysomies and genetic aberrations characteristic of other atypical meningiomas. Sequencing of over 560 cancer-relevant genes in 16 cases of angiomatous meningioma showed that these tumors lack common mutations found in other variants of meningioma. Our study demonstrates that angiomatous meningiomas have distinct genomic features that may be clinically useful for their diagnosis.
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Affiliation(s)
- Malak S Abedalthagafi
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Parker H Merrill
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert T Jones
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc L Listewnik
- Clinical Cytogenetics Laboratory, Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shakti H Ramkissoon
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Aaron R Thorner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ian F Dunn
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian M Alexander
- Department of Radiation Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Priscilla K Brastianos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua M Francis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca D Folkerth
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Van Hummelen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Azra H Ligon
- Clinical Cytogenetics Laboratory, Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
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17
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Jones RT, Abedalthagafi MS, Brahmandam M, Greenfield EA, Hoang MP, Louis DN, Hornick JL, Santagata S. Cross-reactivity of the BRAF VE1 antibody with epitopes in axonemal dyneins leads to staining of cilia. Mod Pathol 2015; 28:596-606. [PMID: 25412847 DOI: 10.1038/modpathol.2014.150] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/12/2014] [Accepted: 09/13/2014] [Indexed: 11/09/2022]
Abstract
Antibodies that recognize neo-epitopes in tumor cells are valuable tools in the evaluation of tissue biopsy or resection specimens. The VE1 antibody that recognizes the V600E-mutant BRAF protein is one such example. We have recently shown that the vast majority of papillary craniopharyngiomas-tumors that arise in the sellar or suprasellar regions of the brain-harbor BRAF V600E mutations. The VE1 antibody can be effective in discriminating papillary craniopharyngioma from adamantinomatous craniopharyngioma, which harbors mutations in CTNNB1 and not BRAF. While further characterizing the use of the VE1 antibody in the differential diagnosis of suprasellar lesions, we found that the VE1 antibody stains the epithelial cells lining Rathke's cleft cysts with very strong staining of the cilia of these cells. We used targeted sequencing to show that Rathke's cleft cysts do not harbor the BRAF V600E mutation. Moreover, we found that the VE1 antibody reacts strongly with cilia in various structures-the bronchial airways, the fallopian tubes, the nasopharynx, and the epididymis-as well as with the flagella of sperm. In addition, VE1 reacts strongly with the cilia of the ependymal lining of the brain and with the cilia-containing microlumens of ependymoma tumors. There is significant sequence homology between the synthetic peptide (amino acid 596-606 of BRAF V600E: GLATEKSRWSG) that was used to generate the VE1 antibody and regions of multiple axonemal dynein heavy chain proteins (eg, DNAH2, DNAH7, and DNAH12). These proteins are major components of the axonemes of cilia and flagella where they drive the sliding of microtubules. In ELISA assays, we show that the VE1 antibody recognizes epitopes from these proteins. A familiarity with the cross-reactivity of the VE1 antibody with epitopes of proteins in cilia is of value when evaluating tissues stained with this important clinical antibody.
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Affiliation(s)
- Robert T Jones
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Malak S Abedalthagafi
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mohan Brahmandam
- Monoclonal Antibody Core, Dana-Farber Cancer Institute and Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Edward A Greenfield
- Monoclonal Antibody Core, Dana-Farber Cancer Institute and Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David N Louis
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- 1] Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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18
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Abedalthagafi MS, Bi WL, Merrill PH, Gibson WJ, Rose MF, Du Z, Francis JM, Du R, Dunn IF, Ligon AH, Beroukhim R, Santagata S. ARID1A and TERT promoter mutations in dedifferentiated meningioma. Cancer Genet 2015; 208:345-50. [PMID: 25963524 DOI: 10.1016/j.cancergen.2015.03.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [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: 02/05/2015] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 12/30/2022]
Abstract
Unlike patients with World Health Organization (WHO) grade I meningiomas, which are considered benign, patients with WHO grade III meningiomas have very high mortality rates. The principles underlying tumor progression in meningioma are largely unknown, yet a detailed understanding of these mechanisms will be required for effective management of patients with these high grade lethal tumors. We present a case of an intraventricular meningioma that at first presentation displayed remarkable morphologic heterogeneity-composed of distinct regions independently fulfilling histopathologic criteria for WHO grade I, II, and III designations. The lowest grade regions had classic meningothelial features, while the highest grade regions were markedly dedifferentiated. Whereas progression in meningiomas is generally observed during recurrence following radiation and systemic medical therapies, the current case offers us a snapshot of histologic progression and intratumoral heterogeneity in a native pretreatment context. Using whole exome sequencing and high resolution array-based comparative genomic hybridization, we observed marked genetic heterogeneity between the various areas. Notably, in the higher grade regions we found increased aneuploidy with progressive loss of heterozygosity, the emergence of mutations in the TERT promoter, and compromise of ARID1A. These findings provide new insights into intratumoral heterogeneity in the evolution of malignant phenotypes in anaplastic meningiomas and potential pathways of malignant progression.
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Affiliation(s)
- Malak S Abedalthagafi
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Parker H Merrill
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William J Gibson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew F Rose
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ziming Du
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua M Francis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Rose Du
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ian F Dunn
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Azra H Ligon
- Clinical Cytogenetics Laboratory, Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Sandro Santagata
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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