Evaluation of Biomedical Informatics Component of NIGMS Funded IDeA-CTR programs

We believe the NIGMS IDeA-CTR programs would benefit from adopting many of the CTSA innovations. We sought to determine current informatics practices of IDeA-CTR programs through a qualitative study of BMI activity and organization. We recommend possible convergence of NIGMS IDeA-CTR BMI activity towards NCATS CTSA BMI functionality.https://digitalcommons.unmc.edu/com_emerg_pres/1002/thumbnail.jp

Interoperable Knowledge Modeling in Emergency Care: Application of the HL7 Emergency Care Domain Analysis Model

The Emergency Care System (ECS) in the United States provides intermittent unscheduled care to an increasing number of patients annually. Every ECS patient encounter generates data in a myriad of unlinked systems at regional emergency services and hospitals. Often, their prior health records are not available in a timely manner, fragmented, or not found. To address availability and interoperability data relevant to emergency care, the Health Level Seven (HL7) Emergency Care Workgroup seeks to ensure evolving health data interoperability standards incorporate ECS considerations. Foundational to that effort is a comprehensive model of Emergency Care information. This emergency care domain analysis model consists of interlinked layers of vocabulary, information models, health record functions and emergency department workflow. This poster will describe the HL7 Emergency Care Domain Analysis Model (EC-DAM), the design considerations and the impact of the EC-DAM on related information standards such as FHIR resources in prehospital care, trauma care, disease surveillance, and clinical research. The EC-DAM provides an integrated, standardized platform for creation of interoperable EC related knowledge tools. This poster presentation is particularly relevant to developers of health information standards and health information systems that involve the ECS.https://digitalcommons.unmc.edu/com_emerg_pres/1000/thumbnail.jp

Reorganizing Emergency Department Information Systems to Reduce Physician Cognitive Load

https://digitalcommons.unmc.edu/com_emerg_pres/1003/thumbnail.jp

Maintenance of ONC Terminology for i2b2 Metadata

ONC terminologies are constantly adding new content and deactivating existing codes. The University of Nebraska Medical Center (UNMC) deploys three primary code sets that require regular updating to support research: SNOMED CT, RXNORM / NDC, and LOINC. A problem across the i2b2 community is keeping these terminologies up-to-date and loading them into i2b2 for timely analysis of EHR data. We have developed tool kits for rapid deployment of SNOMED CT metadata and will be extending the work to RXNORM/NDC and LOINC.https://digitalcommons.unmc.edu/com_emerg_pres/1001/thumbnail.jp

Beyond Safe Harbor: Risk of Exposing Location in De-Identified Clinical Data

The use of de-identified EHR data for clinical and translational research has increased significantly since the HIPAA Privacy Rule De-Identification standards went into effect -Inclusion of SDOH measures in de-identified research is increasing as well, which presents an inherent risk of re-identifying PHI (primarily location units smaller than the state) -Data warehouse architecture and institutional policies need to recognize the risk associated with providing multiple location-based indices -Research interests are secondary to privacy concerns throughout biomedical research, but particularly in de-identified research, which is intended to promote more secure access to EHR data while allowing for expedient access (fewer institutional barriers to entry)https://digitalcommons.unmc.edu/com_neuro_pres/1000/thumbnail.jp

Associations between COVID-19 therapies and inpatient gastrointestinal bleeding: A multisite retrospective study.

Little data is available regarding the incidence of gastrointestinal bleeding in adults hospitalized with COVID-19 infection and the influence of patient comorbidities and demographics, COVID-19 therapies, and typical medications used. In this retrospective study, we utilized the National COVID Cohort Collaborative to investigate the primary outcome of the development of gastrointestinal bleeding in 512 467 hospitalized US adults (age \u3e18 years) within 14 days of a COVID-19 infection and the influence of demographics, comorbidities, and selected medications. Gastrointestinal bleeding developed in 0.44% of patients hospitalized with COVID-19. Comorbidities associated with gastrointestinal bleeding include peptic ulcer disease (adjusted odds ratio [aOR] 10.2), obesity (aOR 1.27), chronic kidney disease (aOR 1.20), and tobacco use disorder (aOR 1.28). Lower risk of gastrointestinal bleeding was seen among women (aOR 0.76), Latinx (aOR 0.85), and vaccinated patients (aOR 0.74). Dexamethasone alone or with remdesivir was associated with lower risk of gastrointestinal bleeding (aOR 0.69 and aOR 0.83, respectively). Remdesivir monotherapy was associated with upper gastrointestinal bleeding (aOR 1.25). Proton pump inhibitors were more often prescribed in patients with gastrointestinal bleeding, likely representing treatment for gastrointestinal bleeding rather than a risk factor for its development. In adult patients hospitalized with COVID-19, the use of dexamethasone alone or in combination with remdesivir is negatively associated with gastrointestinal bleeding. Remdesivir monotherapy is associated with increased risk of upper gastrointestinal bleeding

Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction

Chronic obstructive pulmonary disease (COPD) is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1) despite many years of heavy smoking. We # hypothesised that these ‘‘resistant smokers’’ may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the ‘‘resistant smokers’’ and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.3461024) in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial epithelium may affect growth of cilia or the extent of damage caused by tobacco smoke

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead