OHDSI MEETINGS THIS WEEK
OHDSI Community Call - Tuesday at 12pm EThttps://meetings.webex.com/collabs/#/meetings/detail?uuid=M59X2V1U61WC9ASID2Z5N3UT95-D1JL&rnd=811649.9868221
Population-Level Estimation (Eastern hemisphere) workgroup meeting - Wednesday at 3pm Hong Kong timehttps://meetings.webex.com/collabs/meetings/join?uuid=M6WE9AOKFETH2VEFPVCZWWBIT0-D1JL
Architecture Working Group - Thursday at 10am EThttps://jjconferencing.webex.com/jjconferencing/j.php?MTID=m3e1ceeca56f1e94c9fcf1ae98c10e02e
GIS working group meeting - Monday (January 29th) at 10am ET
Simple, modern video meetings for the global workforce. Join from anywhere, including your desktop, browser, mobile device, or video room device.
ANNOUNCEMENTS
2018 OHDSI Symposium - SAVE THE DATE!
2018 OHDSI F2F: It’s official! The next OHDSI face-to-face will take place on May 2-3rd 2018 at Columbia University Medical Center in New York. More details to come.
This is the strangest life I’ve ever known.
COMMUNITY PUBLICATIONS
The Next Generation of Drug Safety Science: Coupling Detection, Corroboration, and Validation to Discover Novel Drug Effects and Drug–Drug Interactionshttp://onlinelibrary.wiley.com/doi/10.1002/cpt.949/full
Computational methods for birth-death processeshttp://onlinelibrary.wiley.com/doi/10.1002/wics.1423/full
The Impact of Censoring Drug Switching in Medication Adherence Measures of Chronic Single Ingredient Oral Drugs.
VJ Zhu, JM Overhage, Q Ma and PB Ryan,
Studies in health technology and informatics , 2017
We explored how drug switching impacts adherence measures for common chronic oral medications. Switching between ingredients with the same indication was detected within a 30-day grace period. The proportion of days covered (PDC) and adherent status (cutoff 0.8) for each ingredient was calculated and compared between different censoring approaches: censoring drug switching (PDCswitch), censoring the end of dispensing (PDCend), and fixed 365-day period (PDC365). Overall, 854,380 (15.9%) patients in the Optum ClinFormatics (Optum) and 150,785 (22.0%) patients in the MarketScan Multi-state Medicaid (MDCD) had at least one switch within one year. Compared with PDC365 in Optum, PDCswitch means were higher: 0.85 vs. 0.41 for antihypertensive, 0.82 vs. 0.46 for antihyperglycemics, and 0.84 vs. 0.33 for antihyerlipidemia. Further, the percentages of adherent patients were higher: 95.8% vs. 17.9% for antihypertensive, 85.5% vs. 18.9% for antihyperglycemics, and 72.1% vs. 5.3% for antihyerlipidemia. Significant and modest changes were observed between PDCswitch and PDCend.
The Effect of Safety Warnings on Antipsychotic Drug Prescribing in Elderly Persons with Dementia in the United Kingdom and Italy: A Population-Based Study.
J Sultana, A Fontana, F Giorgianni, A Pasqua, C Cricelli, E Spina, G Gambassi, J Ivanovic, C Ferrajolo, M Molokhia, C Ballard, S Sharp, M Sturkenboom and G Trifirò,
CNS drugs , 2016 11
Antipsychotic (AP) drugs are commonly used to manage the behavioural symptoms of dementia. Nevertheless, international (i.e. the European Medicines Agency in Europe) and national (i.e. the Medicines and Healthcare products Regulatory Agency in the UK and the Italian Drug Agency) regulatory agencies issued safety warnings against AP use in dementia in 2004 and 2009.The aim of this study is to investigate the short- and long-term impact of safety warnings on the use of APs in UK and Italian persons with dementia using two nationwide databases: The Health Improvement Network (THIN) from the UK and the Health Search Database-Cegedim-Strategic Data-Longitudinal Patient Database (HSD-CSD-LPD) from Italy.We calculated the overall quarterly prevalence of AP use by class and by individual drug in persons with dementia aged ≥65 years and used generalized linear models to explore the effect of the safety warnings.We identified 58,497 and 10,857 individuals aged ≥65 years with dementia from the THIN and HSD-CSD-LPD databases, respectively, over the period 2000-2012. After the 2004 warnings, the use of atypical APs decreased, whereas the use of conventional APs increased, in Italy and the UK until 2009. However, the trend for APs individually showed that the use of risperidone/olanzapine decreased, whereas the use of quetiapine increased in both countries. After the 2009 warnings (until 2012), the use of atypical and conventional APs decreased in the UK (from 11 to 9 and 5 to 3 %, respectively), but such use increased in Italy (from 11 to 18 and 9 to 14 %, respectively).The 2004 warnings led to a reduction in the use of olanzapine and risperidone and increased the use of quetiapine/conventional APs in both countries. From 2009, the use of APs decreased in persons with dementia in the UK but not in Italy. Possible reasons for the difference in AP use between the two countries include a more proactive approach towards reducing the use of APs in the UK than in Italy.
Genetic and Non-Genetic Factors Affecting the Quality of Anticoagulation Control and Vascular Events in Atrial Fibrillation.
YK Park, MJ Lee, JH Kim, JS Lee, RW Park, GM Kim, CS Chung, KH Lee, JS Kim, SY Lee and OY Bang,
Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association , Jun 2017
Warfarin has a narrow therapeutic window. We hypothesized that genetic factors related to warfarin metabolism (CYP2C9) and activity (VKORC1) would show stronger associations than modifiable factors with the quality of anticoagulation control and risks for thromboembolism and hemorrhage.In this retrospective cohort analysis, clinical and genetic data were collected from 380 patients with atrial fibrillation (AF) who were followed for an average observation period of 4 years. We evaluated the factors associated with time in therapeutic range (TTR, international normalized ratio [INR]: 2-3) and vascular events (either thromboembolic or hemorrhagic), including both genetic (CYP2C9 and VKORC1 genotype) and modifiable factors (anticoagulation service and warfarin dose assessment interval).The genotypic frequency of CYP2C9*3 (rs1057910) was 9.5% and that of VKORC1 1173C>T (rs9934438) was 16.3%. TTR showed dependence on VKORC1 polymorphism: TTR was higher in carriers of the VKORC1 1173C>T than of the VKORC1 TT genotype (61.7 ± 16.0% versus 56.7 ± 17.4%, P = .031). Multivariate testing showed that the VKORC1 genotype and anticoagulation service were independently related to labile INRs (TTR <65%). Vascular events were observed in 66 patients (18.4%) during the study period. A Cox proportional hazard model showed that the use of anticoagulation service and patients' characteristics, such as AF-thromboembolic risk (CHA2DS2-VASc score: Congestive heart failure, Hypertension, Age 75 years or older, Diabetes mellitus, previous Stroke or transient ischemic attack, Vascular disease, Age 65 to 74 years, female) and consequence (neurologic disability), but not genetic factors, were independently associated with vascular events.Both genetic factor (VKORC1 genotype) and clinical efforts (anticoagulation service) influenced the quality of anticoagulation control. However, clinical events were more strongly associated with patient characteristics and clinical efforts than with genetic factors.
Assessing the readiness of precision medicine interoperabilty: An exploratory study of the National Institutes of Health genetic testing registry.
JG Ronquillo, C Weng and WT Lester,
Journal of innovation in health informatics , Nov 2017 17
Precision medicine involves three major innovations currently taking place in healthcare: electronic health records, genomics, and big data. A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine. To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats. We performed an exploratory analysis of the National Institutes of Health Genetic Testing Registry. Relevant standards included Health Level Seven International Version 3 Implementation Guide for Family History, the Human Genome Organization Gene Nomenclature Committee (HGNC) database, and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT). We analyzed the distribution of genetic testing laboratories, genetic test characteristics, and standardized genome/clinical code mappings, stratified by laboratory setting.There were a total of 25472 genetic tests from 240 laboratories testing for approximately 3632 distinct genes. Most tests focused on diagnosis, mutation confirmation, and/or risk assessment of germline mutations that could be passed to offspring. Genes were successfully mapped to all HGNC identifiers, but less than half of tests mapped to SNOMED CT codes, highlighting significant gaps when linking genetic tests to standardized clinical codes that explain the medical motivations behind test ordering. Conclusion: While precision medicine could potentially transform healthcare, successful practical and clinical application will first require the comprehensive and responsible adoption of interoperable standards, terminologies, and formats across all aspects of the precision medicine pipeline.
Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).
M Panahiazar, M Dumontier and O Gevaert,
Journal of biomedical informatics , 2017 08
A crucial and limiting factor in data reuse is the lack of accurate, structured, and complete descriptions of data, known as metadata. Towards improving the quantity and quality of metadata, we propose a novel metadata prediction framework to learn associations from existing metadata that can be used to predict metadata values. We evaluate our framework in the context of experimental metadata from the Gene Expression Omnibus (GEO). We applied four rule mining algorithms to the most common structured metadata elements (sample type, molecular type, platform, label type and organism) from over 1.3million GEO records. We examined the quality of well supported rules from each algorithm and visualized the dependencies among metadata elements. Finally, we evaluated the performance of the algorithms in terms of accuracy, precision, recall, and F-measure. We found that PART is the best algorithm outperforming Apriori, Predictive Apriori, and Decision Table. All algorithms perform significantly better in predicting class values than the majority vote classifier. We found that the performance of the algorithms is related to the dimensionality of the GEO elements. The average performance of all algorithm increases due of the decreasing of dimensionality of the unique values of these elements (2697 platforms, 537 organisms, 454 labels, 9 molecules, and 5 types). Our work suggests that experimental metadata such as present in GEO can be accurately predicted using rule mining algorithms. Our work has implications for both prospective and retrospective augmentation of metadata quality, which are geared towards making data easier to find and reuse.
