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Callahan TJ, Stefanski AL, Wyrwa JM, Zeng C, Ostropolets A, Banda JM, Baumgartner WA, Boyce RD, Casiraghi E, Coleman BD, Collins JH, Deakyne Davies SJ, Feinstein JA, Lin AY, Martin B, Matentzoglu NA, Meeker D, Reese J, Sinclair J, Taneja SB, Trinkley KE, Vasilevsky NA, Williams AE, Zhang XA, Denny JC, Ryan PB, Hripcsak G, Bennett TD, Haendel MA, Robinson PN, Hunter LE, Kahn MG. Ontologizing health systems data at scale: making translational discovery a reality. NPJ Digit Med 2023; 6:89. [PMID: 37208468 PMCID: PMC10196319 DOI: 10.1038/s41746-023-00830-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.
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Affiliation(s)
- Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Adrianne L Stefanski
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jordan M Wyrwa
- Department of Physical Medicine and Rehabilitation, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anna Ostropolets
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Juan M Banda
- Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA
| | - William A Baumgartner
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Richard D Boyce
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Elena Casiraghi
- Computer Science, Università degli Studi di Milano, Milan, Italy
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ben D Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Janine H Collins
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sara J Deakyne Davies
- Department of Research Informatics & Data Science, Analytics Resource Center, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - James A Feinstein
- Adult and Child Center for Health Outcomes Research and Delivery Science (ACCORDS), University of Colorado Anschutz School of Medicine, Aurora, CO, 80045, USA
| | - Asiyah Y Lin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Blake Martin
- Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | | | | | - Justin Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Sanya B Taneja
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Katy E Trinkley
- Department of Family Medicine, University of Colorado Anschutz School of Medicine, Aurora, CO, 80045, USA
| | - Nicole A Vasilevsky
- Translational and Integrative Sciences Lab, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Andrew E Williams
- Tufts Institute for Clinical Research and Health Policy Studies, Tufts University, Boston, MA, 02155, USA
| | - Xingmin A Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Patrick B Ryan
- Janssen Research and Development, Raritan, NJ, 08869, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tellen D Bennett
- Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Melissa A Haendel
- Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Lawrence E Hunter
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael G Kahn
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
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Giunta EF, Signori A, West HJ, Metro G, Friedlaender A, Parikh K, Banna GL, Addeo A. Beyond Crizotinib: A Systematic Review and Meta-Analysis of the Next-Generation ALK Inhibitors as First-Line Treatment for ALK-Translocated Lung Cancer. Front Oncol 2022; 12:921854. [PMID: 35774122 PMCID: PMC9239548 DOI: 10.3389/fonc.2022.921854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/10/2022] [Indexed: 12/27/2022] Open
Abstract
Background Second and third-generation ALK inhibitors (ALKIs) have been recently approved for ALK-translocated lung cancer treatment, improving - and expanding - the first-line scenario. Methods In this systematic review and metanalysis, we investigated the efficacy and safety of next-generation ALKIs in untreated advanced ALK-translocated lung cancer patients, searching for randomized phase III controlled trials through databases (PubMed, EMBASE, and the Cochrane Library). Inclusion and exclusion of studies, quality assessment, data extraction, and synthesis were independently accomplished by two reviewers, with discrepancies adjudicated by a third reviewer. Stata (StataCorp., v.16) software was used for the metanalysis. Results In total, seven randomized controlled trials met our inclusion criteria. Comparing the results of next-generation ALKIs and control therapy (crizotinib or chemotherapy), next-generation ALKIs significantly improved progression-free survival (PFS), overall survival (OS), objective response rate (ORR), disease control rate (DCR), any lesion (aCNSRR) and measurable lesions of central nervous system response rate (mCNSRR). Safety results were similar between the experimental and control groups. Conclusion Our analysis confirmed that next-generation ALKIs are the preferred first-line treatment option for ALK-translocated lung cancer. They are superior to crizotinib or chemotherapy in several clinical endpoints, including OS, PFS, ORR and CNS disease control, without increased toxicity. In the absence of head-to-head data, the choice between these molecules should be guided by physician experience and preference, drug-specific safety profile and schedule.
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Affiliation(s)
| | - Alessio Signori
- Department of Health Sciences, University of Genova, Genoa, Italy
| | - Howard Jack West
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Giulio Metro
- Medical Oncology, Santa Maria Della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Alex Friedlaender
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
| | - Kaushal Parikh
- Hackensack University Medical Center, Hackensack, NJ, United States
| | - Giuseppe Luigi Banna
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (Turin), Italy
- *Correspondence: Giuseppe Luigi Banna,
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
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Rijavec E, Biello F, Indini A, Grossi F, Genova C. Current Insights on the Treatment of Anaplastic Lymphoma Kinase-Positive Metastatic Non-Small Cell Lung Cancer: Focus on Brigatinib. Clin Pharmacol 2022; 14:1-9. [PMID: 35082536 PMCID: PMC8786362 DOI: 10.2147/cpaa.s284850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022] Open
Abstract
Rearrangement of anaplastic lymphoma kinase (ALK) gene is detected in approximately 5% of non-small cell lung cancer (NSCLC) patients. Tyrosine kinase inhibitors targeting ALK have significantly improved the prognosis of these patients. However, most patients experienced disease progression within a few years due to acquired resistance. Brigatinib is a second-generation ALK inhibitor effective in presence of several ALK mutations with demonstrated activity against central nervous system metastases. Currently, brigatinib is approved to treat ALK-positive metastatic NSCLC patients not previously treated with ALK inhibitors and patients who have progressed on or are intolerant to crizotinib. In this review, we provide a summary of results from clinical trials involving brigatinib, and we discuss its possible role in the management of ALK-positive NSCLC in the following years.
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Affiliation(s)
- Erika Rijavec
- Medical Oncology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Correspondence: Erika Rijavec, Email
| | - Federica Biello
- Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Alice Indini
- Division of Medical Oncology, University of Insubria, ASST dei Sette Laghi, Varese, Italy
| | - Francesco Grossi
- Division of Medical Oncology, University of Insubria, ASST dei Sette Laghi, Varese, Italy
| | - Carlo Genova
- UO Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), Università degli Studi di Genova, Genova, Italy
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