Linking Genomic and Clinical Data for Discovery and Personalized Care

作者: Joshua C. Denny , Hua Xu

DOI: 10.1016/B978-0-12-401678-1.00012-9

关键词: Data scienceRepurposingOperationalizationHealth care qualityDecision support systemMedicineData miningMedical diagnosisDocumentationPersonalized medicineBiobank

摘要: Electronic Health Records (EHRs) are a powerful tool to improve health care quality while reducing its costs. As longitudinal repository of patient diagnoses, treatments, and responses treatment, EHRs also being increasingly recognized as an important for research well clinical care. By coupling with DNA biobanks, can provide phenotypes genomic studies. This chapter summarizes the role needed methods use EHR data discovery implementation into There number challenges accurate interpretation repurposing research. Typically, investigators employ multimodal “phenotype algorithms” find cases controls. Such algorithms integrate billing codes, medication records, laboratory test result data, notes achieve necessary recall precision. Since much content in record is unstructured (narrative) documentation, natural language processing often required. Despite these challenges, researchers have been successful replicating known genetic associations making new discoveries using data. Early demonstration projects show that EHR, coupled advanced genome-enabled decision support, may be ideal operationalize use.

参考文章(93)
Chunhua Weng, Herbert S. Chase, Carol Friedman, Li Li, Chintan O. Patel, Comparing ICD9-encoded diagnoses and NLP-processed discharge summaries for clinical trials pre-screening: a case study. american medical informatics association annual symposium. ,vol. 2008, pp. 404- 408 ,(2008)
George Hripcsak, Adam S Rothschild, Agreement, the F-Measure, and Reliability in Information Retrieval Journal of the American Medical Informatics Association. ,vol. 12, pp. 296- 298 ,(2005) , 10.1197/JAMIA.M1733
J.-W. Fan, C. Friedman, Semantic Classification of Biomedical Concepts Using Distributional Similarity Journal of the American Medical Informatics Association. ,vol. 14, pp. 467- 477 ,(2007) , 10.1197/JAMIA.M2314
Edward H Shortliffe, Edward H Shortliffe, James J Cimino, James J Cimino, None, Biomedical informatics : computer applications in health care and biomedicine Springer. ,(2001)
Hua Xu, Min Jiang, Matt Oetjens, Erica A Bowton, Andrea H Ramirez, Janina M Jeff, Melissa A Basford, Jill M Pulley, James D Cowan, Xiaoming Wang, Marylyn D Ritchie, Daniel R Masys, Dan M Roden, Dana C Crawford, Joshua C Denny, Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. Journal of the American Medical Informatics Association. ,vol. 18, pp. 387- 391 ,(2011) , 10.1136/AMIAJNL-2011-000208
Jonathan S. Schildcrout, Dawood Darbar, S. Trent Rosenbloom, Anderson Spickard, Josh F. Peterson, Joshua C. Denny, Randolph A. Miller, Identifying UMLS concepts from ECG Impressions using KnowledgeMap american medical informatics association annual symposium. ,vol. 2005, pp. 196- 200 ,(2005)
S. T. Rosenbloom, J. C. Denny, H. Xu, N. Lorenzi, W. W. Stead, K. B. Johnson, Data from clinical notes: a perspective on the tension between structure and flexible documentation. Journal of the American Medical Informatics Association. ,vol. 18, pp. 181- 186 ,(2011) , 10.1136/JAMIA.2010.007237
Alan R. Aronson, Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program american medical informatics association annual symposium. pp. 17- 21 ,(2001)
Min-Woong Sohn, Huiyuan Zhang, Noreen Arnold, Kevin Stroupe, Brent C Taylor, Timothy J Wilt, Denise M Hynes, Transition to the new race/ethnicity data collection standards in the Department of Veterans Affairs Population Health Metrics. ,vol. 4, pp. 7- 7 ,(2006) , 10.1186/1478-7954-4-7
Clement J. McDonald, Paul C. Tang, George Hripcsak, Electronic Health Record Systems Springer London. pp. 391- 421 ,(2014) , 10.1007/978-1-4471-4474-8_12