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Wang X, Liu M, Nogues IE, Chen T, Xiong X, Bonzel CL, Zhang H, Hong C, Xia Y, Dahal K, Costa L, Cui J, Gaziano JM, Kim SC, Ho YL, Cho K, Cai T, Liao KP. Heterogeneous associations between interleukin-6 receptor variants and phenotypes across ancestries and implications for therapy. Sci Rep 2024; 14:8021. [PMID: 38580710 PMCID: PMC10997791 DOI: 10.1038/s41598-024-54063-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/08/2024] [Indexed: 04/07/2024] Open
Abstract
The Phenome-Wide Association Study (PheWAS) is increasingly used to broadly screen for potential treatment effects, e.g., IL6R variant as a proxy for IL6R antagonists. This approach offers an opportunity to address the limited power in clinical trials to study differential treatment effects across patient subgroups. However, limited methods exist to efficiently test for differences across subgroups in the thousands of multiple comparisons generated as part of a PheWAS. In this study, we developed an approach that maximizes the power to test for heterogeneous genotype-phenotype associations and applied this approach to an IL6R PheWAS among individuals of African (AFR) and European (EUR) ancestries. We identified 29 traits with differences in IL6R variant-phenotype associations, including a lower risk of type 2 diabetes in AFR (OR 0.96) vs EUR (OR 1.0, p-value for heterogeneity = 8.5 × 10-3), and higher white blood cell count (p-value for heterogeneity = 8.5 × 10-131). These data suggest a more salutary effect of IL6R blockade for T2D among individuals of AFR vs EUR ancestry and provide data to inform ongoing clinical trials targeting IL6 for an expanding number of conditions. Moreover, the method to test for heterogeneity of associations can be applied broadly to other large-scale genotype-phenotype screens in diverse populations.
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Affiliation(s)
- Xuan Wang
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Molei Liu
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Tony Chen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Xin Xiong
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Clara-Lea Bonzel
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Harrison Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Chuan Hong
- Department of Biostatistics, Duke University, Durham, NC, USA
| | - Yin Xia
- Department of Statistics and Data Science, Fudan University, Shanghai, China
| | - Kumar Dahal
- Department of Biostatistics, Duke University, Durham, NC, USA
| | - Lauren Costa
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Jing Cui
- Department of Biostatistics, Duke University, Durham, NC, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Boston, MA, USA
| | - Seoyoung C Kim
- Division of Pharmacoepidemiology and Pharmacoeconomics, Brigham and Women's Hospital, Boston, MA, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Boston, MA, USA
| | - Tianxi Cai
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Katherine P Liao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA.
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA.
- Rheumatology Section, VA Boston Healthcare System, Boston, USA.
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2
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Hutch MR, Son J, Le TT, Hong C, Wang X, Shakeri Hossein Abad Z, Morris M, Gutiérrez-Sacristán A, Klann JG, Spiridou A, Batugo A, Bellazzi R, Benoit V, Bonzel CL, Bryant WA, Chiudinelli L, Cho K, Das P, González González T, Hanauer DA, Henderson DW, Ho YL, Loh NHW, Makoudjou A, Makwana S, Malovini A, Moal B, Mowery DL, Neuraz A, Samayamuthu MJ, Sanz Vidorreta FJ, Schriver ER, Schubert P, Talbert J, Tan ALM, Tan BWL, Tan BWQ, Tibollo V, Tippman P, Verdy G, Yuan W, Avillach P, Gehlenborg N, Omenn GS, Visweswaran S, Cai T, Luo Y, Xia Z. Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study. PLOS Digit Health 2024; 3:e0000484. [PMID: 38620037 PMCID: PMC11018281 DOI: 10.1371/journal.pdig.0000484] [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] [Received: 08/17/2023] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
Few studies examining the patient outcomes of concurrent neurological manifestations during acute COVID-19 leveraged multinational cohorts of adults and children or distinguished between central and peripheral nervous system (CNS vs. PNS) involvement. Using a federated multinational network in which local clinicians and informatics experts curated the electronic health records data, we evaluated the risk of prolonged hospitalization and mortality in hospitalized COVID-19 patients from 21 healthcare systems across 7 countries. For adults, we used a federated learning approach whereby we ran Cox proportional hazard models locally at each healthcare system and performed a meta-analysis on the aggregated results to estimate the overall risk of adverse outcomes across our geographically diverse populations. For children, we reported descriptive statistics separately due to their low frequency of neurological involvement and poor outcomes. Among the 106,229 hospitalized COVID-19 patients (104,031 patients ≥18 years; 2,198 patients <18 years, January 2020-October 2021), 15,101 (14%) had at least one CNS diagnosis, while 2,788 (3%) had at least one PNS diagnosis. After controlling for demographics and pre-existing conditions, adults with CNS involvement had longer hospital stay (11 versus 6 days) and greater risk of (Hazard Ratio = 1.78) and faster time to death (12 versus 24 days) than patients with no neurological condition (NNC) during acute COVID-19 hospitalization. Adults with PNS involvement also had longer hospital stay but lower risk of mortality than the NNC group. Although children had a low frequency of neurological involvement during COVID-19 hospitalization, a substantially higher proportion of children with CNS involvement died compared to those with NNC (6% vs 1%). Overall, patients with concurrent CNS manifestation during acute COVID-19 hospitalization faced greater risks for adverse clinical outcomes than patients without any neurological diagnosis. Our global informatics framework using a federated approach (versus a centralized data collection approach) has utility for clinical discovery beyond COVID-19.
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Affiliation(s)
- Meghan R. Hutch
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Jiyeon Son
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Trang T. Le
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Xuan Wang
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Zahra Shakeri Hossein Abad
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alba Gutiérrez-Sacristán
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jeffrey G. Klann
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Anastasia Spiridou
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, London, United Kingdom
| | - Ashley Batugo
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Vincent Benoit
- IT Department, Innovation & Data, APHP Greater Paris University Hospital, Paris, France
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - William A. Bryant
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, London, United Kingdom
| | - Lorenzo Chiudinelli
- UOC Ricerca, Innovazione e Brand reputation, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Kelly Cho
- Population Health and Data Science, VA Boston Healthcare System, Boston Massachusetts, United States of America
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston Massachusetts, United States of America
| | - Priyam Das
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - David A. Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Darren W. Henderson
- Center for Clinical and Translational Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston Massachusetts, United States of America
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health System, Kent Ridge, Singapore
| | - Adeline Makoudjou
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Simran Makwana
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Bertrand Moal
- IAM Unit, Bordeaux University Hospital, Bordeaux, France
| | - Danielle L. Mowery
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Antoine Neuraz
- Department of biomedical informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | | | - Fernando J. Sanz Vidorreta
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Emily R. Schriver
- Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, United States of America
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston Massachusetts, United States of America
| | - Jeffery Talbert
- Division of Biomedical Informatics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Amelia L. M. Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Byorn W. L. Tan
- Department of Medicine, National University Hospital, Singapore, Kent Ridge, Singapore
| | - Bryce W. Q. Tan
- Department of Medicine, National University Hospital, Singapore, Kent Ridge, Singapore
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Patric Tippman
- Institute of Medical Biometry and University of Freiburg, Medical Center, Freiburg, Germany
| | | | - William Yuan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Wu XF, Sun TT, Lin JL, Guo WL, Li XY, Hong C. [Pulmonary artery stenting in chronic thromboembolic pulmonary hypertension: a report of 2 cases]. Zhonghua Jie He He Hu Xi Za Zhi 2024; 47:228-232. [PMID: 38448172 DOI: 10.3760/cma.j.cn112147-20230921-00184] [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] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Chronic thromboembolic pulmonary hypertension (CTEPH) is a pulmonary vascular disease characterized by an insidious onset, progressive deterioration, and poor prognosis. It is distinguished by the thrombotic organization within the pulmonary arteries, leading to vascular stenosis or occlusion. This results in a progressive increase in pulmonary vascular resistance and pulmonary arterial pressure, ultimately leading to right heart failure. In recent years, balloon pulmonary angioplasty (BPA) has emerged as an effective treatment option for patients ineligible for pulmonary endarterectomy (PEA). However, the use of stents in patients with suboptimal balloon dilation remains controversial. This article describes two cases of chronic thromboembolic pulmonary hypertension (CTEPH) in which balloon angioplasty yielded unsatisfactory results, subsequently leading to stent placement. Following stent implantation, there was improved blood flow, significant reduction in pulmonary arterial pressure, and notable alleviation of patient symptoms. One-year follow-up showed no recurrence of stenosis within the stent, suggesting potential guidance for the use of pulmonary artery stenting as a treatment modality for CTEPH. This report provided new insights into the therapeutic approach for CTEPH.
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Affiliation(s)
- X F Wu
- Guangzhou Institute of Respiratory Health (National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine), The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - T T Sun
- Guangzhou Institute of Respiratory Health (National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine), The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - J L Lin
- Department of Radiology and Interventianl, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - W L Guo
- Guangzhou Institute of Respiratory Health (National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine), The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - X Y Li
- Guangzhou Institute of Respiratory Health (National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine), The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - C Hong
- Guangzhou Institute of Respiratory Health (National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, National Center for Respiratory Medicine), The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
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4
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Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy Z, Baharuddin B, Bakonyi J, Broders K, Cacciola S, Chang TT, Chi N, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu CH, Garcia L, Hieno A, Ho HH, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira L, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu P, Tomić Z, Tomšovský M, Uematsu S, Webber J, Zeng HC, Zheng FC, Brasier C, Horta Jung M. Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Stud Mycol 2024; 107:251-388. [PMID: 38600961 PMCID: PMC11003442 DOI: 10.3114/sim.2024.107.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 04/12/2024] Open
Abstract
During 25 surveys of global Phytophthora diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of Phytophthora major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels ca. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the Phytophthora clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single Phytophthora clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in Phytophthora. Taxonomic novelties: New species: Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenković, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M. Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora furcata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I. Milenković, Phytophthora indonesiensis T. Jung, M. Tarigan, L. Oliveira & I. Milenković, Phytophthora japonensis T. Jung, A. Hieno, H. Masuya & J.F. Webber, Phytophthora limosa T. Corcobado, T. Majek, M. Ferreira & T. Jung, Phytophthora macroglobulosa H.-C. Zeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenković & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora nimia T. Jung, H. Masuya, A. Hieno & C.M. Brasier, Phytophthora oblonga T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora obovoidea T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora obturata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora penetrans T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora platani T. Jung, A. Pérez-Sierra, S.O. Cacciola & M. Horta Jung, Phytophthora proliferata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora pseudocapensis T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pseudocitrophthora T. Jung, S.O. Cacciola, J. Bakonyi & M. Horta Jung, Phytophthora pseudofrigida T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora pseudoccultans T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pyriformis T. Jung, Y. Balci, K.D. Boders & M. Horta Jung, Phytophthora sumatera T. Jung, M. Tarigan, M. Junaid & A. Durán, Phytophthora transposita T. Jung, K. Kageyama, C.M. Brasier & H. Masuya, Phytophthora vacuola T. Jung, H. Masuya, K. Kageyama & J.F. Webber, Phytophthora valdiviana T. Jung, E. Sanfuentes von Stowasser, A. Durán & M. Horta Jung, Phytophthora variepedicellata T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora vietnamensis T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora ×australasiatica T. Jung, N.M. Chi, M. Tarigan & M. Horta Jung, Phytophthora ×lusitanica T. Jung, M. Horta Jung, C. Maia & I. Milenković, Phytophthora ×taiwanensis T. Jung, T.-T. Chang, H.-S. Fu & M. Horta Jung. Citation: Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy ZÁ, Baharuddin B, Bakonyi J, Broders KD, Cacciola SO, Chang T-T, Chi NM, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu C-H, Garcia L, Hieno A, Ho H-H, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira LSS, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu PQ, Tomić Z, Tomšovský M, Uematsu S, Webber JF, Zeng H-C, Zheng F-C, Brasier CM, Horta Jung M (2024). Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Studies in Mycology 107: 251-388. doi: 10.3114/sim.2024.107.04.
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Affiliation(s)
- T. Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
| | - I. Milenković
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Belgrade, Faculty of Forestry, 11030 Belgrade, Serbia
| | - Y. Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, Maryland, 20737 USA
| | - J. Janoušek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - T. Kudláček
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Greifswald, Institute for Mathematics and Computer Science & Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Z.Á. Nagy
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - B. Baharuddin
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - J. Bakonyi
- HUN-REN Centre for Agricultural Research, Plant Protection Institute, ELKH, 1022 Budapest, Hungary
| | - K.D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, República de Panamá
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA
| | - S.O. Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - T.-T. Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - N.M. Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - T. Corcobado
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Cravador
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, University of Algarve, 8005-130 Faro, Portugal
| | - B. Đorđević
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Durán
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - M. Ferreira
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - C.-H. Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - L. Garcia
- Universidad Nacional Agraria, Carretera Norte, Managua 11065, Nicaragua
| | - A. Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - H.-H. Ho
- Department of Biology, State University of New York, New Paltz, New York 12561, USA
| | - C. Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| | - M. Junaid
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - K. Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - T. Kuswinanti
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - C. Maia
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
| | - T. Májek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - H. Masuya
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687, Japan
| | - G. Magnano di San Lio
- University Mediterranea of Reggio Calabria, Department of Agriculture, 89124 Reggio Calabria, Italy
| | | | - N. Nasri
- The United Graduate School of Agricultural Science, Ehime University, Matsuyama, 790-8566, Japan
| | - L.S.S. Oliveira
- Research and Development, Bracell, Alagoinhas, Bahia 48030-300, Brazil
| | - A. Pane
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - A. Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - A. Rosmana
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - E. Sanfuentes von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de Biotecnología, Universidad de Concepción, 4030000 Concepción, Chile
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39A, 07100 Sassari, Italy
| | - R. Singh
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Z. Stanivuković
- University of Banja Luka, Faculty of Forestry, 78000 Banja Luka, Bosnia and Herzegovina
| | - M. Tarigan
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - P.Q. Thu
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - Z. Tomić
- Center for Plant Protection, Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia
| | - M. Tomšovský
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - S. Uematsu
- Laboratory of Molecular and Cellular Biology, Dept. of Bioregulation and Bio-interaction, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - J.F. Webber
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - H.-C. Zeng
- The Institute of Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - F.-C. Zheng
- College of Environment and Plant Protection, Hainan University, Baodoa Xincun, Danzhou City, Hainan 571737, China
| | - C.M. Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - M. Horta Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
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Hao S, Dempsey K, Matos J, Cox CE, Rotemberg V, Gichoya JW, Kibbe W, Hong C, Wong I. Utility of skin tone on pulse oximetry in critically ill patients: a prospective cohort study. medRxiv 2024:2024.02.24.24303291. [PMID: 38464170 PMCID: PMC10925348 DOI: 10.1101/2024.02.24.24303291] [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: 03/12/2024]
Abstract
Importance Pulse oximetry, a ubiquitous vital sign in modern medicine, has inequitable accuracy that disproportionately affects Black and Hispanic patients, with associated increases in mortality, organ dysfunction, and oxygen therapy. Although the root cause of these clinical performance discrepancies is believed to be skin tone, previous retrospective studies used self-reported race or ethnicity as a surrogate for skin tone. Objective To determine the utility of objectively measured skin tone in explaining pulse oximetry discrepancies. Design Setting and Participants Admitted hospital patients at Duke University Hospital were eligible for this prospective cohort study if they had pulse oximetry recorded up to 5 minutes prior to arterial blood gas (ABG) measurements. Skin tone was measured across sixteen body locations using administered visual scales (Fitzpatrick Skin Type, Monk Skin Tone, and Von Luschan), reflectance colorimetry (Delfin SkinColorCatch [L*, individual typology angle {ITA}, Melanin Index {MI}]), and reflectance spectrophotometry (Konica Minolta CM-700D [L*], Variable Spectro 1 [L*]). Main Outcomes and Measures Mean directional bias, variability of bias, and accuracy root mean square (ARMS), comparing pulse oximetry and ABG measurements. Linear mixed-effects models were fitted to estimate mean directional bias while accounting for clinical confounders. Results 128 patients (57 Black, 56 White) with 521 ABG-pulse oximetry pairs were recruited, none with hidden hypoxemia. Skin tone data was prospectively collected using 6 measurement methods, generating 8 measurements. The collected skin tone measurements were shown to yield differences among each other and overlap with self-reported racial groups, suggesting that skin tone could potentially provide information beyond self-reported race. Among the eight skin tone measurements in this study, and compared to self-reported race, the Monk Scale had the best relationship with differences in pulse oximetry bias (point estimate: -2.40%; 95% CI: -4.32%, -0.48%; p=0.01) when comparing patients with lighter and dark skin tones. Conclusions and relevance We found clinical performance differences in pulse oximetry, especially in darker skin tones. Additional studies are needed to determine the relative contributions of skin tone measures and other potential factors on pulse oximetry discrepancies.
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Affiliation(s)
- Sicheng Hao
- Duke University, Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Durham, NC, USA
| | - Katelyn Dempsey
- Duke University, Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Durham, NC, USA
| | - João Matos
- Duke University, Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Durham, NC, USA
| | - Christopher E. Cox
- Duke University, Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Durham, NC, USA
| | | | - Judy W. Gichoya
- Emory University School of Medicine, Department of Radiology, Atlanta, USA
| | - Warren Kibbe
- Duke University, Department of Biostatistics and Bioinformatics, Division of Translational Biomedical Informatics, Durham, NC, USA
| | - Chuan Hong
- Duke University, Department of Biostatistics and Bioinformatics, Division of Translational Biomedical Informatics, Durham, NC, USA
| | - Ian Wong
- Duke University, Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Durham, NC, USA
- Duke University, Department of Biostatistics and Bioinformatics, Division of Translational Biomedical Informatics, Durham, NC, USA
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Gao J, Bonzel CL, Hong C, Varghese P, Zakir K, Gronsbell J. Semi-supervised ROC analysis for reliable and streamlined evaluation of phenotyping algorithms. J Am Med Inform Assoc 2024; 31:640-650. [PMID: 38128118 PMCID: PMC10873838 DOI: 10.1093/jamia/ocad226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/22/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVE High-throughput phenotyping will accelerate the use of electronic health records (EHRs) for translational research. A critical roadblock is the extensive medical supervision required for phenotyping algorithm (PA) estimation and evaluation. To address this challenge, numerous weakly-supervised learning methods have been proposed. However, there is a paucity of methods for reliably evaluating the predictive performance of PAs when a very small proportion of the data is labeled. To fill this gap, we introduce a semi-supervised approach (ssROC) for estimation of the receiver operating characteristic (ROC) parameters of PAs (eg, sensitivity, specificity). MATERIALS AND METHODS ssROC uses a small labeled dataset to nonparametrically impute missing labels. The imputations are then used for ROC parameter estimation to yield more precise estimates of PA performance relative to classical supervised ROC analysis (supROC) using only labeled data. We evaluated ssROC with synthetic, semi-synthetic, and EHR data from Mass General Brigham (MGB). RESULTS ssROC produced ROC parameter estimates with minimal bias and significantly lower variance than supROC in the simulated and semi-synthetic data. For the 5 PAs from MGB, the estimates from ssROC are 30% to 60% less variable than supROC on average. DISCUSSION ssROC enables precise evaluation of PA performance without demanding large volumes of labeled data. ssROC is also easily implementable in open-source R software. CONCLUSION When used in conjunction with weakly-supervised PAs, ssROC facilitates the reliable and streamlined phenotyping necessary for EHR-based research.
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Affiliation(s)
- Jianhui Gao
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, United States
| | - Paul Varghese
- Health Informatics, Verily Life Sciences, Cambridge, MA, United States
| | - Karim Zakir
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Jessica Gronsbell
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
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Wen J, Hou J, Bonzel CL, Zhao Y, Castro VM, Gainer VS, Weisenfeld D, Cai T, Ho YL, Panickan VA, Costa L, Hong C, Gaziano JM, Liao KP, Lu J, Cho K, Cai T. LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. Patterns (N Y) 2024; 5:100906. [PMID: 38264714 PMCID: PMC10801250 DOI: 10.1016/j.patter.2023.100906] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/06/2023] [Accepted: 12/01/2023] [Indexed: 01/25/2024]
Abstract
Electronic health record (EHR) data are increasingly used to support real-world evidence studies but are limited by the lack of precise timings of clinical events. Here, we propose a label-efficient incident phenotyping (LATTE) algorithm to accurately annotate the timing of clinical events from longitudinal EHR data. By leveraging the pre-trained semantic embeddings, LATTE selects predictive features and compresses their information into longitudinal visit embeddings through visit attention learning. LATTE models the sequential dependency between the target event and visit embeddings to derive the timings. To improve label efficiency, LATTE constructs longitudinal silver-standard labels from unlabeled patients to perform semi-supervised training. LATTE is evaluated on the onset of type 2 diabetes, heart failure, and relapses of multiple sclerosis. LATTE consistently achieves substantial improvements over benchmark methods while providing high prediction interpretability. The event timings are shown to help discover risk factors of heart failure among patients with rheumatoid arthritis.
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Affiliation(s)
- Jun Wen
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Jue Hou
- University of Minnesota, Minneapolis, MN, USA
| | - Clara-Lea Bonzel
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | | | | | | | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA, USA
- Mass General Brigham, Boston, MA, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Vidul A. Panickan
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | | | - J. Michael Gaziano
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Katherine P. Liao
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Junwei Lu
- VA Boston Healthcare System, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kelly Cho
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Tianxi Cai
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Hong C, Liu M, Wojdyla DM, Hickey J, Pencina M, Henao R. Trans-Balance: Reducing demographic disparity for prediction models in the presence of class imbalance. J Biomed Inform 2024; 149:104532. [PMID: 38070817 PMCID: PMC10850917 DOI: 10.1016/j.jbi.2023.104532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/21/2023] [Accepted: 10/28/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Risk prediction, including early disease detection, prevention, and intervention, is essential to precision medicine. However, systematic bias in risk estimation caused by heterogeneity across different demographic groups can lead to inappropriate or misinformed treatment decisions. In addition, low incidence (class-imbalance) outcomes negatively impact the classification performance of many standard learning algorithms which further exacerbates the racial disparity issues. Therefore, it is crucial to improve the performance of statistical and machine learning models in underrepresented populations in the presence of heavy class imbalance. METHOD To address demographic disparity in the presence of class imbalance, we develop a novel framework, Trans-Balance, by leveraging recent advances in imbalance learning, transfer learning, and federated learning. We consider a practical setting where data from multiple sites are stored locally under privacy constraints. RESULTS We show that the proposed Trans-Balance framework improves upon existing approaches by explicitly accounting for heterogeneity across demographic subgroups and cohorts. We demonstrate the feasibility and validity of our methods through numerical experiments and a real application to a multi-cohort study with data from participants of four large, NIH-funded cohorts for stroke risk prediction. CONCLUSION Our findings indicate that the Trans-Balance approach significantly improves predictive performance, especially in scenarios marked by severe class imbalance and demographic disparity. Given its versatility and effectiveness, Trans-Balance offers a valuable contribution to enhancing risk prediction in biomedical research and related fields.
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Affiliation(s)
- Chuan Hong
- Duke University, Department of Biostatistics and Bioinformatics, Durham, NC, USA; Duke Clinical Research Institute, Durham, NC, USA.
| | - Molei Liu
- Columbia University, Department of Biostatistics, New York, NY, USA
| | | | - Jimmy Hickey
- North Carolina State University, Department of Statistics, Raleigh, NC, USA
| | - Michael Pencina
- Duke University, Department of Biostatistics and Bioinformatics, Durham, NC, USA; Duke Clinical Research Institute, Durham, NC, USA
| | - Ricardo Henao
- Duke University, Department of Biostatistics and Bioinformatics, Durham, NC, USA; Duke Clinical Research Institute, Durham, NC, USA
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Li S, Liu P, Nascimento GG, Wang X, Leite FRM, Chakraborty B, Hong C, Ning Y, Xie F, Teo ZL, Ting DSW, Haddadi H, Ong MEH, Peres MA, Liu N. Federated and distributed learning applications for electronic health records and structured medical data: a scoping review. J Am Med Inform Assoc 2023; 30:2041-2049. [PMID: 37639629 PMCID: PMC10654866 DOI: 10.1093/jamia/ocad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/19/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVES Federated learning (FL) has gained popularity in clinical research in recent years to facilitate privacy-preserving collaboration. Structured data, one of the most prevalent forms of clinical data, has experienced significant growth in volume concurrently, notably with the widespread adoption of electronic health records in clinical practice. This review examines FL applications on structured medical data, identifies contemporary limitations, and discusses potential innovations. MATERIALS AND METHODS We searched 5 databases, SCOPUS, MEDLINE, Web of Science, Embase, and CINAHL, to identify articles that applied FL to structured medical data and reported results following the PRISMA guidelines. Each selected publication was evaluated from 3 primary perspectives, including data quality, modeling strategies, and FL frameworks. RESULTS Out of the 1193 papers screened, 34 met the inclusion criteria, with each article consisting of one or more studies that used FL to handle structured clinical/medical data. Of these, 24 utilized data acquired from electronic health records, with clinical predictions and association studies being the most common clinical research tasks that FL was applied to. Only one article exclusively explored the vertical FL setting, while the remaining 33 explored the horizontal FL setting, with only 14 discussing comparisons between single-site (local) and FL (global) analysis. CONCLUSIONS The existing FL applications on structured medical data lack sufficient evaluations of clinically meaningful benefits, particularly when compared to single-site analyses. Therefore, it is crucial for future FL applications to prioritize clinical motivations and develop designs and methodologies that can effectively support and aid clinical practice and research.
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Affiliation(s)
- Siqi Li
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Pinyan Liu
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gustavo G Nascimento
- National Dental Research Institute Singapore, National Dental Centre Singapore, Singapore 168938, Singapore
- Oral Health Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Xinru Wang
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Fabio Renato Manzolli Leite
- National Dental Research Institute Singapore, National Dental Centre Singapore, Singapore 168938, Singapore
- Oral Health Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Bibhas Chakraborty
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore 117546, Singapore
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, United States
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, United States
| | - Yilin Ning
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Feng Xie
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Zhen Ling Teo
- Singapore National Eye Centre, Singapore, Singapore Eye Research Institute, Singapore 168751, Singapore
| | - Daniel Shu Wei Ting
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
- Singapore National Eye Centre, Singapore, Singapore Eye Research Institute, Singapore 168751, Singapore
| | - Hamed Haddadi
- Department of Computing, Imperial College London, London SW7 2AZ, England, United Kingdom
| | - Marcus Eng Hock Ong
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Emergency Medicine, Singapore General Hospital, Singapore 169608, Singapore
| | - Marco Aurélio Peres
- National Dental Research Institute Singapore, National Dental Centre Singapore, Singapore 168938, Singapore
- Oral Health Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Nan Liu
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore
- Institute of Data Science, National University of Singapore, Singapore 117602, Singapore
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Zhang R, Weschler LB, Ye J, Wang Z, Deng Q, Li B, HuaQian, Zhao Z, Zhang Y, Huang S, Hong C. Associations between home environmental factors and childhood eczema and related symptoms in different cities in China. Heliyon 2023; 9:e21718. [PMID: 38027650 PMCID: PMC10661510 DOI: 10.1016/j.heliyon.2023.e21718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Previous studies have shown significant associations between home environmental factors and childhood eczema. However, few studies have compared how associations differ in different regions. This study investigated associations between home environmental factors and childhood eczema ever, and related symptoms including itchy rash (IR) and being awakened by itchy rash at night (awake by IR) in 4 cities located in different regions of China, based on cross-sectional investigations during 2010-2012. We used two-step analysis to explore the associations between influencing factors and eczema/related symptoms: first, group Least Absolute Shrinkage and Selection Operator (LASSO) was conducted to identify important factors among a list of candidates; then, the associations in total study population and in each city were estimated using logistic regression. We found these home environmental factors to be risk factors for eczema or related symptoms: large residence size, shared room, air cleaner at home, abnormal smell, perceived dry air, visible mold or damp stains, cooking with coal or wood, painted wall, incense, mice, new furniture during pregnancy, abnormal smell at birth, window condensation at birth and environmental tobacco smoke at birth. Environmental protective factors were rural house location and window ventilation. Associations of factors with eczema/related symptoms differed across cities. For example, air conditioning was protective for eczema in Beijing and awakening by IR in Shanghai with ORs of 0.70 (95%CI: 0.52, 0.95) and 0.33 (95%CI: 0.14, 0.81) respectively, but not significant in other cities. Our results have implications for improving home environments to reduce the risk of childhood eczema/related symptoms in different regions of China.
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Affiliation(s)
- Ruosu Zhang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | | | - Jin Ye
- School of Energy and Power, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Zhaokun Wang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Qihong Deng
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Baizhan Li
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Chongqing University, Chongqing 400030, China
| | - HuaQian
- School of Energy & Environment, Southeast University, Nanjing 210096, China
| | - Zhuohui Zhao
- School of Public Health, Fudan University, Shanghai 200032, China
| | - Yinping Zhang
- Department of Building Science, Tsinghua University, Beijing 100084, China
| | - Shaodan Huang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, China
| | - Chuan Hong
- Department of Biostatistics & Bioinformatics, School of Medicine, Duke University, North Carolina, USA
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Mallya P, Stevens LM, Zhao J, Hong C, Henao R, Economou-Zavlanos N, Wojdyla DM, Schibler T, Manchanda V, Pencina MJ, Hall JL. Facilitating Harmonization of Variables in Framingham, MESA, ARIC, and REGARDS Studies Through a Metadata Repository. Circ Cardiovasc Qual Outcomes 2023; 16:e009938. [PMID: 37850400 PMCID: PMC10841164 DOI: 10.1161/circoutcomes.123.009938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
BACKGROUND High-quality research in cardiovascular prevention, as in other fields, requires inclusion of a broad range of data sets from different sources. Integrating and harmonizing different data sources are essential to increase generalizability, sample size, and representation of understudied populations-strengthening the evidence for the scientific questions being addressed. METHODS Here, we describe an effort to build an open-access repository and interactive online portal for researchers to access the metadata and code harmonizing data from 4 well-known cohort studies-the REGARDS (Reasons for Geographic and Racial Differences in Stroke) study, FHS (Framingham Heart Study), MESA (Multi-Ethnic Study of Atherosclerosis), and ARIC (Atherosclerosis Risk in Communities) study. We introduce a methodology and a framework used for preprocessing and harmonizing variables from multiple studies. RESULTS We provide a real-case study and step-by-step guidance to demonstrate the practical utility of our repository and interactive web page. In addition to our successful development of such an open-access repository and interactive web page, this exercise in harmonizing data from multiple cohort studies has revealed several key themes. These themes include the importance of careful preprocessing and harmonization of variables, the value of creating an open-access repository to facilitate collaboration and reproducibility, and the potential for using harmonized data to address important scientific questions and disparities in cardiovascular disease research. CONCLUSIONS By integrating and harmonizing these large-scale cohort studies, such a repository may improve the statistical power and representation of understudied cohorts, enabling development and validation of risk prediction models, identification and investigation of risk factors, and creating a platform for racial disparities research. REGISTRATION URL: https://precision.heart.org/duke-ninds.
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Affiliation(s)
- Pratheek Mallya
- American Heart Association, Dallas, TX (P.M., J.Z., V.M., J.L.H.)
| | - Laura M Stevens
- University of Colorado Anschutz Medical School, Aurora (L.M.S.)
| | - Juan Zhao
- American Heart Association, Dallas, TX (P.M., J.Z., V.M., J.L.H.)
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC (C.H., R.H., M.P.)
- Duke Clinical Research Institute, Durham, NC (C.H., R.H., D.W., T.S.)
| | - Ricardo Henao
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC (C.H., R.H., M.P.)
- Duke Clinical Research Institute, Durham, NC (C.H., R.H., D.W., T.S.)
| | | | - Daniel M Wojdyla
- Duke Clinical Research Institute, Durham, NC (C.H., R.H., D.W., T.S.)
| | - Tony Schibler
- Duke Clinical Research Institute, Durham, NC (C.H., R.H., D.W., T.S.)
| | - Vihaan Manchanda
- American Heart Association, Dallas, TX (P.M., J.Z., V.M., J.L.H.)
| | - Michael J Pencina
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC (C.H., R.H., M.P.)
| | - Jennifer L Hall
- American Heart Association, Dallas, TX (P.M., J.Z., V.M., J.L.H.)
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Guo WL, Hou P, Tan WG, Lei YX, Wu XF, Huang HQ, Hong C. [A case of metastatic breast cancer complicated by pulmonary tumor thrombotic microangiopathy]. Zhonghua Jie He He Hu Xi Za Zhi 2023; 46:1014-1018. [PMID: 37752045 DOI: 10.3760/cma.j.cn112147-20230521-00253] [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] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Pulmonary tumor thrombotic microangiopathy is a malignancy-related complication with rapid progression and high mortality. To improve the understanding of the disease, early diagnosis and treatment are key to successful treatment. A 39-year-old patient with pulmonary hypertension transferred from another hospital was admitted to the First Affiliated Hospital of Guangzhou Medical University on September 26, 2021. The patient developed shortness of breath and progressive exacerbation over the past month. No pulmonary artery embolism was seen on computed tomography pulmonary angiography (CTPA) at the outside hospital where the breast cancer was diagnosed. Pulmonary tumor thrombotic microangiopathy was immediately considered on admission and oncological endocrine therapy was started. After treatment, the patient's dyspnoea improved, PET-CT showed significant tumor regression, and cardiac ultrasound showed a significant decrease in pulmonary artery pressure. The successful treatment experience of this case was summarized for reference.
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Affiliation(s)
- W L Guo
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
| | - P Hou
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Nuclear Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
| | - W G Tan
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
| | - Y X Lei
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
| | - X F Wu
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
| | - H Q Huang
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
| | - C Hong
- State Key Laboratory of Respiratory Diseases/National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510163, China
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Xiong X, Sweet SM, Liu M, Hong C, Bonzel CL, Panickan VA, Zhou D, Wang L, Costa L, Ho YL, Geva A, Mandl KD, Cheng S, Xia Z, Cho K, Gaziano JM, Liao KP, Cai T, Cai T. Knowledge-Driven Online Multimodal Automated Phenotyping System. medRxiv 2023:2023.09.29.23296239. [PMID: 37873131 PMCID: PMC10593060 DOI: 10.1101/2023.09.29.23296239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Though electronic health record (EHR) systems are a rich repository of clinical information with large potential, the use of EHR-based phenotyping algorithms is often hindered by inaccurate diagnostic records, the presence of many irrelevant features, and the requirement for a human-labeled training set. In this paper, we describe a knowledge-driven online multimodal automated phenotyping (KOMAP) system that i) generates a list of informative features by an online narrative and codified feature search engine (ONCE) and ii) enables the training of a multimodal phenotyping algorithm based on summary data. Powered by composite knowledge from multiple EHR sources, online article corpora, and a large language model, features selected by ONCE show high concordance with the state-of-the-art AI models (GPT4 and ChatGPT) and encourage large-scale phenotyping by providing a smaller but highly relevant feature set. Validation of the KOMAP system across four healthcare centers suggests that it can generate efficient phenotyping algorithms with robust performance. Compared to other methods requiring patient-level inputs and gold-standard labels, the fully online KOMAP provides a significant opportunity to enable multi-center collaboration.
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14
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Li S, Ning Y, Ong MEH, Chakraborty B, Hong C, Xie F, Yuan H, Liu M, Buckland DM, Chen Y, Liu N. FedScore: A privacy-preserving framework for federated scoring system development. J Biomed Inform 2023; 146:104485. [PMID: 37660960 DOI: 10.1016/j.jbi.2023.104485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/08/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
OBJECTIVE We propose FedScore, a privacy-preserving federated learning framework for scoring system generation across multiple sites to facilitate cross-institutional collaborations. MATERIALS AND METHODS The FedScore framework includes five modules: federated variable ranking, federated variable transformation, federated score derivation, federated model selection and federated model evaluation. To illustrate usage and assess FedScore's performance, we built a hypothetical global scoring system for mortality prediction within 30 days after a visit to an emergency department using 10 simulated sites divided from a tertiary hospital in Singapore. We employed a pre-existing score generator to construct 10 local scoring systems independently at each site and we also developed a scoring system using centralized data for comparison. RESULTS We compared the acquired FedScore model's performance with that of other scoring models using the receiver operating characteristic (ROC) analysis. The FedScore model achieved an average area under the curve (AUC) value of 0.763 across all sites, with a standard deviation (SD) of 0.020. We also calculated the average AUC values and SDs for each local model, and the FedScore model showed promising accuracy and stability with a high average AUC value which was closest to the one of the pooled model and SD which was lower than that of most local models. CONCLUSION This study demonstrates that FedScore is a privacy-preserving scoring system generator with potentially good generalizability.
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Affiliation(s)
- Siqi Li
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
| | - Yilin Ning
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
| | - Marcus Eng Hock Ong
- Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore; Health Services Research Centre, Singapore Health Services, Singapore, Singapore; Department of Emergency Medicine, Singapore General Hospital, Singapore, Singapore
| | - Bibhas Chakraborty
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore; Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Feng Xie
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore; Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Han Yuan
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
| | - Mingxuan Liu
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
| | - Daniel M Buckland
- Department of Emergency Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan Liu
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore; Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore; Institute of Data Science, National University of Singapore, Singapore, Singapore.
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15
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Hong C, Liang L, Yuan Q, Cho K, Liao KP, Pencina MJ, Christiani DC, Cai T. Semi-supervised calibration of noisy event risk (SCANER) with electronic health records. J Biomed Inform 2023; 144:104425. [PMID: 37331495 PMCID: PMC10478159 DOI: 10.1016/j.jbi.2023.104425] [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: 10/16/2022] [Revised: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 06/20/2023]
Abstract
OBJECTIVE Electronic health records (EHR), containing detailed longitudinal clinical information on a large number of patients and covering broad patient populations, open opportunities for comprehensive predictive modeling of disease progression and treatment response. However, since EHRs were originally constructed for administrative purposes not for research, in the EHR-linked studies, it is often not feasible to capture reliable information for analytical variables, especially in the survival setting, when both accurate event status and event times are needed for model building. For example, progression-free survival (PFS), a commonly used survival outcome for cancer patients, often involves complex information embedded in free-text clinical notes and cannot be extracted reliably. Proxies of PFS time such as time to the first mention of progression in the notes are at best good approximations to the true event time. This leads to difficulty in efficiently estimating event rates for an EHR patient cohort. Estimating survival rates based on error-prone outcome definitions can lead to biased results and hamper the power in the downstream analysis. On the other hand, extracting accurate event time information via manual annotation is time and resource intensive. The objective of this study is to develop a calibrated survival rate estimator using noisy outcomes from EHR data. MATERIALS AND METHODS In this paper, we propose a two-stage semi-supervised calibration of noisy event rate (SCANER) estimator that can effectively overcome censoring induced dependency and attains more robust performance (i.e., not sensitive to misspecification of the imputation model) by fully utilizing both a small-labeled set of gold-standard survival outcomes annotated via manual chart review and a set of proxy features automatically captured via EHR in the unlabeled set. We validate the SCANER estimator by estimating the PFS rates for a virtual cohort of lung cancer patients from one large tertiary care center and the ICU-free survival rates for COVID patients from two large tertiary care centers. RESULTS In terms of survival rate estimates, the SCANER had very similar point estimates compared to the complete-case Kaplan Meier estimator. On the other hand, other benchmark methods for comparison, which fail to account for the induced dependency between event time and the censoring time conditioning on surrogate outcomes, produced biased results across all three case studies. In terms of standard errors, the SCANER estimator was more efficient than the KM estimator, with up to 50% efficiency gain. CONCLUSION The SCANER estimator achieves more efficient, robust, and accurate survival rate estimates compared to existing approaches. This promising new approach can also improve the resolution (i.e., granularity of event time) by using labels conditioning on multiple surrogates, particularly among less common or poorly coded conditions.
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Affiliation(s)
- Chuan Hong
- Duke University, Durham, NC, USA; Harvard Medical School, Boston, MA, USA
| | - Liang Liang
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qianyu Yuan
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kelly Cho
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine P Liao
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | | | - David C Christiani
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; Massachusetts General Hospital, Boston, MA, USA
| | - Tianxi Cai
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; Massachusetts General Hospital, Boston, MA, USA.
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16
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Zhang HG, McDermott G, Seyok T, Huang S, Dahal K, L'Yi S, Lea-Bonzel C, Stratton J, Weisenfeld D, Monach P, Raychaudhuri S, Yu KH, Cai T, Cui J, Hong C, Cai T, Liao KP. Identifying shared genetic architecture between rheumatoid arthritis and other conditions: a phenome-wide association study with genetic risk scores. EBioMedicine 2023; 92:104581. [PMID: 37121095 PMCID: PMC10173154 DOI: 10.1016/j.ebiom.2023.104581] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 03/19/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) shares genetic variants with other autoimmune conditions, but existing studies test the association between RA variants with a pre-defined set of phenotypes. The objective of this study was to perform a large-scale, systemic screen to determine phenotypes that share genetic architecture with RA to inform our understanding of shared pathways. METHODS In the UK Biobank (UKB), we constructed RA genetic risk scores (GRS) incorporating human leukocyte antigen (HLA) and non-HLA risk alleles. Phenotypes were defined using groupings of International Classification of Diseases (ICD) codes. Patients with an RA code were excluded to mitigate the possibility of associations being driven by the diagnosis or management of RA. We performed a phenome-wide association study, testing the association between the RA GRS with phenotypes using multivariate generalized estimating equations that adjusted for age, sex, and first five principal components. Statistical significance was defined using Bonferroni correction. Results were replicated in an independent cohort and replicated phenotypes were validated using medical record review of patients. FINDINGS We studied n = 316,166 subjects from UKB without evidence of RA and screened for association between the RA GRS and n = 1317 phenotypes. In the UKB, 20 phenotypes were significantly associated with the RA GRS, of which 13 (65%) were immune mediated conditions including polymyalgia rheumatica, granulomatosis with polyangiitis (GPA), type 1 diabetes, and multiple sclerosis. We further identified a novel association in Celiac disease where the HLA and non-HLA alleles had strong associations in opposite directions. Strikingly, we observed that the non-HLA GRS was exclusively associated with greater risk of the validated conditions, suggesting shared underlying pathways outside the HLA region. INTERPRETATION This study replicated and identified novel autoimmune phenotypes verified by medical record review that share immune pathways with RA and may inform opportunities for shared treatment targets, as well as risk assessment for conditions with a paucity of genomic data, such as GPA. FUNDING This research was funded by the US National Institutes of Health (P30AR072577, R21AR078339, R35GM142879, T32AR007530) and the Harold and DuVal Bowen Fund.
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Affiliation(s)
- Harrison G Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Greg McDermott
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Thany Seyok
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sicong Huang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kumar Dahal
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clara Lea-Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jacklyn Stratton
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dana Weisenfeld
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul Monach
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Data Science, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kun-Hsing Yu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tianrun Cai
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA.
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17
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Hou J, Zhao R, Gronsbell J, Lin Y, Bonzel CL, Zeng Q, Zhang S, Beaulieu-Jones BK, Weber GM, Jemielita T, Wan SS, Hong C, Cai T, Wen J, Ayakulangara Panickan V, Liaw KL, Liao K, Cai T. Generate Analysis-Ready Data for Real-world Evidence: Tutorial for Harnessing Electronic Health Records With Advanced Informatic Technologies. J Med Internet Res 2023; 25:e45662. [PMID: 37227772 DOI: 10.2196/45662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 05/26/2023] Open
Abstract
Although randomized controlled trials (RCTs) are the gold standard for establishing the efficacy and safety of a medical treatment, real-world evidence (RWE) generated from real-world data has been vital in postapproval monitoring and is being promoted for the regulatory process of experimental therapies. An emerging source of real-world data is electronic health records (EHRs), which contain detailed information on patient care in both structured (eg, diagnosis codes) and unstructured (eg, clinical notes and images) forms. Despite the granularity of the data available in EHRs, the critical variables required to reliably assess the relationship between a treatment and clinical outcome are challenging to extract. To address this fundamental challenge and accelerate the reliable use of EHRs for RWE, we introduce an integrated data curation and modeling pipeline consisting of 4 modules that leverage recent advances in natural language processing, computational phenotyping, and causal modeling techniques with noisy data. Module 1 consists of techniques for data harmonization. We use natural language processing to recognize clinical variables from RCT design documents and map the extracted variables to EHR features with description matching and knowledge networks. Module 2 then develops techniques for cohort construction using advanced phenotyping algorithms to both identify patients with diseases of interest and define the treatment arms. Module 3 introduces methods for variable curation, including a list of existing tools to extract baseline variables from different sources (eg, codified, free text, and medical imaging) and end points of various types (eg, death, binary, temporal, and numerical). Finally, module 4 presents validation and robust modeling methods, and we propose a strategy to create gold-standard labels for EHR variables of interest to validate data curation quality and perform subsequent causal modeling for RWE. In addition to the workflow proposed in our pipeline, we also develop a reporting guideline for RWE that covers the necessary information to facilitate transparent reporting and reproducibility of results. Moreover, our pipeline is highly data driven, enhancing study data with a rich variety of publicly available information and knowledge sources. We also showcase our pipeline and provide guidance on the deployment of relevant tools by revisiting the emulation of the Clinical Outcomes of Surgical Therapy Study Group Trial on laparoscopy-assisted colectomy versus open colectomy in patients with early-stage colon cancer. We also draw on existing literature on EHR emulation of RCTs together with our own studies with the Mass General Brigham EHR.
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Affiliation(s)
- Jue Hou
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Rachel Zhao
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jessica Gronsbell
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Yucong Lin
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Qingyi Zeng
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Sinian Zhang
- School of Statistics, Renmin University of China, Bejing, China
| | | | - Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | | | | | - Chuan Hong
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, United States
| | - Tianrun Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Jun Wen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | | | | | - Katherine Liao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, United States
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18
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Gan Z, Zhou D, Rush E, Panickan VA, Ho YL, Ostrouchov G, Xu Z, Shen S, Xiong X, Greco KF, Hong C, Bonzel CL, Wen J, Costa L, Cai T, Begoli E, Xia Z, Gaziano JM, Liao KP, Cho K, Cai T, Lu J. ARCH: Large-scale Knowledge Graph via Aggregated Narrative Codified Health Records Analysis. medRxiv 2023:2023.05.14.23289955. [PMID: 37293026 PMCID: PMC10246054 DOI: 10.1101/2023.05.14.23289955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Objective Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes, covering hundreds of thousands of clinical concepts available for research and clinical care. The complex, massive, heterogeneous, and noisy nature of EHR data imposes significant challenges for feature representation, information extraction, and uncertainty quantification. To address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods The ARCH algorithm first derives embedding vectors from a co-occurrence matrix of all EHR concepts and then generates cosine similarities along with associated p -values to measure the strength of relatedness between clinical features with statistical certainty quantification. In the final step, ARCH performs a sparse embedding regression to remove indirect linkage between entity pairs. We validated the clinical utility of the ARCH knowledge graph, generated from 12.5 million patients in the Veterans Affairs (VA) healthcare system, through downstream tasks including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer's disease patients. Results ARCH produces high-quality clinical embeddings and KG for over 60,000 EHR concepts, as visualized in the R-shiny powered web-API (https://celehs.hms.harvard.edu/ARCH/). The ARCH embeddings attained an average area under the ROC curve (AUC) of 0.926 and 0.861 for detecting pairs of similar EHR concepts when the concepts are mapped to codified data and to NLP data; and 0.810 (codified) and 0.843 (NLP) for detecting related pairs. Based on the p -values computed by ARCH, the sensitivity of detecting similar and related entity pairs are 0.906 and 0.888 under false discovery rate (FDR) control of 5%. For detecting drug side effects, the cosine similarity based on the ARCH semantic representations achieved an AUC of 0.723 while the AUC improved to 0.826 after few-shot training via minimizing the loss function on the training data set. Incorporating NLP data substantially improved the ability to detect side effects in the EHR. For example, based on unsupervised ARCH embeddings, the power of detecting drug-side effects pairs when using codified data only was 0.15, much lower than the power of 0.51 when using both codified and NLP concepts. Compared to existing large-scale representation learning methods including PubmedBERT, BioBERT and SAPBERT, ARCH attains the most robust performance and substantially higher accuracy in detecting these relationships. Incorporating ARCH selected features in weakly supervised phenotyping algorithms can improve the robustness of algorithm performance, especially for diseases that benefit from NLP features as supporting evidence. For example, the phenotyping algorithm for depression attained an AUC of 0.927 when using ARCH selected features but only 0.857 when using codified features selected via the KESER network[1]. In addition, embeddings and knowledge graphs generated from the ARCH network were able to cluster AD patients into two subgroups, where the fast progression subgroup had a much higher mortality rate. Conclusions The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.
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Affiliation(s)
| | - Doudou Zhou
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Everett Rush
- Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Vidul A Panickan
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Zhiwei Xu
- University of Michigan, Ann Arbor, MI, USA
| | - Shuting Shen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xin Xiong
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Clara-Lea Bonzel
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Jun Wen
- Harvard Medical School, Boston, MA, USA
| | | | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Edmon Begoli
- Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Zongqi Xia
- University of Pittsburgh, Pittsburgh, USA
| | - J Michael Gaziano
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine P Liao
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Kelly Cho
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Tianxi Cai
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Junwei Lu
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
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19
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Tan ALM, Getzen EJ, Hutch MR, Strasser ZH, Gutiérrez-Sacristán A, Le TT, Dagliati A, Morris M, Hanauer DA, Moal B, Bonzel CL, Yuan W, Chiudinelli L, Das P, Zhang HG, Aronow BJ, Avillach P, Brat GA, Cai T, Hong C, La Cava WG, Hooi Will Loh H, Luo Y, Murphy SN, Yuan Hgiam K, Omenn GS, Patel LP, Jebathilagam Samayamuthu M, Shriver ER, Shakeri Hossein Abad Z, Tan BWL, Visweswaran S, Wang X, Weber GM, Xia Z, Verdy B, Long Q, Mowery DL, Holmes JH. Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? J Biomed Inform 2023; 139:104306. [PMID: 36738870 PMCID: PMC10849195 DOI: 10.1016/j.jbi.2023.104306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/21/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND In electronic health records, patterns of missing laboratory test results could capture patients' course of disease as well as reflect clinician's concerns or worries for possible conditions. These patterns are often understudied and overlooked. This study aims to identify informative patterns of missingness among laboratory data collected across 15 healthcare system sites in three countries for COVID-19 inpatients. METHODS We collected and analyzed demographic, diagnosis, and laboratory data for 69,939 patients with positive COVID-19 PCR tests across three countries from 1 January 2020 through 30 September 2021. We analyzed missing laboratory measurements across sites, missingness stratification by demographic variables, temporal trends of missingness, correlations between labs based on missingness indicators over time, and clustering of groups of labs based on their missingness/ordering pattern. RESULTS With these analyses, we identified mapping issues faced in seven out of 15 sites. We also identified nuances in data collection and variable definition for the various sites. Temporal trend analyses may support the use of laboratory test result missingness patterns in identifying severe COVID-19 patients. Lastly, using missingness patterns, we determined relationships between various labs that reflect clinical behaviors. CONCLUSION In this work, we use computational approaches to relate missingness patterns to hospital treatment capacity and highlight the heterogeneity of looking at COVID-19 over time and at multiple sites, where there might be different phases, policies, etc. Changes in missingness could suggest a change in a patient's condition, and patterns of missingness among laboratory measurements could potentially identify clinical outcomes. This allows sites to consider missing data as informative to analyses and help researchers identify which sites are better poised to study particular questions.
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Affiliation(s)
| | - Emily J Getzen
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | - Trang T Le
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | - Priam Das
- Harvard Medical School, Cambridge, MA, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Tianxi Cai
- Harvard Medical School, Cambridge, MA, USA
| | - Chuan Hong
- Harvard Medical School, Cambridge, MA, USA; Duke University, Durham, NC, USA
| | - William G La Cava
- Harvard Medical School, Cambridge, MA, USA; Boston Children's Hospital, Boston, MA, USA
| | | | - Yuan Luo
- Northwestern University, Chicago, IL, USA
| | | | | | | | - Lav P Patel
- University of Kansas Medical Center, United States
| | | | - Emily R Shriver
- University of Pennsylvania Health System, Philadelphia, PA, USA
| | | | | | | | - Xuan Wang
- Harvard Medical School, Cambridge, MA, USA
| | | | - Zongqi Xia
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Qi Long
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Danielle L Mowery
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John H Holmes
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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20
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Wen J, Zhang X, Rush E, Panickan VA, Li X, Cai T, Zhou D, Ho YL, Costa L, Begoli E, Hong C, Gaziano JM, Cho K, Lu J, Liao KP, Zitnik M, Cai T. Multimodal representation learning for predicting molecule-disease relations. Bioinformatics 2023; 39:7034101. [PMID: 36805623 PMCID: PMC9940625 DOI: 10.1093/bioinformatics/btad085] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/23/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
MOTIVATION Predicting molecule-disease indications and side effects is important for drug development and pharmacovigilance. Comprehensively mining molecule-molecule, molecule-disease and disease-disease semantic dependencies can potentially improve prediction performance. METHODS We introduce a Multi-Modal REpresentation Mapping Approach to Predicting molecular-disease relations (M2REMAP) by incorporating clinical semantics learned from electronic health records (EHR) of 12.6 million patients. Specifically, M2REMAP first learns a multimodal molecule representation that synthesizes chemical property and clinical semantic information by mapping molecule chemicals via a deep neural network onto the clinical semantic embedding space shared by drugs, diseases and other common clinical concepts. To infer molecule-disease relations, M2REMAP combines multimodal molecule representation and disease semantic embedding to jointly infer indications and side effects. RESULTS We extensively evaluate M2REMAP on molecule indications, side effects and interactions. Results show that incorporating EHR embeddings improves performance significantly, for example, attaining an improvement over the baseline models by 23.6% in PRC-AUC on indications and 23.9% on side effects. Further, M2REMAP overcomes the limitation of existing methods and effectively predicts drugs for novel diseases and emerging pathogens. AVAILABILITY AND IMPLEMENTATION The code is available at https://github.com/celehs/M2REMAP, and prediction results are provided at https://shiny.parse-health.org/drugs-diseases-dev/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jun Wen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,VA Boston Healthcare System, Boston, MA 02130, USA
| | - Xiang Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Everett Rush
- Department of Energy, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Vidul A Panickan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,VA Boston Healthcare System, Boston, MA 02130, USA
| | - Xingyu Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA 02130, USA.,Mass General Brigham, Boston, MA 02130, USA
| | - Doudou Zhou
- Department of Statistics, University of California, Davis, CA 95616, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Lauren Costa
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Edmon Begoli
- Department of Energy, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chuan Hong
- VA Boston Healthcare System, Boston, MA 02130, USA.,Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - J Michael Gaziano
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,VA Boston Healthcare System, Boston, MA 02130, USA.,Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kelly Cho
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,VA Boston Healthcare System, Boston, MA 02130, USA.,Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Junwei Lu
- VA Boston Healthcare System, Boston, MA 02130, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Katherine P Liao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,VA Boston Healthcare System, Boston, MA 02130, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Data Science Initiative, Cambridge, MA 02138, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,VA Boston Healthcare System, Boston, MA 02130, USA.,Mass General Brigham, Boston, MA 02130, USA
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21
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Cui H, Zeng L, Li R, Li Q, Hong C, Zhu H, Chen L, Liu L, Zou X, Xiao L. Radiomics signature based on CECT for non-invasive prediction of response to anti-PD-1 therapy in patients with hepatocellular carcinoma. Clin Radiol 2023; 78:e37-e44. [PMID: 36257868 DOI: 10.1016/j.crad.2022.09.113] [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: 05/09/2022] [Revised: 08/07/2022] [Accepted: 09/02/2022] [Indexed: 01/18/2023]
Abstract
PURPOSE This study aimed to develop a radiomics signature (RS) based on contrast-enhanced computed tomography (CECT) and evaluate its potential predictive value in hepatocellular carcinoma (HCC) patients receiving anti-PD-1 therapy. METHOD CECT scans of 76 HCC patients who received anti-PD-1 therapy were obtained in this study (training group = 53 and validation group = 23). The least absolute shrinkage and selection operator (LASSO) regression was applied to select radiomics features of primary and metastatic lesions and establish a RS to predict lesion-level response. Then, a nomogram combined the mean RS (MRS) and clinical variables with patient-level response as the end point. RESULTS In the lesion-level analysis, the area under the curves (AUCs) of RS in the training and validation groups were 0.751 (95% CI, 0.668-0.835) and 0.734 (95% CI, 0.604-0.864), respectively. In the patient-level analysis, the AUCs of the nomogram in the training and validation groups were 0.897 (95% CI, 0.798-0.996) and 0.889 (95% CI, 0.748-1.000), respectively. The nomogram stratified patients into low- and high-risk groups, which showed a significant difference in progression-free survival (PFS) (p<0.05). CONCLUSIONS The RS is a noninvasive biomarker for predicting anti-PD-1 therapy response in patients with HCC. The nomogram may be of clinical use for identifying high-risk patients and formulating individualised treatments.
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Affiliation(s)
- H Cui
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - L Zeng
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - R Li
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Q Li
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - C Hong
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - H Zhu
- Department of Medical Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - L Chen
- Department of Medical Quality Management, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - L Liu
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - X Zou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - L Xiao
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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22
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Loo G, Yap J, Hon JS, Ismail A, Lim CL, Sumanthy P, Ruan W, Sewa DW, Phua GC, Ng SA, Hong C, Low A, Lim ST, Tan JL. Real-world outcomes of Selexipag for treatment of pulmonary hypertension in an Asian population. Eur Heart J 2023. [DOI: 10.1093/eurheartj/ehac779.081] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Introduction
Selexipag is an oral selective prostacyclin IP receptor agonist indicated for treatment of pulmonary arterial hypertension (PAH). Data on its real-world safety and efficacy in Asians is lacking.
Purpose
We sought to evaluate the clinical characteristics, treatment regimens and outcomes of patients initiated on selexipag in a tertiary cardiac centre in Asia.
Methods
This was a retrospective study on all patients initiated on selexipag from January 2017 to December 2020. Baseline and follow up characteristics including demographics, functional status and clinical data were collected. Clinical outcomes evaluated included hospitalisation for PH related complications and all-cause mortality. Patients were risk stratified using the COMPERA 2.0 risk scores.
Results
A total of 36 PAH patients were treated with selexipag. At baseline, most patients were WHO functional class II or III (36.4% and 51.5% respectively), with a NT-proBNP of 1335 pg/ml (557 – 2918) and 6 minute walk test (6MWT) duration of 327.5 ±126.4 meters. Selexipag was initiated at 200mcg twice daily dosage for all except one patient (started at 200mcg once daily) and the maximum tolerated dose ranged from 200mcg twice daily to 1400mcg twice daily, with majority tolerating up to a dose of 600mcg twice daily (58.3%). Side effects were reported in 23 patients (63.9%), of which headache (27.8%), diarrhea (30.6%) or musculoskeletal symptoms (27.8%) were predominant. After a median follow up duration of 25.9 ± 23.1 months, selexipag was stopped in 20 patients (55.6%), of which eight patients were due to PAH progression requiring alternative therapy, and 12 patients due to side effects from selexipag. At baseline, patients were classified into low (8.3%), intermediate-low (30.6%), intermediate-high (33.3%) and high risk (27.8%) respectively. Patients who continued on selexipag at follow up showed no change (46.2%), improvement (15.4%) and deterioration (38.5%) in risk score. In the overall cohort of 36 patients, majority (75%) had at least one hospitalisation for PAH related complications and 15 patients (41.7%) demised.
Conclusion
In this real-world study, while selexipag was associated with a stable or improved PAH risk scores in majority of patients, there was a subset of patients with disease progression or intolerance to the medication. Further studies are warranted to identify patients who will benefit most from this therapy.
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Affiliation(s)
- G Loo
- National Heart Centre Singapore , Singapore , Singapore
| | - J Yap
- National Heart Centre Singapore , Singapore , Singapore
| | - J S Hon
- National Heart Centre Singapore , Singapore , Singapore
| | - A Ismail
- National Heart Centre Singapore , Singapore , Singapore
| | - C L Lim
- National Heart Centre Singapore , Singapore , Singapore
| | - P Sumanthy
- National Heart Centre Singapore , Singapore , Singapore
| | - W Ruan
- National Heart Centre Singapore , Singapore , Singapore
| | - D W Sewa
- Singapore General Hospital , Singapore , Singapore
| | - G C Phua
- Singapore General Hospital , Singapore , Singapore
| | - S A Ng
- Singapore General Hospital , Singapore , Singapore
| | - C Hong
- Singapore General Hospital , Singapore , Singapore
| | - A Low
- Singapore General Hospital , Singapore , Singapore
| | - S T Lim
- National Heart Centre Singapore , Singapore , Singapore
| | - J L Tan
- National Heart Centre Singapore , Singapore , Singapore
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23
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Hong C, Pencina MJ, Wojdyla DM, Hall JL, Judd SE, Cary M, Engelhard MM, Berchuck S, Xian Y, D’Agostino R, Howard G, Kissela B, Henao R. Predictive Accuracy of Stroke Risk Prediction Models Across Black and White Race, Sex, and Age Groups. JAMA 2023; 329:306-317. [PMID: 36692561 PMCID: PMC10408266 DOI: 10.1001/jama.2022.24683] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/26/2022] [Indexed: 01/25/2023]
Abstract
Importance Stroke is the fifth-highest cause of death in the US and a leading cause of serious long-term disability with particularly high risk in Black individuals. Quality risk prediction algorithms, free of bias, are key for comprehensive prevention strategies. Objective To compare the performance of stroke-specific algorithms with pooled cohort equations developed for atherosclerotic cardiovascular disease for the prediction of new-onset stroke across different subgroups (race, sex, and age) and to determine the added value of novel machine learning techniques. Design, Setting, and Participants Retrospective cohort study on combined and harmonized data from Black and White participants of the Framingham Offspring, Atherosclerosis Risk in Communities (ARIC), Multi-Ethnic Study for Atherosclerosis (MESA), and Reasons for Geographical and Racial Differences in Stroke (REGARDS) studies (1983-2019) conducted in the US. The 62 482 participants included at baseline were at least 45 years of age and free of stroke or transient ischemic attack. Exposures Published stroke-specific algorithms from Framingham and REGARDS (based on self-reported risk factors) as well as pooled cohort equations for atherosclerotic cardiovascular disease plus 2 newly developed machine learning algorithms. Main Outcomes and Measures Models were designed to estimate the 10-year risk of new-onset stroke (ischemic or hemorrhagic). Discrimination concordance index (C index) and calibration ratios of expected vs observed event rates were assessed at 10 years. Analyses were conducted by race, sex, and age groups. Results The combined study sample included 62 482 participants (median age, 61 years, 54% women, and 29% Black individuals). Discrimination C indexes were not significantly different for the 2 stroke-specific models (Framingham stroke, 0.72; 95% CI, 0.72-073; REGARDS self-report, 0.73; 95% CI, 0.72-0.74) vs the pooled cohort equations (0.72; 95% CI, 0.71-0.73): differences 0.01 or less (P values >.05) in the combined sample. Significant differences in discrimination were observed by race: the C indexes were 0.76 for all 3 models in White vs 0.69 in Black women (all P values <.001) and between 0.71 and 0.72 in White men and between 0.64 and 0.66 in Black men (all P values ≤.001). When stratified by age, model discrimination was better for younger (<60 years) vs older (≥60 years) adults for both Black and White individuals. The ratios of observed to expected 10-year stroke rates were closest to 1 for the REGARDS self-report model (1.05; 95% CI, 1.00-1.09) and indicated risk overestimation for Framingham stroke (0.86; 95% CI, 0.82-0.89) and pooled cohort equations (0.74; 95% CI, 0.71-0.77). Performance did not significantly improve when novel machine learning algorithms were applied. Conclusions and Relevance In this analysis of Black and White individuals without stroke or transient ischemic attack among 4 US cohorts, existing stroke-specific risk prediction models and novel machine learning techniques did not significantly improve discriminative accuracy for new-onset stroke compared with the pooled cohort equations, and the REGARDS self-report model had the best calibration. All algorithms exhibited worse discrimination in Black individuals than in White individuals, indicating the need to expand the pool of risk factors and improve modeling techniques to address observed racial disparities and improve model performance.
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Affiliation(s)
- Chuan Hong
- Duke AI Health, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - Michael J. Pencina
- Duke AI Health, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, North Carolina
- Duke Clinical Research Institute, Durham, North Carolina
| | | | | | - Suzanne E. Judd
- School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michael Cary
- Duke AI Health, Durham, North Carolina
- Duke University School of Nursing, Durham, North Carolina
| | - Matthew M. Engelhard
- Duke AI Health, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - Samuel Berchuck
- Department of Statistical Science, Duke University School of Medicine, Durham, North Carolina
| | - Ying Xian
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas
| | - Ralph D’Agostino
- Department of Mathematics & Statistics, Boston University Arts and Sciences, Boston, Massachusetts
| | - George Howard
- School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brett Kissela
- College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ricardo Henao
- Duke AI Health, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, North Carolina
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina
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24
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Moal B, Orieux A, Ferté T, Neuraz A, Brat GA, Avillach P, Bonzel CL, Cai T, Cho K, Cossin S, Griffier R, Hanauer DA, Haverkamp C, Ho YL, Hong C, Hutch MR, Klann JG, Le TT, Loh NHW, Luo Y, Makoudjou A, Morris M, Mowery DL, Olson KL, Patel LP, Samayamuthu MJ, Sanz Vidorreta FJ, Schriver ER, Schubert P, Verdy G, Visweswaran S, Wang X, Weber GM, Xia Z, Yuan W, Zhang HG, Zöller D, Kohane IS, Boyer A, Jouhet V. Acute respiratory distress syndrome after SARS-CoV-2 infection on young adult population: International observational federated study based on electronic health records through the 4CE consortium. PLoS One 2023; 18:e0266985. [PMID: 36598895 DOI: 10.1371/journal.pone.0266985] [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: 04/05/2022] [Accepted: 11/09/2022] [Indexed: 01/05/2023] Open
Abstract
PURPOSE In young adults (18 to 49 years old), investigation of the acute respiratory distress syndrome (ARDS) after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been limited. We evaluated the risk factors and outcomes of ARDS following infection with SARS-CoV-2 in a young adult population. METHODS A retrospective cohort study was conducted between January 1st, 2020 and February 28th, 2021 using patient-level electronic health records (EHR), across 241 United States hospitals and 43 European hospitals participating in the Consortium for Clinical Characterization of COVID-19 by EHR (4CE). To identify the risk factors associated with ARDS, we compared young patients with and without ARDS through a federated analysis. We further compared the outcomes between young and old patients with ARDS. RESULTS Among the 75,377 hospitalized patients with positive SARS-CoV-2 PCR, 1001 young adults presented with ARDS (7.8% of young hospitalized adults). Their mortality rate at 90 days was 16.2% and they presented with a similar complication rate for infection than older adults with ARDS. Peptic ulcer disease, paralysis, obesity, congestive heart failure, valvular disease, diabetes, chronic pulmonary disease and liver disease were associated with a higher risk of ARDS. We described a high prevalence of obesity (53%), hypertension (38%- although not significantly associated with ARDS), and diabetes (32%). CONCLUSION Trough an innovative method, a large international cohort study of young adults developing ARDS after SARS-CoV-2 infection has been gather. It demonstrated the poor outcomes of this population and associated risk factor.
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Affiliation(s)
- Bertrand Moal
- IAM Unit, Bordeaux University Hospital, Bordeaux, France
| | - Arthur Orieux
- Medical Intensive Care Unit, Bordeaux University Hospital, Bordeaux, France
| | - Thomas Ferté
- Inserm Bordeaux Population Health Research Center UMR 1219, Inria BSO, Team SISTM, University of Bordeaux, Bordeaux, France
| | - Antoine Neuraz
- Department of Biomedical Informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kelly Cho
- Population Health and Data Science, MAVERIC, VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Sébastien Cossin
- INSERM Bordeaux Population Health ERIAS TEAM, Bordeaux University Hospital / ERIAS - Inserm U1219 BPH, Bordeaux, France
| | - Romain Griffier
- Institute of Digitalization in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - David A Hanauer
- IAM Unit, INSERM Bordeaux Population Health ERIAS TEAM, Bordeaux University Hospital / ERIAS - Inserm U1219 BPH, Bordeaux, France
| | - Christian Haverkamp
- Department of Learning Health Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuk-Lam Ho
- Institute of Digitalization in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Meghan R Hutch
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Jeffrey G Klann
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Trang T Le
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ne Hooi Will Loh
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Yuan Luo
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Adeline Makoudjou
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michele Morris
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Danielle L Mowery
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karen L Olson
- Department of Anaesthesia, National University Health System, Singapore, Singapore
| | - Lav P Patel
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Malarkodi J Samayamuthu
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Fernando J Sanz Vidorreta
- Computational Health Informatics Program, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Emily R Schriver
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Petra Schubert
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | | | - Shyam Visweswaran
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xuan Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zongqi Xia
- Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, United States of America
| | - William Yuan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Harrison G Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniela Zöller
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexandre Boyer
- Medical Intensive Care Unit, Bordeaux University Hospital, Bordeaux, France
| | - Vianney Jouhet
- Institute of Digitalization in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
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Tan BW, Tan BW, Tan AL, Schriver ER, Gutiérrez-Sacristán A, Das P, Yuan W, Hutch MR, García Barrio N, Pedrera Jimenez M, Abu-el-rub N, Morris M, Moal B, Verdy G, Cho K, Ho YL, Patel LP, Dagliati A, Neuraz A, Klann JG, South AM, Visweswaran S, Hanauer DA, Maidlow SE, Liu M, Mowery DL, Batugo A, Makoudjou A, Tippmann P, Zöller D, Brat GA, Luo Y, Avillach P, Bellazzi R, Chiovato L, Malovini A, Tibollo V, Samayamuthu MJ, Serrano Balazote P, Xia Z, Loh NHW, Chiudinelli L, Bonzel CL, Hong C, Zhang HG, Weber GM, Kohane IS, Cai T, Omenn GS, Holmes JH, Ngiam KY. Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study. EClinicalMedicine 2023; 55:101724. [PMID: 36381999 PMCID: PMC9640184 DOI: 10.1016/j.eclinm.2022.101724] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/12/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
Background While acute kidney injury (AKI) is a common complication in COVID-19, data on post-AKI kidney function recovery and the clinical factors associated with poor kidney function recovery is lacking. Methods A retrospective multi-centre observational cohort study comprising 12,891 hospitalized patients aged 18 years or older with a diagnosis of SARS-CoV-2 infection confirmed by polymerase chain reaction from 1 January 2020 to 10 September 2020, and with at least one serum creatinine value 1-365 days prior to admission. Mortality and serum creatinine values were obtained up to 10 September 2021. Findings Advanced age (HR 2.77, 95%CI 2.53-3.04, p < 0.0001), severe COVID-19 (HR 2.91, 95%CI 2.03-4.17, p < 0.0001), severe AKI (KDIGO stage 3: HR 4.22, 95%CI 3.55-5.00, p < 0.0001), and ischemic heart disease (HR 1.26, 95%CI 1.14-1.39, p < 0.0001) were associated with worse mortality outcomes. AKI severity (KDIGO stage 3: HR 0.41, 95%CI 0.37-0.46, p < 0.0001) was associated with worse kidney function recovery, whereas remdesivir use (HR 1.34, 95%CI 1.17-1.54, p < 0.0001) was associated with better kidney function recovery. In a subset of patients without chronic kidney disease, advanced age (HR 1.38, 95%CI 1.20-1.58, p < 0.0001), male sex (HR 1.67, 95%CI 1.45-1.93, p < 0.0001), severe AKI (KDIGO stage 3: HR 11.68, 95%CI 9.80-13.91, p < 0.0001), and hypertension (HR 1.22, 95%CI 1.10-1.36, p = 0.0002) were associated with post-AKI kidney function impairment. Furthermore, patients with COVID-19-associated AKI had significant and persistent elevations of baseline serum creatinine 125% or more at 180 days (RR 1.49, 95%CI 1.32-1.67) and 365 days (RR 1.54, 95%CI 1.21-1.96) compared to COVID-19 patients with no AKI. Interpretation COVID-19-associated AKI was associated with higher mortality, and severe COVID-19-associated AKI was associated with worse long-term post-AKI kidney function recovery. Funding Authors are supported by various funders, with full details stated in the acknowledgement section.
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Affiliation(s)
- Byorn W.L. Tan
- Department of Medicine, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block Level 10, Singapore 119228
| | - Bryce W.Q. Tan
- Department of Medicine, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block Level 10, Singapore 119228
| | - Amelia L.M. Tan
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Emily R. Schriver
- Data Analytics Center, University of Pennsylvania Health System, 3600 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Alba Gutiérrez-Sacristán
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Priyam Das
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - William Yuan
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Meghan R. Hutch
- Department of Preventive Medicine, Northwestern University, 750 North Lake Shore Drive, Chicago, IL 60611, USA
| | - Noelia García Barrio
- Department of Health Informatics, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n 28041 Madrid, Spain
| | - Miguel Pedrera Jimenez
- Department of Health Informatics, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n 28041 Madrid, Spain
| | - Noor Abu-el-rub
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Pittsburgh, PA 15206, USA
| | - Bertrand Moal
- IAM Unit, Bordeaux University Hospital, Place Amélie Rabat Léon, 33076 Bordeaux, France
| | - Guillaume Verdy
- IAM Unit, Bordeaux University Hospital, Place Amélie Rabat Léon, 33076 Bordeaux, France
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, 2 Avenue De Lafayette, Boston, MA 02130, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, 2 Avenue De Lafayette, Boston, MA 02130, USA
| | - Lav P. Patel
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Arianna Dagliati
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy, Via Ferrata 5, 27100 Pavia, Italy
| | - Antoine Neuraz
- Department of Biomedical Informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris, University of Paris, 149 Rue de Sèvres, 75015 Paris, France
| | - Jeffrey G. Klann
- Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Andrew M. South
- Department of Pediatrics-Section of Nephrology, Brenner Children's Hospital, Wake Forest School of Medicine, Medical Center Boulevard, Winston Salem, NC 27157, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Pittsburgh, PA 15206, USA
| | - David A. Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA, 100-107 NCRC, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Sarah E. Maidlow
- Michigan Institute for Clinical and Health Research (MICHR) Informatics, University of Michigan, NCRC Bldg 400, 2800 Plymouth Road, Ann Arbor, MI, United States
| | - Mei Liu
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Danielle L. Mowery
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk, Richards Hall, A202, Philadelphia, PA 19104, USA
| | - Ashley Batugo
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, 401 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104, USA
| | - Adeline Makoudjou
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Zinkmattenstraße 6a, DE79108 Freiburg, Germany
| | - Patric Tippmann
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Zinkmattenstraße 6a, DE79108 Freiburg, Germany
| | - Daniela Zöller
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Zinkmattenstraße 6a, DE79108 Freiburg, Germany
| | - Gabriel A. Brat
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, 750 North Lake Shore Drive, Chicago, IL 60611, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy, Via Ferrata 5, 27100 Pavia, Italy
| | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy., Via Maugeri 4, 27100 Pavia, Italy
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy., Via Maugeri 4, 27100 Pavia, Italy
| | | | - Pablo Serrano Balazote
- Department of Health Informatics, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n 28041 Madrid, Spain
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, 3501 5th Avenue, BST-3 Suite 7014, Pittsburgh, PA 15260, USA
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health System, 5 Lower Kent Ridge Road, Singapore 119074
| | - Lorenzo Chiudinelli
- UOC Ricerca, Innovazione e Brand reputation, ASST Papa Giovanni XXIII, Bergamo, P.zza OMS 1 - 24127 Bergamo, Italy
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
- Department of Biostatistics and Bioinformatics, Duke University, 2424 Erwin Road, Durham, NC, United States
| | - Harrison G. Zhang
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Griffin M. Weber
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine & Bioinformatics, University of Michigan, 2017B Palmer Commons, 100 Washtenaw, Ann Arbor, MI 48109-2218
| | - John H. Holmes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk, Richards Hall, A202, Philadelphia, PA 19104, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, 401 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104, USA
| | - Kee Yuan Ngiam
- Department of Biomedical Informatics, WiSDM, National University Health Systems Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 8, Singapore 119228
- Corresponding author. Department of Biomedical Informatics, WiSDM, National University Health Systems Singapore, 1E Kent Ridge Road, NUHS Tower Block Level 8, Singapore 119228.
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Yoon A, Faldu J, Hong C. Craniofacial Growth Modification Protocol for Pediatric OSA. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yoon A, Bockow R, Abdelwahab M, Vakili A, Lovell K, Ganguly R, Liu S, Kushida C, Hong C. Impact of Rapid Maxillary Expansion on Adenotonsillar Hypertrophy in Children. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Santiago S, Hong C, As-Sanie S, Till S. 8258 Does Uterine Size Matter? the Relationship between Surgeon Volume, Surgical Approach, and Uterine Weight for Benign Hysterectomy. J Minim Invasive Gynecol 2022. [DOI: 10.1016/j.jmig.2022.09.391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Paller A, Blauvelt A, Soong W, Hong C, Schuttelaar M, Schneider S, Moerch M, Simpson E. MEANINGFUL RESPONSES IN TRALOKINUMAB-TREATED ADOLESCENTS WITH ATOPIC DERMATITIS NOT ACHIEVING IGA 0/1 AT WEEK-16. Ann Allergy Asthma Immunol 2022. [DOI: 10.1016/j.anai.2022.08.715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Punshon T, Jackson BP, Donohue A, Hong C, Rothenberg SE. Distribution and accumulation of mercury in pot-grown African rice cultivars (Oryza glaberrima Steud. and Oryza sativa L.) determined via LA-ICP-MS. Environ Geochem Health 2022; 44:4077-4089. [PMID: 34981270 PMCID: PMC9376884 DOI: 10.1007/s10653-021-01169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
There is limited information concerning the distribution of mercury in rice, particularly in African rice. The objective was to compare the distribution of total mercury (THg) and methylmercury (MeHg) in African rice (Oryza glaberrima Steud.) and Asian rice (O. sativa L.). It is hypothesized that increased mineral accumulation and greater stress tolerance in O. glaberrima will affect the uptake and distribution of THg and MeHg, compared to O. sativa. Rice varieties from the Republic of Mali, including O. glaberrima (n =1) and O. sativa (n = 2), were cultivated in a greenhouse, in mercury-spiked soil (50 mg/kg) (n =3 replicates/variety). THg and MeHg concentrations were analyzed in the grain (brown rice), and the THg distribution was analyzed using laser ablation inductively coupled-plasma mass spectrometry (LA-ICP-MS). THg and MeHg concentrations did not differ between O. glaberrima and O. sativa grain. However, in both O. sativa varieties, THg was highly concentrated in the scutellum, which surrounds the embryo and is removed during polishing. Conversely, in O. glaberrima grain, THg was widely distributed throughout the endosperm, the edible portion of the grain. Differences in the THg distribution in O. glaberrima grain, compared to O. sativa, may elevate the risk of mercury exposure through ingestion of polished rice. The novelty of this study includes the investigation of a less-studied rice species (O. glaberrima), the use of a highly sensitive elemental imaging technique (LA-ICP-MS), and its finding of a different grain THg distribution in O. glaberrima than has been observed in O. sativa.
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Affiliation(s)
- Tracy Punshon
- Dartmouth College, Hanover, New Hampshire, 03755, USA
| | | | - Alexis Donohue
- University of South Carolina, Arnold School of Public Health, Columbia, South Carolina, 29208, USA
| | - Chuan Hong
- University of South Carolina, Arnold School of Public Health, Columbia, South Carolina, 29208, USA
| | - Sarah E Rothenberg
- University of South Carolina, Arnold School of Public Health, Columbia, South Carolina, 29208, USA.
- College of Public Health and Human Sciences, Oregon State University, 103 Milam Hall, Corvallis, Oregon, 97331, USA.
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Ahuja Y, Wen J, Hong C, Xia Z, Huang S, Cai T. A semi-supervised adaptive Markov Gaussian embedding process (SAMGEP) for prediction of phenotype event times using the electronic health record. Sci Rep 2022; 12:17737. [PMID: 36273240 PMCID: PMC9588081 DOI: 10.1038/s41598-022-22585-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/17/2022] [Indexed: 01/18/2023] Open
Abstract
While there exist numerous methods to identify binary phenotypes (i.e. COPD) using electronic health record (EHR) data, few exist to ascertain the timings of phenotype events (i.e. COPD onset or exacerbations). Estimating event times could enable more powerful use of EHR data for longitudinal risk modeling, including survival analysis. Here we introduce Semi-supervised Adaptive Markov Gaussian Embedding Process (SAMGEP), a semi-supervised machine learning algorithm to estimate phenotype event times using EHR data with limited observed labels, which require resource-intensive chart review to obtain. SAMGEP models latent phenotype states as a binary Markov process, and it employs an adaptive weighting strategy to map timestamped EHR features to an embedding function that it models as a state-dependent Gaussian process. SAMGEP's feature weighting achieves meaningful feature selection, and its predictions significantly improve AUCs and F1 scores over existing approaches in diverse simulations and real-world settings. It is particularly adept at predicting cumulative risk and event counting process functions, and is robust to diverse generative model parameters. Moreover, it achieves high accuracy with few (50-100) labels, efficiently leveraging unlabeled EHR data to maximize information gain from costly-to-obtain event time labels. SAMGEP can be used to estimate accurate phenotype state functions for risk modeling research.
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Affiliation(s)
- Yuri Ahuja
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Harvard Medical School, Boston, MA, USA. .,Department of Medicine, NYU Langone Health, New York, NY, USA.
| | - Jun Wen
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Chuan Hong
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Zongqi Xia
- grid.21925.3d0000 0004 1936 9000Department of Neurology, University of Pittsburgh, Pittsburgh, PA USA
| | - Sicong Huang
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.62560.370000 0004 0378 8294Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA USA ,grid.410370.10000 0004 4657 1992VA Boston Healthcare System, Boston, MA USA
| | - Tianxi Cai
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.410370.10000 0004 4657 1992VA Boston Healthcare System, Boston, MA USA
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Hong C, Li H, Parel PM, Berg AR, Rodante J, Keel A, Teague HL, Playford MP, Chen MY, Zhou W, Sorokin AV, Bluemke DA, Mehta NN. Application of machine learning to identify top determinants of fibrofatty plaque burden by CCTA in humans with psoriasis. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.213] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Fibrofatty plaque burden (FFB) is a high-risk, vulnerable plaque feature comprised of an atheromatous core and fibrous cap with increased risk of coronary artery disease (CAD) [1]. Psoriasis (PSO) is a chronic inflammatory disease linked with atherosclerotic risk and premature cardiovascular disease, driven in part by vulnerable plaque rupture [2,3]. Machine learning (ML) previously showed the prognostic value of FFB in predicting 5-year risk of cardiac-related mortality in patients with CAD [4]. Whether ML can predict FFB in psoriasis is understudied.
Purpose
To use ML to identify top determinants of FFB by CCTA in PSO.
Methods
320 consecutive participants with psoriasis were recruited as part of an ongoing cohort study, of whom 307 had FFB analyzed with coronary computed tomography angiography (CCTA) and quantified by QAngio CT (Medis, The Netherlands). 140 out of 182 potential determinants were subjected to ML algorithms analyzed by random forest and validated by 5-fold cross validation to select the top determinants based on R-square criteria. Lipid concentration and size were measured by nuclear magnetic resonance (NMR) and sdLDL-C was calculated by Sampson's formula.
Results
The top 21 determinants of FFB at baseline were grouped into 3 categories: cardiometabolic risk factors (BMI, sex, DBP, mean arterial pressure, exercise, heart rate, glucose, anxiety, psoriasis disease duration), clinical measurements (basophils, platelets, hemoglobin, RBC, alkaline phosphatase, ALT, creatinine, neutrophil-to-lymphocyte ratio), and lipoproteins (LDL particle size, apolipoprotein A1, apolipoprotein B-to-A1 ratio, calculated sdLDL-C).
Conclusion
ML confirmed that FFB strongly correlates with cardiometabolic risk factors, clinical measurements, and lipoproteins. Further investigations into these top determinants of FFB over time may provide insight into potential therapeutic interventions that decrease cardiovascular risk in patients with chronic inflammatory diseases and should be validated in larger studies.
Funding Acknowledgement
Type of funding sources: Public Institution(s). Main funding source(s): This study was supported by the National Heart, Lung and Blood Institute (NHLBI) IntramuralResearch Program (ZIA-HL-06193). This research was made possible through the NIH MedicalResearch Scholars Program, a public-private partnership supported jointly by the NIH andcontributions to the Foundation for the NIH from the Doris Duke Charitable Foundation,Genentech, the American Association for Dental Research, the Colgate-Palmolive Company, andother private donors.
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Affiliation(s)
- C Hong
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - H Li
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - P M Parel
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - A R Berg
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - J Rodante
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - A Keel
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - H L Teague
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - M P Playford
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - M Y Chen
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - W Zhou
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - A V Sorokin
- National Heart Lung and Blood Institute , Bethesda , United States of America
| | - D A Bluemke
- University of Wisconsin-Madison, Department of Radiology , Madison , United States of America
| | - N N Mehta
- National Heart Lung and Blood Institute , Bethesda , United States of America
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Gustafson MS, Patel A, Hong C, Meline M, Peña D, Tang C, Fernandez Lynch H. Estimated Clinical Trial Capacity of Sites Participating in the COVID-19 Convalescent Plasma Expanded Access Program. JAMA Netw Open 2022; 5:e2237540. [PMID: 36260335 PMCID: PMC9582895 DOI: 10.1001/jamanetworkopen.2022.37540] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This cross-sectional study estimates the trial capacity of sites participating in the COVID-19 convalescent plasma expanded access program.
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Affiliation(s)
| | - Aman Patel
- University of Southern California, Los Angeles, California
| | - Chuan Hong
- Department of Population Health, NYU Langone Health, New York, New York
| | - Miles Meline
- University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Holly Fernandez Lynch
- Department of Medical Ethics and Health Policy Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Nogues IE, Wen J, Lin Y, Liu M, Tedeschi SK, Geva A, Cai T, Hong C. Weakly Semi-supervised phenotyping using Electronic Health records. J Biomed Inform 2022; 134:104175. [PMID: 36064111 PMCID: PMC10112494 DOI: 10.1016/j.jbi.2022.104175] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 12/07/2021] [Revised: 04/23/2022] [Accepted: 08/15/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Electronic Health Record (EHR) based phenotyping is a crucial yet challenging problem in the biomedical field. Though clinicians typically determine patient-level diagnoses via manual chart review, the sheer volume and heterogeneity of EHR data renders such tasks challenging, time-consuming, and prohibitively expensive, thus leading to a scarcity of clinical annotations in EHRs. Weakly supervised learning algorithms have been successfully applied to various EHR phenotyping problems, due to their ability to leverage information from large quantities of unlabeled samples to better inform predictions based on a far smaller number of patients. However, most weakly supervised methods are subject to the challenge to choose the right cutoff value to generate an optimal classifier. Furthermore, since they only utilize the most informative features (i.e., main ICD and NLP counts) they may fail for episodic phenotypes that cannot be consistently detected via ICD and NLP data. In this paper, we propose a label-efficient, weakly semi-supervised deep learning algorithm for EHR phenotyping (WSS-DL), which overcomes the limitations above. MATERIALS AND METHODS WSS-DL classifies patient-level disease status through a series of learning stages: 1) generating silver standard labels, 2) deriving enhanced-silver-standard labels by fitting a weakly supervised deep learning model to data with silver standard labels as outcomes and high dimensional EHR features as input, and 3) obtaining the final prediction score and classifier by fitting a supervised learning model to data with a minimal number of gold standard labels as the outcome, and the enhanced-silver-standard labels and a minimal set of most informative EHR features as input. To assess the generalizability of WSS-DL across different phenotypes and medical institutions, we apply WSS-DL to classify a total of 17 diseases, including both acute and chronic conditions, using EHR data from three healthcare systems. Additionally, we determine the minimum quantity of training labels required by WSS-DL to outperform existing supervised and semi-supervised phenotyping methods. RESULTS The proposed method, in combining the strengths of deep learning and weakly semi-supervised learning, successfully leverages the crucial phenotyping information contained in EHR features from unlabeled samples. Indeed, the deep learning model's ability to handle high-dimensional EHR features allows it to generate strong phenotype status predictions from silver standard labels. These predictions, in turn, provide highly effective features in the final logistic regression stage, leading to high phenotyping accuracy in notably small subsets of labeled data (e.g. n = 40 labeled samples). CONCLUSION Our method's high performance in EHR datasets with very small numbers of labels indicates its potential value in aiding doctors to diagnose rare diseases as well as conditions susceptible to misdiagnosis.
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Affiliation(s)
| | - Jun Wen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yucong Lin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Statistical Science, Tsinghua University, Beijing, China
| | - Molei Liu
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sara K Tedeschi
- Department of Medicine, Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Alon Geva
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Department of Anesthesiology, Critical Care, and Pain Medicine, and Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA; Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Tianxi Cai
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Hong C, Wang E, Turgeon R, Wong G. COMPARING DUAL ANTIPLATELET THERAPY STRATEGIES POST-ACUTE CORONARY SYNDROME: NETWORK META-ANALYSIS. Can J Cardiol 2022. [DOI: 10.1016/j.cjca.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Wang X, Zhang HG, Xiong X, Hong C, Weber GM, Brat GA, Bonzel CL, Luo Y, Duan R, Palmer NP, Hutch MR, Gutiérrez-Sacristán A, Bellazzi R, Chiovato L, Cho K, Dagliati A, Estiri H, García-Barrio N, Griffier R, Hanauer DA, Ho YL, Holmes JH, Keller MS, Klann MEng JG, L'Yi S, Lozano-Zahonero S, Maidlow SE, Makoudjou A, Malovini A, Moal B, Moore JH, Morris M, Mowery DL, Murphy SN, Neuraz A, Yuan Ngiam K, Omenn GS, Patel LP, Pedrera-Jiménez M, Prunotto A, Jebathilagam Samayamuthu M, Sanz Vidorreta FJ, Schriver ER, Schubert P, Serrano-Balazote P, South AM, Tan ALM, Tan BWL, Tibollo V, Tippmann P, Visweswaran S, Xia Z, Yuan W, Zöller D, Kohane IS, Avillach P, Guo Z, Cai T. SurvMaximin: Robust federated approach to transporting survival risk prediction models. J Biomed Inform 2022; 134:104176. [PMID: 36007785 PMCID: PMC9707637 DOI: 10.1016/j.jbi.2022.104176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/01/2022] [Revised: 07/18/2022] [Accepted: 08/15/2022] [Indexed: 10/15/2022]
Abstract
OBJECTIVE For multi-center heterogeneous Real-World Data (RWD) with time-to-event outcomes and high-dimensional features, we propose the SurvMaximin algorithm to estimate Cox model feature coefficients for a target population by borrowing summary information from a set of health care centers without sharing patient-level information. MATERIALS AND METHODS For each of the centers from which we want to borrow information to improve the prediction performance for the target population, a penalized Cox model is fitted to estimate feature coefficients for the center. Using estimated feature coefficients and the covariance matrix of the target population, we then obtain a SurvMaximin estimated set of feature coefficients for the target population. The target population can be an entire cohort comprised of all centers, corresponding to federated learning, or a single center, corresponding to transfer learning. RESULTS Simulation studies and a real-world international electronic health records application study, with 15 participating health care centers across three countries (France, Germany, and the U.S.), show that the proposed SurvMaximin algorithm achieves comparable or higher accuracy compared with the estimator using only the information of the target site and other existing methods. The SurvMaximin estimator is robust to variations in sample sizes and estimated feature coefficients between centers, which amounts to significantly improved estimates for target sites with fewer observations. CONCLUSIONS The SurvMaximin method is well suited for both federated and transfer learning in the high-dimensional survival analysis setting. SurvMaximin only requires a one-time summary information exchange from participating centers. Estimated regression vectors can be very heterogeneous. SurvMaximin provides robust Cox feature coefficient estimates without outcome information in the target population and is privacy-preserving.
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Affiliation(s)
- Xuan Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Harrison G Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Xin Xiong
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yuan Luo
- Department of Preventive Medicine Northwestern University, Chicago, IL, USA
| | - Rui Duan
- Department of Biostatistics, Harvard University, Boston, MA, USA
| | - Nathan P Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Meghan R Hutch
- Department of Preventive Medicine Northwestern University, Chicago, IL, USA
| | | | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Kelly Cho
- Population Health and Data Science, VA Boston Healthcare System, Boston, MA, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Arianna Dagliati
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Hossein Estiri
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Romain Griffier
- IAM unit, Bordeaux University Hospital, Bordeaux, France; INSERM Bordeaux Population Health ERIAS TEAM, ERIAS - Inserm U1219 BPH, Bordeaux, France
| | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark S Keller
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sara Lozano-Zahonero
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Sarah E Maidlow
- Michigan Institute for Clinical and Health Research (MICHR) Informatics, University of Michigan, Ann Arbor, MI, USA
| | - Adeline Makoudjou
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Bertrand Moal
- IAM unit, Bordeaux University Hospital, Bordeaux, France
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Danielle L Mowery
- Department of Biostatistics, Epidemiology, and Informatics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Antoine Neuraz
- Department of biomedical informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | - Kee Yuan Ngiam
- Department of Biomedical informatics, WiSDM, National University Health Systems, Singapore
| | - Gilbert S Omenn
- Depts of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, Public Health University of Michigan, Ann Arbor, MI, USA
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University Of Kansas Medical Center
| | | | - Andrea Prunotto
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | | | | | - Emily R Schriver
- Data Analytics Center, University of Pennsylvania Health System, Philadelphia, PA, USA
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | | | - Andrew M South
- Department of Pediatrics-Section of Nephrology, Brenner Children's, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Byorn W L Tan
- Department of Medicine, National University Hospital, Singapore
| | - Valentina Tibollo
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Patric Tippmann
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - William Yuan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniela Zöller
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zijian Guo
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Hong C, Xie HY, Ge WK, Yu M, Lin SN, Liu CJ. The efficacy of parecoxib in improving pain after total knee or total hip arthroplasty: Systematic review and meta-analysis. Medicine (Baltimore) 2022; 101:e30748. [PMID: 36197263 PMCID: PMC9509050 DOI: 10.1097/md.0000000000030748] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The cyclooxygenase-2 (COX-2) selective inhibitor parecoxib is widely used in the treatment of pain and inflammation. Parecoxib has been adopted for use for postoperative analgesia following a range of surgical procedures (orthopedic, general, gynecological, and dental surgery). Total knee or total hip arthroplasty (THA) surgery is mostly done in older patients, so postoperative analgesics need to be used more carefully, and the safety and efficacy of parecoxib in this type of surgery need to be further verified. The aim of this study was to investigate the effects of parecoxib on patient safety, cumulative morphine consumption and was at 24 and 48 hours in the analgesic treatment of total knee or THA for meta-analysis and systematic review, with few studies in this area so far. METHODS We searched the Online Database Cochrane Library, PubMed, Web of Science, EMBASE, and CBM (SinoMed), CNKI, VIP, WANFANG up to January 2021. According to the value of I2, the random-effect model or fixed-effect model was supposed to combine data from studies, respectively. Publication bias was assessed through funneling plot and Beggs test. Review Manager 5.3 and Stata 16.0 software were applied to perform the statistical analyses. RESULTS Eleven RCTs which involved 1690 participants were included in this study. The meta-analysis indicated parecoxib sodium could not significantly reduce the incidence of adverse events after total knee or THA compared with placebo. There was no statistical significance in incidence of nausea and vomiting. 24 hours resting VAS score was statistically significant between the group. The 48-hour resting VAS scores did not indicate a significant difference between the groups. CONCLUSION Parecoxib can reduce the incidence of adverse events after total knee or total hip surgery to some extent but cannot reduce the incidence of nausea and vomiting. Twenty-four hour postoperative analgesia is better than placebo, but 48 hours after operation analgesia is the same as placebo.
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Affiliation(s)
- Chuan Hong
- Department of Orthopedics, Ninghai First Hospital, Ningbo, Zhejiang, China
| | - Hai-Yan Xie
- Department of Pharmacy, The Third Hospital of Quzhou, Zhejiang, China
| | - Wu-Kun Ge
- Department of Pharmacy, Ninghai First Hospital, Ningbo, Zhejiang, China
- * Correspondence: Wu-Kun Ge, Department of Pharmacy, Ninghai First Hospital, No. 142, Taoyuan Middle Road, Ninghai County, Ningbo City, Zhejiang Province, China (e-mail: )
| | - Min Yu
- Department of Pharmacy, Ninghai First Hospital, Ningbo, Zhejiang, China
| | - Shuai-nan Lin
- Department of Pharmacy, Ninghai First Hospital, Ningbo, Zhejiang, China
| | - Cheng-Jiang Liu
- Department of General Medicine, Affiliated Anqing First People’s Hospital of Anhui Medical University, Anhui, China
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He Z, Guo Q, Ling Y, Hong C, Liu Y, Jin X, Thanaporn P, Zhao D, Wang L, Liu L, Yan LL. Aldehyde dehydrogenase 2 rs671 polymorphism and multiple diseases: protocol for a quantitative umbrella review of meta-analyses. Syst Rev 2022; 11:185. [PMID: 36050775 PMCID: PMC9438126 DOI: 10.1186/s13643-022-02050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/08/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The mutant allele (*2) of aldehyde dehydrogenase type 2 (ALDH2) caused by a single nucleotide variant (rs671) inhibits enzymatic activity and is associated with multiple diseases. In recent years, an explosive number of original studies and meta-analyses have been conducted to examine the associations of ALDH2 rs671 polymorphism with diseases. Due to conflicting results, the overall associations of ALDH2 rs671 polymorphism and multiple diseases remain unclear. METHODS A quantitative umbrella review will be conducted on meta-analyses of genetic association studies to examine the pleiotropic effects of ALDH2 rs671, mainly including cardio-cerebral vascular disease, diabetes mellitus, cancer, neurodegenerative disease, and alcohol-induced medical disease. A search of relevant literature according to comprehensive search strategies will be performed on studies published before July 1st, 2022 in PubMed, MEDLINE Ovid, Embase, Cochrane Database of Systematic Reviews, and Web of Science. Study selection, data extraction, methodology quality assessment, and strength of evidence assessment will be conducted by two reviewers independently and in duplicate. Included meta-analyses will be grouped by outcomes. Data conflicts and overlap between meta-analyses will be managed through updated standardized and customized methods including the calculation of CCA for study selection reference, application of Doi plots to assess small-study effects and others. Evidence from included meta-analyses will be quantitatively synthesized by overlap-corrected analyses and meta-analysis using primary studies. DISCUSSION This umbrella review is expected to generate systematic evidence on the association between ALDH2 rs671 and diseases. Specific approaches were developed to address key challenges in conducting an umbrella review, including assessment tools of methodology and evidence quality of meta-analyses, methods to manage overlap between meta-analyses, a "stop-light" plot to summarize key findings. These approaches provide applicable methods for future umbrella reviews of meta-analyses on genetic association studies. TRIAL REGISTRATION CRD42021223812.
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Affiliation(s)
- Zhengting He
- Global Health Research Center, Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Qi Guo
- Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China
| | - Yikai Ling
- Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China
| | - Chuan Hong
- Department of Biostatistics & Bioinformatics, Duke University, 2424 Erwin Road, Durham, NC, 27705, USA
| | - Yuqing Liu
- Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China
| | - Xurui Jin
- MindRank AI Ltd., Hangzhou, Zhejiang, 310000, China
| | - Porama Thanaporn
- Department of Internal Medicine, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Duan Zhao
- Global Health Research Center, Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China.,School of Public Health, Hong Kong University, 7 Sassoon Road, Pokfulam, Hong Kong
| | - Leiting Wang
- Global Health Research Center, Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China
| | - Liang Liu
- Global Health Research Center, Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China
| | - Lijing L Yan
- Global Health Research Center, Duke Kunshan University, No. 8 Duke Avenue, Kunshan, Jiangsu, 215316, China. .,Duke Global Health Institute, Duke University, 310 Trent Drive, Durham, NC, 27710, USA. .,School of Public Health, Wuhan University, No. 115 Donghu Road, Wuhan, Hubei, 430071, China. .,Institute for Global Health and Development, Peking University, No. 5 Yiheyuan Road, Beijing, 100871, China.
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Gonzalez-Cantero Á, Patel N, Hong C, Abbad-Jaime de Aragón C, Berna-Rico E, Solis J, Ballester A, Sorokin A, Teague H, Playford M, Barderas M, Fernandez-Friera L, Mehta N. 845 HDL composition, particle number and size is associated with non-calcified coronary plaque in psoriasis. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cai T, He Z, Hong C, Zhang Y, Ho YL, Honerlaw J, Geva A, Ayakulangara Panickan V, King A, Gagnon DR, Gaziano M, Cho K, Liao K, Cai T. Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review. J Biomed Inform 2022; 132:104109. [PMID: 35660521 DOI: 10.1016/j.jbi.2022.104109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/30/2022] [Accepted: 05/29/2022] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Accurately assigning phenotype information to individual patients via computational phenotyping using Electronic Health Records (EHRs) has been seen as the first step towards enabling EHRs for precision medicine research. Chart review labels annotated by clinical experts, also known as "gold standard" labels, are essential for the development and validation of computational phenotyping algorithms. However, given the complexity of EHR systems, the process of chart review is both labor intensive and time consuming. We propose a fully automated algorithm, referred to as pGUESS, to rank EHR notes according to their relevance to a given phenotype. By identifying the most relevant notes, pGUESS can greatly improve the efficiency and accuracy of chart reviews. METHOD pGUESS uses prior guided semantic similarity to measure the informativeness of a clinical note to a given phenotype. We first select candidate clinical concepts from a pool of comprehensive medical concepts using public knowledge sources and then derive the semantic embedding vector (SEV) for a reference article (SEVref) and each note (SEVnote). The algorithm scores the relevance of a note as the cosine similarity between SEVnote and SEVref. RESULTS The algorithm was validated against four sets of 200 notes that were manually annotated by clinical experts to assess their informativeness to one of three disease phenotypes. pGUESS algorithm substantially outperforms existing unsupervised approaches for classifying the relevance status with respect to both accuracy and scalability across phenotypes. Averaging over the three phenotypes, the rank correlation between the algorithm ranking and gold standard label was 0.64 for pGUESS, but only 0.47 and 0.35 for the next two best performing algorithms. pGUESS is also much more computationally scalable compared to existing algorithms. CONCLUSION pGUESS algorithm can substantially reduce the burden of chart review and holds potential in improving the efficiency and accuracy of human annotation.
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Affiliation(s)
- Tianrun Cai
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, USA; Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, USA; VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA.
| | - Zeling He
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Chuan Hong
- Department of Biostatistics & Bioinformatics, Duke University, Duke University Medical Center 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721, Durham, NC, USA
| | - Yichi Zhang
- Department of Computer Science and Statistics, University of Rhode Island, Tyler Hall, 9 Greenhouse Road, Suite 2, Kingston, RI, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA
| | | | - Alon Geva
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, USA; Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Avenue, Bader, 6th Floor, Boston, MA, USA
| | | | - Amanda King
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - David R Gagnon
- VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA; Department of Biostatistics, Boston University, School of Public Health, 801 Massachusetts Ave Crosstown Center, Boston, MA, USA
| | - Michael Gaziano
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, USA; VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA
| | - Kelly Cho
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, USA; Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, USA; VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA
| | - Katherine Liao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, USA; Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, USA; VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, USA; VA Boston Healthcare System, 150 S Huntington Ave, Boston, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
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Lin E, Tu H, Hong C. 160 Halved incidence of scrub typhus after travel restriction to confine a surge of COVID-19 in Taiwan in 2021. J Invest Dermatol 2022. [PMCID: PMC9296970 DOI: 10.1016/j.jid.2022.05.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Zhou D, Gan Z, Shi X, Patwari A, Rush E, Bonzel CL, Panickan VA, Hong C, Ho YL, Cai T, Costa L, Li X, Castro VM, Murphy SN, Brat G, Weber G, Avillach P, Gaziano JM, Cho K, Liao KP, Lu J, Cai T. Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization. J Biomed Inform 2022; 133:104147. [PMID: 35872266 DOI: 10.1016/j.jbi.2022.104147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/31/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The growing availability of electronic health records (EHR) data opens opportunities for integrative analysis of multi-institutional EHR to produce generalizable knowledge. A key barrier to such integrative analyses is the lack of semantic interoperability across different institutions due to coding differences. We propose a Multiview Incomplete Knowledge Graph Integration (MIKGI) algorithm to integrate information from multiple sources with partially overlapping EHR concept codes to enable translations between healthcare systems. METHODS The MIKGI algorithm combines knowledge graph information from (i) embeddings trained from the co-occurrence patterns of medical codes within each EHR system and (ii) semantic embeddings of the textual strings of all medical codes obtained from the Self-Aligning Pretrained BERT (SAPBERT) algorithm. Due to the heterogeneity in the coding across healthcare systems, each EHR source provides partial coverage of the available codes. MIKGI synthesizes the incomplete knowledge graphs derived from these multi-source embeddings by minimizing a spherical loss function that combines the pairwise directional similarities of embeddings computed from all available sources. MIKGI outputs harmonized semantic embedding vectors for all EHR codes, which improves the quality of the embeddings and enables direct assessment of both similarity and relatedness between any pair of codes from multiple healthcare systems. RESULTS With EHR co-occurrence data from Veteran Affairs (VA) healthcare and Mass General Brigham (MGB), MIKGI algorithm produces high quality embeddings for a variety of downstream tasks including detecting known similar or related entity pairs and mapping VA local codes to the relevant EHR codes used at MGB. Based on the cosine similarity of the MIKGI trained embeddings, the AUC was 0.918 for detecting similar entity pairs and 0.809 for detecting related pairs. For cross-institutional medical code mapping, the top 1 and top 5 accuracy were 91.0% and 97.5% when mapping medication codes at VA to RxNorm medication codes at MGB; 59.1% and 75.8% when mapping VA local laboratory codes to LOINC hierarchy. When trained with 500 labels, the lab code mapping attained top 1 and 5 accuracy at 77.7% and 87.9%. MIKGI also attained best performance in selecting VA local lab codes for desired laboratory tests and COVID-19 related features for COVID EHR studies. Compared to existing methods, MIKGI attained the most robust performance with accuracy the highest or near the highest across all tasks. CONCLUSIONS The proposed MIKGI algorithm can effectively integrate incomplete summary data from biomedical text and EHR data to generate harmonized embeddings for EHR codes for knowledge graph modeling and cross-institutional translation of EHR codes.
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Affiliation(s)
| | | | - Xu Shi
- University of Michigan, MI, USA
| | | | - Everett Rush
- Department of Energy, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Clara-Lea Bonzel
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Vidul A Panickan
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Chuan Hong
- VA Boston Healthcare System, Boston, MA, USA; Duke University, Durham, NC, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | | | - Gabriel Brat
- Harvard Medical School, Boston, MA, USA; Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | - J Michael Gaziano
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Kelly Cho
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine P Liao
- VA Boston Healthcare System, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Junwei Lu
- VA Boston Healthcare System, Boston, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tianxi Cai
- Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Zhang HG, Dagliati A, Shakeri Hossein Abad Z, Xiong X, Bonzel CL, Xia Z, Tan BWQ, Avillach P, Brat GA, Hong C, Morris M, Visweswaran S, Patel LP, Gutiérrez-Sacristán A, Hanauer DA, Holmes JH, Samayamuthu MJ, Bourgeois FT, L'Yi S, Maidlow SE, Moal B, Murphy SN, Strasser ZH, Neuraz A, Ngiam KY, Loh NHW, Omenn GS, Prunotto A, Dalvin LA, Klann JG, Schubert P, Vidorreta FJS, Benoit V, Verdy G, Kavuluru R, Estiri H, Luo Y, Malovini A, Tibollo V, Bellazzi R, Cho K, Ho YL, Tan ALM, Tan BWL, Gehlenborg N, Lozano-Zahonero S, Jouhet V, Chiovato L, Aronow BJ, Toh EMS, Wong WGS, Pizzimenti S, Wagholikar KB, Bucalo M, Cai T, South AM, Kohane IS, Weber GM. International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. NPJ Digit Med 2022; 5:81. [PMID: 35768548 PMCID: PMC9242995 DOI: 10.1038/s41746-022-00623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
The risk profiles of post-acute sequelae of COVID-19 (PASC) have not been well characterized in multi-national settings with appropriate controls. We leveraged electronic health record (EHR) data from 277 international hospitals representing 414,602 patients with COVID-19, 2.3 million control patients without COVID-19 in the inpatient and outpatient settings, and over 221 million diagnosis codes to systematically identify new-onset conditions enriched among patients with COVID-19 during the post-acute period. Compared to inpatient controls, inpatient COVID-19 cases were at significant risk for angina pectoris (RR 1.30, 95% CI 1.09–1.55), heart failure (RR 1.22, 95% CI 1.10–1.35), cognitive dysfunctions (RR 1.18, 95% CI 1.07–1.31), and fatigue (RR 1.18, 95% CI 1.07–1.30). Relative to outpatient controls, outpatient COVID-19 cases were at risk for pulmonary embolism (RR 2.10, 95% CI 1.58–2.76), venous embolism (RR 1.34, 95% CI 1.17–1.54), atrial fibrillation (RR 1.30, 95% CI 1.13–1.50), type 2 diabetes (RR 1.26, 95% CI 1.16–1.36) and vitamin D deficiency (RR 1.19, 95% CI 1.09–1.30). Outpatient COVID-19 cases were also at risk for loss of smell and taste (RR 2.42, 95% CI 1.90–3.06), inflammatory neuropathy (RR 1.66, 95% CI 1.21–2.27), and cognitive dysfunction (RR 1.18, 95% CI 1.04–1.33). The incidence of post-acute cardiovascular and pulmonary conditions decreased across time among inpatient cases while the incidence of cardiovascular, digestive, and metabolic conditions increased among outpatient cases. Our study, based on a federated international network, systematically identified robust conditions associated with PASC compared to control groups, underscoring the multifaceted cardiovascular and neurological phenotype profiles of PASC.
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Affiliation(s)
- Harrison G Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Arianna Dagliati
- Department of Electrical Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | | | - Xin Xiong
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryce W Q Tan
- Department of Medicine, National University Hospital, Singapore, Singapore
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University Of Kansas Medical Center, Kansas City, MO, USA
| | | | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sarah E Maidlow
- Michigan Institute for Clinical and Health Research (MICHR) Informatics, University of Michigan, Ann Arbor, MI, USA
| | - Bertrand Moal
- IAM unit, Bordeaux University Hospital, Bordeaux, France
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Antoine Neuraz
- Department of biomedical informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | - Kee Yuan Ngiam
- Department of Biomedical informatics, WiSDM, National University Health Systems Singapore, Singapore, Singapore
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health Systems Singapore, Singapore, Singapore
| | - Gilbert S Omenn
- Department of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Prunotto
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Lauren A Dalvin
- Department of Ophthalmology, Mayo Clinic, Rochester, NY, USA
| | - Jeffrey G Klann
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | | | - Vincent Benoit
- IT Department, Innovation & Data, APHP Greater Paris University Hospital, Paris, France
| | | | - Ramakanth Kavuluru
- Division of Biomedical Informatics (Department of Internal Medicine), University of Kentucky, Lexington, KY, USA
| | - Hossein Estiri
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA.,Population Health and Data Science, VA Boston Healthcare System, Boston, MA, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Byorn W L Tan
- Department of Medicine, National University Hospital, Singapore, Singapore
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sara Lozano-Zahonero
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Vianney Jouhet
- IAM unit, INSERM Bordeaux Population Health ERIAS TEAM, Bordeaux University Hospital / ERIAS - Inserm, U1219 BPH, Bordeaux, France
| | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Emma M S Toh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wei Gen Scott Wong
- Department of Medicine, National University Health Systems Singapore, Singapore, Singapore
| | - Sara Pizzimenti
- Scientific Direction, IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | | | - Mauro Bucalo
- BIOMERIS (BIOMedical Research Informatics Solutions), Pavia, Italy
| | | | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andrew M South
- Department of Pediatrics-Section of Nephrology, Brenner Children's, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Hong C, Zhang HG, L'Yi S, Weber G, Avillach P, Tan BWQ, Gutiérrez-Sacristán A, Bonzel CL, Palmer NP, Malovini A, Tibollo V, Luo Y, Hutch MR, Liu M, Bourgeois F, Bellazzi R, Chiovato L, Sanz Vidorreta FJ, Le TT, Wang X, Yuan W, Neuraz A, Benoit V, Moal B, Morris M, Hanauer DA, Maidlow S, Wagholikar K, Murphy S, Estiri H, Makoudjou A, Tippmann P, Klann J, Follett RW, Gehlenborg N, Omenn GS, Xia Z, Dagliati A, Visweswaran S, Patel LP, Mowery DL, Schriver ER, Samayamuthu MJ, Kavuluru R, Lozano-Zahonero S, Zöller D, Tan ALM, Tan BWL, Ngiam KY, Holmes JH, Schubert P, Cho K, Ho YL, Beaulieu-Jones BK, Pedrera-Jiménez M, García-Barrio N, Serrano-Balazote P, Kohane I, South A, Brat GA, Cai T. Changes in laboratory value improvement and mortality rates over the course of the pandemic: an international retrospective cohort study of hospitalised patients infected with SARS-CoV-2. BMJ Open 2022; 12:e057725. [PMID: 35738646 PMCID: PMC9226470 DOI: 10.1136/bmjopen-2021-057725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/12/2022] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE To assess changes in international mortality rates and laboratory recovery rates during hospitalisation for patients hospitalised with SARS-CoV-2 between the first wave (1 March to 30 June 2020) and the second wave (1 July 2020 to 31 January 2021) of the COVID-19 pandemic. DESIGN, SETTING AND PARTICIPANTS This is a retrospective cohort study of 83 178 hospitalised patients admitted between 7 days before or 14 days after PCR-confirmed SARS-CoV-2 infection within the Consortium for Clinical Characterization of COVID-19 by Electronic Health Record, an international multihealthcare system collaborative of 288 hospitals in the USA and Europe. The laboratory recovery rates and mortality rates over time were compared between the two waves of the pandemic. PRIMARY AND SECONDARY OUTCOME MEASURES The primary outcome was all-cause mortality rate within 28 days after hospitalisation stratified by predicted low, medium and high mortality risk at baseline. The secondary outcome was the average rate of change in laboratory values during the first week of hospitalisation. RESULTS Baseline Charlson Comorbidity Index and laboratory values at admission were not significantly different between the first and second waves. The improvement in laboratory values over time was faster in the second wave compared with the first. The average C reactive protein rate of change was -4.72 mg/dL vs -4.14 mg/dL per day (p=0.05). The mortality rates within each risk category significantly decreased over time, with the most substantial decrease in the high-risk group (42.3% in March-April 2020 vs 30.8% in November 2020 to January 2021, p<0.001) and a moderate decrease in the intermediate-risk group (21.5% in March-April 2020 vs 14.3% in November 2020 to January 2021, p<0.001). CONCLUSIONS Admission profiles of patients hospitalised with SARS-CoV-2 infection did not differ greatly between the first and second waves of the pandemic, but there were notable differences in laboratory improvement rates during hospitalisation. Mortality risks among patients with similar risk profiles decreased over the course of the pandemic. The improvement in laboratory values and mortality risk was consistent across multiple countries.
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Affiliation(s)
- Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Harrison G Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Griffin Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Bryce W Q Tan
- Department of Medicine, National University Hospital, Singapore
| | | | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathan P Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Lombardia, Italy
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Lombardia, Italy
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Evanston, Illinois, USA
| | - Meghan R Hutch
- Department of Preventive Medicine, Northwestern University, Evanston, Illinois, USA
| | - Molei Liu
- Department of Biostatistics, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Florence Bourgeois
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Lombardia, Italy
| | | | - Trang T Le
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xuan Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - William Yuan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Antoine Neuraz
- Department of Biomedical Informatics, Hopital Universitaire Necker-Enfants Malades, Paris, Île-de-France, France
| | - Vincent Benoit
- IT department, Innovation & Data, APHP Greater Paris University Hospital, Paris, France
| | - Bertrand Moal
- IAM unit, Bordeaux University Hospital, Bordeaux, France
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sarah Maidlow
- MICHR Informatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Kavishwar Wagholikar
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shawn Murphy
- Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hossein Estiri
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Adeline Makoudjou
- Institute of Medical Biometry and Statistics, University of Freiburg Faculty of Medicine, Freiburg, Baden-Württemberg, Germany
| | - Patric Tippmann
- Institute of Medical Biometry and Statistics, Medical Center-University of Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Jeffery Klann
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert W Follett
- Department of Medicine, David Geffen School of Medicine, Los Angeles, California, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gilbert S Omenn
- Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Arianna Dagliati
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Kansas, USA
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Danielle L Mowery
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily R Schriver
- Data Analytics Center, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA
| | | | - Ramakanth Kavuluru
- Institute for Biomedical Informatics, University of Kentucky, Lexington, Kentucky, USA
| | - Sara Lozano-Zahonero
- Institute of Medical Biometry and Statistics, University of Freiburg Faculty of Medicine, Freiburg, Baden-Württemberg, Germany
| | - Daniela Zöller
- Institute of Medical Biometry and Statistics, University of Freiburg Faculty of Medicine, Freiburg, Baden-Württemberg, Germany
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Byorn W L Tan
- Department of Medicine, National University Hospital, Singapore
| | - Kee Yuan Ngiam
- Department of Surgery, National University Hospital, Singapore
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | | | - Miguel Pedrera-Jiménez
- Health Informatics, Hospital Universitario 12 de Octubre, Madrid, Comunidad de Madrid, Spain
| | - Noelia García-Barrio
- Health Informatics, Hospital Universitario 12 de Octubre, Madrid, Comunidad de Madrid, Spain
| | - Pablo Serrano-Balazote
- Health Informatics, Hospital Universitario 12 de Octubre, Madrid, Comunidad de Madrid, Spain
| | - Isaac Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew South
- Department of Pediatrics, Section of Nephrology, Wake Forest University, Winston Salem, North Carolina, USA
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - T Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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45
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Weber GM, Hong C, Xia Z, Palmer NP, Avillach P, L'Yi S, Keller MS, Murphy SN, Gutiérrez-Sacristán A, Bonzel CL, Serret-Larmande A, Neuraz A, Omenn GS, Visweswaran S, Klann JG, South AM, Loh NHW, Cannataro M, Beaulieu-Jones BK, Bellazzi R, Agapito G, Alessiani M, Aronow BJ, Bell DS, Benoit V, Bourgeois FT, Chiovato L, Cho K, Dagliati A, DuVall SL, Barrio NG, Hanauer DA, Ho YL, Holmes JH, Issitt RW, Liu M, Luo Y, Lynch KE, Maidlow SE, Malovini A, Mandl KD, Mao C, Matheny ME, Moore JH, Morris JS, Morris M, Mowery DL, Ngiam KY, Patel LP, Pedrera-Jimenez M, Ramoni RB, Schriver ER, Schubert P, Balazote PS, Spiridou A, Tan ALM, Tan BWL, Tibollo V, Torti C, Trecarichi EM, Wang X, Kohane IS, Cai T, Brat GA. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. NPJ Digit Med 2022; 5:74. [PMID: 35697747 PMCID: PMC9192605 DOI: 10.1038/s41746-022-00601-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/11/2022] [Indexed: 01/08/2023] Open
Abstract
Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach.
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Affiliation(s)
- Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, USA
| | - Nathan P Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Mark S Keller
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, USA
| | | | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Arnaud Serret-Larmande
- Department of biomedical informatics, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Antoine Neuraz
- Department of biomedical informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | - Gilbert S Omenn
- Department of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA
| | - Jeffrey G Klann
- Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Andrew M South
- Department of Pediatrics-Section of Nephrology, Brenner Children's Hospital, Wake Forest School of Medicine, Winston Salem, USA
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health System, Singapore, Singapore, Singapore
| | - Mario Cannataro
- Department of Medical and Surgical Sciences, Data Analytics Research Center, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | | | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy, Pavia, Italy
| | - Giuseppe Agapito
- Department of Legal, Economic and Social Sciences, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | - Mario Alessiani
- Department of Surgery, ASST Pavia, Lombardia Region Health System, Pavia, Italy
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, USA
| | - Douglas S Bell
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Vincent Benoit
- IT department, Innovation & Data, APHP Greater Paris University Hospital, Paris, France
| | | | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | - Arianna Dagliati
- Department of Electrical Computer and Biomedical Engineering, University of Pavia, Italy, Pavia, Italy
| | - Scott L DuVall
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, USA
| | | | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan, Ann Arbor, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Richard W Issitt
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, UK, London, UK
| | - Molei Liu
- Department of Biostatistics, Harvard School of Public Health, Boston, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, USA
| | - Kristine E Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, USA
| | - Sarah E Maidlow
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, USA
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, Boston, USA
| | - Chengsheng Mao
- Department of Preventive Medicine, Northwestern University, Chicago, USA
| | - Michael E Matheny
- VA Informatics and Computing Infrastructure, Tennessee Valley Healthcare System Veterans Affairs Medical Center, Nashville, USA
| | - Jason H Moore
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Jeffrey S Morris
- Department of Biostatistics, Epidemiology, and Biostatistics, University of Pennysylvania Perelman School of Medicine, Philadelphia, USA
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA
| | - Danielle L Mowery
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Kee Yuan Ngiam
- Department of Biomedical informatics, WiSDM, National University Health Systems Singapore, Singapore, Singapore
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, Kansas City, USA
| | | | - Rachel B Ramoni
- Office of Research and Development, Department of Veterans Affairs, Washington, DC, USA
| | - Emily R Schriver
- Data Analytics Center, University of Pennsylvania Health System, Philadelphia, USA
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | | | - Anastasia Spiridou
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, UK, London, UK
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Byorn W L Tan
- Department of Medicine, National University Hospital, Singapore, Singapore, Singapore
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Infectious and Tropical Disease Unit, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | - Enrico M Trecarichi
- Department of Medical and Surgical Sciences, Infectious and Tropical Disease Unit, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | - Xuan Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA.
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA.
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Hong C, Fang L, Yeo YW, Lee HY, Low A, Leung YY. AB0932 Patient and learner experience in a new set up of a rheum-derm combined care model for psoriatic arthritis. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.1954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundPsoriasis (PsO) and musculoskeletal manifestations are common among patients with psoriatic arthritis (PsA). A shared-care model between rheumatologists and dermatologists has been advocated to promote early diagnosis and improve management care. Data from Asia is scanty. Patients’ and learners’ experience of shared-care models are seldom explored.ObjectivesWe described the set-up of a new shared-cared PsA-PsO clinic incorporating service, education and research between rheumatologist and dermatologist for PsA. We describe the patients’ and learners’ experience of this shared-care model.MethodsA combined care clinic was newly set up in 2019. Referrals were internal through either specialty. Each patient was first seen by a trainee, followed by both a dermatologist and rheumatologist simultaneously in the same consultation room. We collected patients’ and learners’ experience through self-administered survey.ResultsFrom May 2019 to January 2020, data from 44 visits (55% new referrals, 45% follow-up) from 28 patients were captured in the PsA-PsO clinic. 50% of cases were referred from either specialty. 34% were referred for diagnostic doubts, 66% were for therapeutic issues. 61% of patients continued follow-up in the PsA-PsO clinic, and 39% discharged back to respective care. From patients’ experience rated on scale from 0-10, median (interquartile range, IQR) rating of the care was 8 (7, 8). 69.2% and 96% of patients would recommend the care to others. Free text comments included enhanced convenience, time saving, and having both specialties input on management. From 20 learners (3 medial students, 12 residents, 4 senior residents and one scientist), 95% reported extremely or very beneficial to training, 77.8% reported improved confidence in care for PsA and/or PsO patients. The PsA-PsO clinic was temporally suspended during the Covid-19 viral pandemic since February 2020 due to lack of manpower and not fulfilling the spacing out requirement for infectious control. The service was resumed gradually from May 2021.ConclusionDespite challenges, we report the setup of a new care model between dermatologists and rheumatologists for care of patients with psoriatic disease. The care model was well received by patients. Learners from various levels reported benefit from the learning experience.Disclosure of InterestsCassandra Hong: None declared, Liwen Fang: None declared, Yi-Wei Yeo: None declared, Haur Yueh Lee: None declared, Andrea Low: None declared, Ying Ying Leung Speakers bureau: Received honorarium from Abbvie, DKSH, Janssen, Novartis and Pfizer.
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Tan YK, Hong C, LI H, Allen JC, Thumboo J. AB1328 A FEASIBILITY STUDY ON A NOVEL COMBINED THERMAL IMAGING AND CLINICAL JOINT ASSESSMENT APPROACH USING ULTRASOUND DETECTED JOINT INFLAMMATION OUTCOMES IN RHEUMATOID ARTHRITIS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundThermal imaging (TI) is a portable, low cost imaging tool with high feasibility for use. Clinical joint assessment.Is routinely performed in rheumatoid arthritis (RA) patient care.ObjectivesTo assess a combined TI and clinical joint assessment (CTCA) approach in comparison with TI alone using ultrasound (US) detected joint inflammation outcomes as a gold standard.MethodsBilateral (BL) hand and wrist (22 joint sites) were assessed in this cross-sectional study. For TI (performed in a draft free room with a controlled temperature of around 22°C), the adjusted maximum (Tmax), minimum (Tmin) and average (Tavg) temperatures were derived by subtracting a control temperature (lowest Tmin at the joints per subject) from the Tmax, Tmin and Tavg per joint. US power Doppler (PD) and greyscale (GS) joint inflammation were graded semi-quantitatively (0-3) using validated scoring methods. Joint swelling and tenderness were graded as yes = 1 or no = 0. To increase the relative weightage of CTCA-MAX, CTCA-MIN and CTCA-AVG on the CTCA scores, if the joint was swollen and/or tender, the adjusted Tmax, Tmin and Tavg at each joint were multiplied by a factor of 2; otherwise, they remained unchanged. Receiver operating characteristic (ROC) analysis assessed the performance of TI and CTCA in identifying joints with US PD score > 1 and GS score > 1. A parameter was selected as a univariate predictor if statistically significant (P < 0.05) with area under the ROC curve (AUC) ≥ 0.70.ResultsThis study included 814 joints from 37 RA patients (mean disease duration, 30.9 months; mean DAS28, 4.43). For both TI and CTCA, out of the 22 joints sites, 3 joint sites were evaluated for PD score > 1 and 14 joint sites for GS score > 1; the remaining joint sites had AUC results unavailable due to small number of outcomes. For TI (Table 1), 3 joint sites had ≥ 1 predictive parameter for either PD score > 1 and/or GS score > 1 as follows: left (L) wrist and right (R) MCPJ 1, AUCs (0.813 to 0.897) for PD score > 1; L wrist and R MCPJs 1 and 3, AUCs (0.808 to 0.947) for GS score > 1. For CTCA (Table 1), 6 joint sites had ≥ 1 predictive parameter for either PD score > 1 and/or GS score > 1 as follows: BL wrists, AUCs (0.726 to 0.899) for PD score > 1; BL wrists, MCPJs 2 and 3, AUCs (0.739 to 0.931) for GS score > 1.Table 1.Identifying joints with ultrasound PD score >1 & GS score >1Thermal Imaging aloneCTCAJointUScriterionParameter (AUC ≥ 0.7& P <0.05)AUC(95% CI)Cut-offJointUScriterionParameter (AUC ≥ 0.7& P <0.05)AUC (95% CI)Cut-offLRLRLPD score >1Adjusted Tmax**0.841 (0.691, 0.992)4.7L & RPD score >1CTCA-MAX**0.899 (0.797, 1)**0.776 (0.578, .973)9.47.3WristAdjusted Tmin**0.813 (0.669, 0.958)2.85WristCTCA-MIN**0.861 (0.735, 0.987)*0.7265.74.45(0.526, 0.926)Adjusted Tavg**0.849 (0.714, 0.985)3.9CTCA-AVG**0.889 (0.781, 0.997)*0.7617.35.95(0.563, 0.959)GS score >1Adjusted Tmax**0.827 (0.687, 0.966)4.7GS score >1CTCA-MAX**0.918 (0.833, 1)**0.81387.3(0.632, 0.994)Adjusted Tmin**0.808 (0.67, 0.947)2.85CTCA-MIN**0.873 (0.761, 0.986)**0.7664.44.45(0.581, 0.951)Adjusted Tavg**0.837 (0.707, 0.967)3.9CTCA-AVG**0.913**0.8025.55.95(0.824, 1)(0.62, 0.985)RPD score >1Adjusted Tmax*0.897 (0.726, 1)5.7L & RGS score >1CTCA-MAX-*0.758-9.8(0.494, 1)MCPJ 1MCPJ 2GS score >1Adjusted Tmax*0.936 (0.813, 1)7.2CTCA-MIN*0.902*0.7392.753.9(0.775, 1)(0.443, 1)Adjusted Tmin*0.932 (0.793, 1)3.95CTCA-AVG*0.931**0.7634.75.5(0.835, 1)(0.474, 1)Adjusted Tavg*0.947 (0.868, 1)4.9L & RGS score >1CTCA-MAX*0.914*0.8736.3512.2(0.735, 1)(0.617, 1)RGS score >1Adjusted Tmax*0.922 (0.76, 1)4.6MCPJ 3CTCA-MIN-*0.902-3.15(0.75, 1)MCPJ 3CTCA-AVG-*0.902-4.1(0.728, 1)Corresponding P-value: statistically significance at *P <0.05, **P<0.01.ConclusionA novel CTCA approach helps discriminate the severity of US detected joint inflammation in RA at more joint sites when compared to TI alone; this includes the commonly affected BL wrists, MCPJs 2 and 3. Further validation work in a larger RA cohort will be required.Disclosure of InterestsNone declared
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Li R, Huang C, Hong C, Wang J, Li Q, Hu C, Cui H, Dong Z, Zhu H, Liu L, Xiao L. [Impact of nonsteroidal anti-inflammatory drugs on efficacy of anti-PD-1 therapy for primary liver cancer]. Nan Fang Yi Ke Da Xue Xue Bao 2022; 42:698-704. [PMID: 35673913 DOI: 10.12122/j.issn.1673-4254.2022.05.10] [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] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To assess the impact of nonsteroidal anti-inflammatory drugs (NSAIDs) on clinical outcomes of patients receiving anti-PD-1 immunotherapy for hepatocellular carcinoma. METHODS We conducted a retrospective study among 215 patients with primary liver cancer receiving immunotherapy between June, 2018 and October, 2020. The patients with balanced baseline characteristics were selected based on propensity matching scores, and among them 33 patients who used NSAIDs were matched at the ratio of 1∶3 with 78 patients who did not use NSAIDs. We compared the overall survival (OS), progression-free survival (PFS), and disease control rate (DCR) between the two groups. RESULTS There was no significant difference in OS between the patients using NSAIDs (29.7%) and those who did not use NSAIDs (70.2%). Univariate and multivariate analyses did not show an a correlation of NSAIDs use with DCR (univariate analysis: OR=0.602, 95% CI: 0.299-1.213, P=0.156; multivariate analysis: OR=0.693, 95% CI: 0.330-1.458, P=0.334), PFS (univariate analysis: HR=1.230, 95% CI: 0.789-1.916, P=0.361; multivariate analysis: HR=1.151, 95% CI: 0.732-1.810, P=9.544), or OS (univariate analysis: HR=0.552, 95% CI: 0.208-1.463, P=0.232; multivariate analysis: HR=1.085, 95% CI: 0.685-1.717, P=0.729). CONCLUSION Our results show no favorable effect of NSAIDs on the efficacy of immunotherapy in patients with advanced primary liver cancer, but this finding still needs to be verified by future prospective studies of large cohorts.
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Affiliation(s)
- R Li
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - C Huang
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - C Hong
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - J Wang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Q Li
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - C Hu
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Infectious Diseases, Guangzhou First People's Hospital, Guangzhou 510180, China
| | - H Cui
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Z Dong
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - H Zhu
- Department of Oncology, First Affiliated Hospital of University of South China, Hengyang 421001, China
| | - L Liu
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - L Xiao
- Big Data Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Luo C, Marks‐Anglin A, Duan R, Lin L, Hong C, Chu H, Chen Y. Accounting for publication bias using a bivariate trim and fill meta‐analysis procedure. Stat Med 2022; 41:3466-3478. [DOI: 10.1002/sim.9428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 03/31/2022] [Accepted: 04/22/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Chongliang Luo
- Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Philadelphia Pennsylvania USA
- Division of Public Health Sciences Washington University in St. Louis St Louis Missouri USA
| | - Arielle Marks‐Anglin
- Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Philadelphia Pennsylvania USA
| | - Rui Duan
- Department of Biostatistics Harvard T.H. Chan School of Public Health Boston Massachusetts USA
| | - Lifeng Lin
- Department of Statistics Florida State University Tallahassee Florida USA
| | - Chuan Hong
- Department of Biostatistics & Bioinformatics Duke University Durham North Carolina USA
| | - Haitao Chu
- Division of Biostatistics, School of Public Health University of Minnesota Minneapolis Minnesota USA
- Statistical Research and Innovation, Global Biometrics and Data Management Pfizer Inc. New York New York USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Philadelphia Pennsylvania USA
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50
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Link NB, Huang S, Cai T, Sun J, Dahal K, Costa L, Cho K, Liao K, Cai T, Hong C. Binary acronym disambiguation in clinical notes from electronic health records with an application in computational phenotyping. Int J Med Inform 2022; 162:104753. [PMID: 35405530 DOI: 10.1016/j.ijmedinf.2022.104753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/18/2022] [Revised: 03/11/2022] [Accepted: 03/27/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The use of electronic health records (EHR) systems has grown over the past decade, and with it, the need to extract information from unstructured clinical narratives. Clinical notes, however, frequently contain acronyms with several potential senses (meanings) and traditional natural language processing (NLP) techniques cannot differentiate between these senses. In this study we introduce a semi-supervised method for binary acronym disambiguation, the task of classifying a target sense for acronyms in the clinical EHR notes. METHODS We developed a semi-supervised ensemble machine learning (CASEml) algorithm to automatically identify when an acronym means a target sense by leveraging semantic embeddings, visit-level text and billing information. The algorithm was validated using note data from the Veterans Affairs hospital system to classify the meaning of three acronyms: RA, MS, and MI. We compared the performance of CASEml against another standard semi-supervised method and a baseline metric selecting the most frequent acronym sense. Along with evaluating the performance of these methods for specific instances of acronyms, we evaluated the impact of acronym disambiguation on NLP-driven phenotyping of rheumatoid arthritis. RESULTS CASEml achieved accuracies of 0.947, 0.911, and 0.706 for RA, MS, and MI, respectively, higher than a standard baseline metric and (on average) higher than a state-of-the-art semi-supervised method. As well, we demonstrated that applying CASEml to medical notes improves the AUC of a phenotype algorithm for rheumatoid arthritis. CONCLUSION CASEml is a novel method that accurately disambiguates acronyms in clinical notes and has advantages over commonly used supervised and semi-supervised machine learning approaches. In addition, CASEml improves the performance of NLP tasks that rely on ambiguous acronyms, such as phenotyping.
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Affiliation(s)
- Nicholas B Link
- VA Boston Healthcare System, Boston, MA, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - Sicong Huang
- VA Boston Healthcare System, Boston, MA, United States; Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, United States
| | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA, United States; Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, United States
| | - Jiehuan Sun
- VA Boston Healthcare System, Boston, MA, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Kumar Dahal
- VA Boston Healthcare System, Boston, MA, United States; Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, United States
| | - Lauren Costa
- VA Boston Healthcare System, Boston, MA, United States
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, United States
| | - Katherine Liao
- VA Boston Healthcare System, Boston, MA, United States; Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, United States
| | - Tianxi Cai
- VA Boston Healthcare System, Boston, MA, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Chuan Hong
- VA Boston Healthcare System, Boston, MA, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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