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Jafari E, Blackman MH, Karnes JH, Van Driest SL, Crawford DC, Choi L, McDonough CW. Using electronic health records for clinical pharmacology research: Challenges and considerations. Clin Transl Sci 2024; 17:e13871. [PMID: 38943244 PMCID: PMC11213823 DOI: 10.1111/cts.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 07/01/2024] Open
Abstract
Electronic health records (EHRs) contain a vast array of phenotypic data on large numbers of individuals, often collected over decades. Due to the wealth of information, EHR data have emerged as a powerful resource to make first discoveries and identify disparities in our healthcare system. While the number of EHR-based studies has exploded in recent years, most of these studies are directed at associations with disease rather than pharmacotherapeutic outcomes, such as drug response or adverse drug reactions. This is largely due to challenges specific to deriving drug-related phenotypes from the EHR. There is great potential for EHR-based discovery in clinical pharmacology research, and there is a critical need to address specific challenges related to accurate and reproducible derivation of drug-related phenotypes from the EHR. This review provides a detailed evaluation of challenges and considerations for deriving drug-related data from EHRs. We provide an examination of EHR-based computable phenotypes and discuss cutting-edge approaches to map medication information for clinical pharmacology research, including medication-based computable phenotypes and natural language processing. We also discuss additional considerations such as data structure, heterogeneity and missing data, rare phenotypes, and diversity within the EHR. By further understanding the complexities associated with conducting clinical pharmacology research using EHR-based data, investigators will be better equipped to design thoughtful studies with more reproducible results. Progress in utilizing EHRs for clinical pharmacology research should lead to significant advances in our ability to understand differential drug response and predict adverse drug reactions.
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Affiliation(s)
- Eissa Jafari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of PharmacyUniversity of FloridaGainesvilleFloridaUSA
- Department of Pharmacy Practice, College of PharmacyJazan UniversityJazanSaudi Arabia
| | - Marisa H. Blackman
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Jason H. Karnes
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Sara L. Van Driest
- Department of PediatricsVanderbilt University Medical Center (VUMC)NashvilleTennesseeUSA
- Present address:
All of US Research Program, National Institutes of HealthBethesdaMarylandUSA
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational BiologyCase Western Reserve UniversityClevelandOhioUSA
- Department of Genetics and Genome Sciences, Cleveland Institute for Computational BiologyCase Western Reserve UniversityClevelandOhioUSA
| | - Leena Choi
- Department of Biostatistics and Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Caitrin W. McDonough
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of PharmacyUniversity of FloridaGainesvilleFloridaUSA
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2
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Mosley JD, Shelley JP, Dickson AL, Zanussi J, Daniel LL, Zheng NS, Bastarache L, Wei WQ, Shi M, Jarvik GP, Rosenthal EA, Khan A, Sherafati A, Kullo IJ, Walunas TL, Glessner J, Hakonarson H, Cox NJ, Roden DM, Frangakis SG, Vanderwerff B, Stein CM, Van Driest SL, Borinstein SC, Shu XO, Zawistowski M, Chung CP, Kawai VK. Clinical associations with a polygenic predisposition to benign lower white blood cell counts. Nat Commun 2024; 15:3384. [PMID: 38649760 PMCID: PMC11035609 DOI: 10.1038/s41467-024-47804-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Polygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is uncharacterized. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio = 0.55 per standard deviation increase in PGSWBC [95%CI, 0.30-0.94], p = 0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n = 1724, hazard ratio [HR] = 0.78 [0.69-0.88], p = 4.0 × 10-5) or immunosuppressant (n = 354, HR = 0.61 [0.38-0.99], p = 0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n = 1,466, HR = 0.62 [0.44-0.87], p = 0.006). Collectively, these findings suggest that there are genetically predisposed individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
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Affiliation(s)
- Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - John P Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacy Zanussi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura L Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil S Zheng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Theresa L Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy J Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephan G Frangakis
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Brett Vanderwerff
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott C Borinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Vivian K Kawai
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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3
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Mosley JD, Shelley JP, Dickson AL, Zanussi J, Daniel LL, Zheng NS, Bastarache L, Wei WQ, Shi M, Jarvik GP, Rosenthal EA, Khan A, Sherafati A, Kullo IJ, Walunas TL, Glessner J, Hakonarson H, Cox NJ, Roden DM, Frangakis SG, Vanderwerff B, Stein CM, Van Driest SL, Borinstein SC, Shu XO, Zawistowski M, Chung CP, Kawai VK. Clinical consequences of a polygenic predisposition to benign lower white blood cell counts: Consequences of benign WBC count genetics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.20.23294331. [PMID: 37662324 PMCID: PMC10473820 DOI: 10.1101/2023.08.20.23294331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Polygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is undefined. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio=0.55 per standard deviation increase in PGSWBC [95%CI, 0.30 - 0.94], p=0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n=1,724, hazard ratio [HR]=0.78 [0.69 - 0.88], p=4.0×10-5) or immunosuppressant (n=354, HR=0.61 [0.38 - 0.99], p=0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n=1,466, HR=0.62 [0.44 - 0.87], p=0.006). Collectively, these findings suggest that a WBC count polygenic score identifies individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
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Affiliation(s)
- Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John P. Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L. Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacy Zanussi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura L. Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil S. Zheng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P. Jarvik
- Department of Genome Sciences, University of Washington Medical Center, Seattle WA, USA
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle WA, USA
| | - Elisabeth A. Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle WA, USA
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester MN USA
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester MN USA
| | - Theresa L. Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joe Glessner
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy J. Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephan G. Frangakis
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brett Vanderwerff
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - C. Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L. Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott C. Borinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Cecilia P. Chung
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vivian K. Kawai
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Bagheri M, Chung CP, Dickson AL, Van Driest SL, Borinstein SC, Mosley JD. White blood cell ranges and frequency of neutropenia by Duffy genotype status. Blood Adv 2023; 7:406-409. [PMID: 35895516 PMCID: PMC9979714 DOI: 10.1182/bloodadvances.2022007680] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/02/2023] Open
Affiliation(s)
- Minoo Bagheri
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Cecilia P. Chung
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Alyson L. Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Sara L. Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Scott C. Borinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
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Chung CP, Karakoc G, Liu G, Gamboa JL, Mosley JD, Cox NJ, Stein CM, Kawai V. Ancestry, ACKR1 and leucopenia in patients with systemic lupus erythematosus. Lupus Sci Med 2022; 9:e000790. [PMID: 36376015 PMCID: PMC9664301 DOI: 10.1136/lupus-2022-000790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVE SLE is more prevalent in populations of African (AA) than European ancestry (EA) and leucopenia is common. A homozygous variant in ACKR1 (rs2814778-CC) is associated with lower white cell counts; the variant is common in AA but not EA populations. We hypothesised that in SLE: (1) leucopenia is more frequent in patients of AA than EA, and (2) the ACKR1-CC genotype accounts for the higher frequency of leucopenia in AA patients. METHODS We performed a retrospective cohort study in patients with SLE at a tertiary care system. Ancestry was defined by genetic principal components. We compared the rate of leucopenia, thrombocytopenia and anaemia between (a) EA and AA patients, and (b) ACKR1-CT/TT and CC genotype in AA patients. RESULTS The cohort included 574 patients of EA and 190 of AA; ACKR1-CC genotype was common in AA (70%) but not EA (0%) patients. Rates of leucopenia for ancestry and genotype were AA 60.0% vs EA 36.8 % (p=1.9E-08); CC 67.7% vs CT/TT 42.1% (p=9.8E-04). The rate of leucopenia did not differ by ancestry comparing EA patients versus AA with CT/TT genotype (p=0.59). Thrombocytopenia (22.2% vs 13.2%, p=0.004) and anaemia (88.4% vs 66.2%, p=3.7E-09) were more frequent in AA patients but were not associated with ACKR1 genotype (p=0.82 and p=0.84, respectively). CONCLUSIONS SLE of AA had higher rates of anaemia, leucopenia, and thrombocytopenia than those of EA; only the difference in leucopenia was explained by ACKR1-CC genotype. This genotype could affect clinical practice.
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Affiliation(s)
- Cecilia P Chung
- Division of Rheumatology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Tennessee Valley Healthcare System - Nashville Campus, Nashville, Tennessee, USA
| | - Gul Karakoc
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ge Liu
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jorge L Gamboa
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jonathan D Mosley
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - C Michael Stein
- Division of Rheumatology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vivian Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Uric Acid to High-Density Lipoprotein Cholesterol Ratio is a Novel Marker to Predict Functionally Significant Coronary Artery Stenosis. J Interv Cardiol 2022; 2022:9057832. [PMID: 36311279 PMCID: PMC9584719 DOI: 10.1155/2022/9057832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/23/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background Intermediate coronary stenosis (ICS) is defined as a visually estimated percentage of diameter stenosis ranging between 40% and 70% by conventional coronary angiography (CAG). Whether to perform percutaneous coronary intervention (PCI) for these lesions is a challenge in clinical practice. The fractional flow reserve (FFR) can guide treatment by determining the functional significance of ICS. Studies have shown that some clinical indicators can be used to predict FFR. However, there is little research on this in the Chinese population. Methods We retrospectively analyzed 690 patients who underwent FFR measurements to determine the functional significance of a single ICS. Patients were divided into 2 groups: FFR ≤0.8 (n = 280) and FFR >0.8 (n = 410). We compared the clinical factors between the two groups and performed multivariate logistic regression analyses to explore the risk factors. In addition, receiver-operating characteristic (ROC) curves were constructed for FFR ≤0.8 diagnoses. Results The mean UHR (uric acid to high-density lipoprotein cholesterol ratio) level was significantly higher in the FFR ≤0.8 group (p < 0.001). UHR corrects negatively with FFR (r = −0.44, p < 0.001). High-level UHR was an independent risk factor for the FFR ≤0.8 (OR = 7.17, 95% CI 4.17–12.34). The area under the curve (AUC) of the UHR diagnostic capacity for the FFR ≤0.8 is 0.77, with 77.3% sensitivity and 68.2% specificity. Conclusion UHR levels were significantly increased in patients with hemodynamically significant coronary lesions. UHR is a novel predictor of functionally significant lesions in patients with a single-vessel disease of ICS.
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