PheMIME: An Interactive Web App and Knowledge Base for Phenome-Wide, Multi-Institutional Multimorbidity Analysis

Motivation

Multimorbidity, characterized by the simultaneous occurrence of multiple diseases in an individual, is an increasing global health concern, posing substantial challenges to healthcare systems. Comprehensive understanding of disease-disease interactions and intrinsic mechanisms behind multimorbidity can offer opportunities for innovative prevention strategies, targeted interventions, and personalized treatments. Yet, there exist limited tools and datasets that characterize multimorbidity patterns across different populations. To bridge this gap, we used large-scale electronic health record (EHR) systems to develop the Phenome-wide Multi-Institutional Multimorbidity Explorer (PheMIME), which facilitates research in exploring and comparing multimorbidity patterns among multiple institutions, potentially leading to the discovery of novel and robust disease associations and patterns that are interoperable across different systems and organizations.

Results

PheMIME integrates summary statistics from phenome-wide analyses of disease multimorbidities. These are currently derived from three major institutions: Vanderbilt University Medical Center, Mass General Brigham, and the UK Biobank. PheMIME offers interactive exploration of multimorbidity through multi-faceted visualization. Incorporating an enhanced version of associationSubgraphs, PheMIME enables dynamic analysis and inference of disease clusters, promoting the discovery of multimorbidity patterns. Once a disease of interest is selected, the tool generates interactive visualizations and tables that users can delve into multimorbidities or multimorbidity networks within a single system or compare across multiple systems. The utility of PheMIME is demonstrated through a case study on schizophrenia.

Availability and implementation

The PheMIME knowledge base and web application are accessible at https://prod.tbilab.org/PheMIME/. A comprehensive tutorial, including a use-case example, is available at https://prod.tbilab.org/PheMIME_supplementary_materials/. Furthermore, the source code for PheMIME can be freely downloaded from https://github.com/tbilab/PheMIME.

Data availability statement

The data underlying this article are available in the article and in its online web application or supplementary material.

Renin-Angiotensin System Modulation With Synthetic Angiotensin (1-7) and Angiotensin II Type 1 Receptor-Biased Ligand in Adults With COVID-19: Two Randomized Clinical Trials

Importance

Preclinical models suggest dysregulation of the renin-angiotensin system (RAS) caused by SARS-CoV-2 infection may increase the relative activity of angiotensin II compared with angiotensin (1-7) and may be an important contributor to COVID-19 pathophysiology.

Objective

To evaluate the efficacy and safety of RAS modulation using 2 investigational RAS agents, TXA-127 (synthetic angiotensin [1-7]) and TRV-027 (an angiotensin II type 1 receptor-biased ligand), that are hypothesized to potentiate the action of angiotensin (1-7) and mitigate the action of the angiotensin II.

Design, Setting, and Participants

Two randomized clinical trials including adults hospitalized with acute COVID-19 and new-onset hypoxemia were conducted at 35 sites in the US between July 22, 2021, and April 20, 2022; last follow-up visit: July 26, 2022.

Interventions

A 0.5-mg/kg intravenous infusion of TXA-127 once daily for 5 days or placebo. A 12-mg/h continuous intravenous infusion of TRV-027 for 5 days or placebo.

Main Outcomes and Measures

The primary outcome was oxygen-free days, an ordinal outcome that classifies a patient's status at day 28 based on mortality and duration of supplemental oxygen use; an adjusted odds ratio (OR) greater than 1.0 indicated superiority of the RAS agent vs placebo. A key secondary outcome was 28-day all-cause mortality. Safety outcomes included allergic reaction, new kidney replacement therapy, and hypotension.

Results

Both trials met prespecified early stopping criteria for a low probability of efficacy. Of 343 patients in the TXA-127 trial (226 [65.9%] aged 31-64 years, 200 [58.3%] men, 225 [65.6%] White, and 274 [79.9%] not Hispanic), 170 received TXA-127 and 173 received placebo. Of 290 patients in the TRV-027 trial (199 [68.6%] aged 31-64 years, 168 [57.9%] men, 195 [67.2%] White, and 225 [77.6%] not Hispanic), 145 received TRV-027 and 145 received placebo. Compared with placebo, both TXA-127 (unadjusted mean difference, -2.3 [95% CrI, -4.8 to 0.2]; adjusted OR, 0.88 [95% CrI, 0.59 to 1.30]) and TRV-027 (unadjusted mean difference, -2.4 [95% CrI, -5.1 to 0.3]; adjusted OR, 0.74 [95% CrI, 0.48 to 1.13]) resulted in no difference in oxygen-free days. In the TXA-127 trial, 28-day all-cause mortality occurred in 22 of 163 patients (13.5%) in the TXA-127 group vs 22 of 166 patients (13.3%) in the placebo group (adjusted OR, 0.83 [95% CrI, 0.41 to 1.66]). In the TRV-027 trial, 28-day all-cause mortality occurred in 29 of 141 patients (20.6%) in the TRV-027 group vs 18 of 140 patients (12.9%) in the placebo group (adjusted OR, 1.52 [95% CrI, 0.75 to 3.08]). The frequency of the safety outcomes was similar with either TXA-127 or TRV-027 vs placebo.

Conclusions and Relevance

In adults with severe COVID-19, RAS modulation (TXA-127 or TRV-027) did not improve oxygen-free days vs placebo. These results do not support the hypotheses that pharmacological interventions that selectively block the angiotensin II type 1 receptor or increase angiotensin (1-7) improve outcomes for patients with severe COVID-19.

Trial Registration

ClinicalTrials.gov Identifier: NCT04924660.

Walk before you run: Feasibility challenges and lessons learned from the PROCLAIM study, a multicenter randomized controlled trial of misoprostol for prevention of recurrent Clostridioides difficile during COVID-19

We analyzed our challenging experience with a randomized controlled trial of misoprostol for prevention of recurrent C. difficile. Despite careful prescreening and thoughtful protocol modifications to facilitate enrollment, we closed the study early after enrolling just 7 participants over 3 years. We share lessons learned, noting the importance of feasibility studies, inclusion of biomarker outcomes, and dissemination of such findings to inform future research design and implementation successes.

Mining 100 million notes to find homelessness and adverse childhood experiences: 2 case studies of rare and severe social determinants of health in electronic health records

Objective

Understanding how to identify the social determinants of health from electronic health records (EHRs) could provide important insights to understand health or disease outcomes. We developed a methodology to capture 2 rare and severe social determinants of health, homelessness and adverse childhood experiences (ACEs), from a large EHR repository.

Materials and Methods

We first constructed lexicons to capture homelessness and ACE phenotypic profiles. We employed word2vec and lexical associations to mine homelessness-related words. Next, using relevance feedback, we refined the 2 profiles with iterative searches over 100 million notes from the Vanderbilt EHR. Seven assessors manually reviewed the top-ranked results of 2544 patient visits relevant for homelessness and 1000 patients relevant for ACE.

Results

word2vec yielded better performance (area under the precision-recall curve [AUPRC] of 0.94) than lexical associations (AUPRC = 0.83) for extracting homelessness-related words. A comparative study of searches for the 2 phenotypes revealed a higher performance achieved for homelessness (AUPRC = 0.95) than ACE (AUPRC = 0.79). A temporal analysis of the homeless population showed that the majority experienced chronic homelessness. Most ACE patients suffered sexual (70%) and/or physical (50.6%) abuse, with the top-ranked abuser keywords being "father" (21.8%) and "mother" (15.4%). Top prevalent associated conditions for homeless patients were lack of housing (62.8%) and tobacco use disorder (61.5%), while for ACE patients it was mental disorders (36.6%-47.6%).

Conclusion

We provide an efficient solution for mining homelessness and ACE information from EHRs, which can facilitate large clinical and genetic studies of these social determinants of health.

The PathLink Acquired Gestational Tissue Bank: Feasibility of Project PLACENTA

BACKGROUND

The Vanderbilt Institute for Clinical and Translational Research piloted the development of Project PLACENTA (PathLink Acquired gEstatioNal Tissue bAnk). This project investigated the feasibility of a fresh gestational tissue biobank, which provides tissue linked to electronic medical records for investigators interested in maternal-fetal health.

METHODS

We developed a pipeline for collection of placental tissue from Labor and Delivery within approximately 30 minutes of delivery. An email alert was developed, to signal delivery, with the ability to specifically flag patients with certain phenotypic traits. Once collected, 4 to 8 mm punch biopsy cores were snap frozen and subsequently used for DNA, RNA and protein extraction. Tissue was also collected for Formalin Fixed Paraffin Embedded (FFPE) histology, flow cytometry, and quality control measures.

RESULTS

Of 60 deliveries using the email notification system, 25 (42%) were sent to Pathology or assigned to other research protocols and were not available for collection, 10 (16%) were discarded prior to arrival at Labor and Delivery, and 25 (42%) were available for collection. Twenty placentas were collected and averaged 38 minutes per collection. DNA extraction yielded an average of 53 µg/µl per sample and RNA extraction yielded 679 ng/µl on average per sample. Proteomic studies showed no degradation of protein, abundant and similar quantities of protein across samples and differentiation between the amnion, decidua, and villi. Histological studies showed good quality for interpretation and occasional pathology including multifocal chronic villitis, meconium laden macrophages, and Stage 2 acute chorioamnionitis. Flow cytometry demonstrated good cell viability after isolation.

Recruitment methods for survey research: Findings from the Mid-South Clinical Data Research Network

PURPOSE

The objective of this study was to report survey response rates and demographic characteristics of eight recruitment approaches to determine acceptability and effectiveness of large-scale patient recruitment among various populations.

METHODS

We conducted a cross sectional analysis of survey data from two large cohorts. Patients were recruited from the Mid-South Clinical Data Research Network using clinic-based recruitment, research registries, and mail, phone, and email approaches. Response rates are reported as patients who consented for the survey divided by the number of eligible patients approached.

RESULTS

We contacted more than 90,000 patients and 13,197 patients completed surveys. Median age was 56.3years (IQR 40.9, 67.4). Racial/ethnic distribution was 84.1% White, non-Hispanic; 9.9% Black, non-Hispanic; 1.8% Hispanic; and 4.0% other, non-Hispanic. Face-to-face recruitment had the highest response rate of 94.3%, followed by participants who "opted-in" to a registry (76%). The lowest response rate was for unsolicited emails from the clinic (6.1%). Face-to-face recruitment enrolled a higher percentage of participants who self-identified as Black, non-Hispanic compared to other approaches (18.6% face-to-face vs. 8.4% for email).

CONCLUSIONS

Technology-enabled recruitment approaches such as registries and emails are effective for recruiting but may yield less racial/ethnic diversity compared to traditional, more time-intensive approaches.

Abstract 1293: ABO blood type and cancer risk: preliminary findings from a phenome analysis

Introduction: ABO blood type has long been implicated in disease susceptibility, including cancer. However, evidence for associations with many malignancies is mixed. We applied a novel phenome approach to test to cancer codes from electronic medical records (EMR) in relation to ABO blood type in a large predominantly Caucasian study population.

Approach: Among adults aged 18-100, cancer case and control status were assigned using 58 general neoplasm related phenome codes to de-identified EMR at the Vanderbilt University Medical Center. Blood type from serologic assays was ascertained from EMR-linked laboratory reports. Associations between blood type and cancer phenomes were quantified with Odds Ratios (OR) and corresponding 95% Confidence Intervals (CI) from logistic regression in models adjusted for sex and stratified by race/ethnicity. Only analyses with at least 100 cases per strata were conducted.

Results: Among 221,015 Non-Hispanic Caucasians, 37,841 Blacks, 7,714 Hispanic Caucasians, and 3,616 Asian subjects with ABO blood type available in linked EMR, we evaluated 56, 37, 4, and 3 general cancer phenome codes, respectively. After employing Bonferroni corrections, ABO blood type was significantly associated with cancers of the pancreas, ovary, cervix, skin, and hematopoietic system. Caucasians with blood type O were less likely to have ovarian cancer (OR: 0.82, 95% CI 0.73-0.91) and pancreatic cancer (OR: 0.83, 95% CI: 0.74-0.92), and more likely to have squamous cell or other skin cancer (OR: 1.08, 95% CI: 1.04-1.13) and myeloid leukemia (OR: 1.15, 95% CI: 1.06-1.25) than those with other blood types (A, B, or AB). Hispanic Caucasians with blood type O were less likely to have cervical cancer (OR: 0.56, 95% CI: 0.38-0.82) than those with other blood types. No associations surpassed correction for multiple comparisons among Blacks or Asians.

Conclusions: Our phenome approach confirmed known associations between blood type and risk of pancreatic and ovarian cancer, and adds to accumulating evidence supporting associations with skin cancer and leukemia. Our novel cervical cancer association among Hispanic Caucasians and other nominally significant findings, especially in understudied non-Caucasians, should be further evaluated in large and diverse populations. In addition, research to determine how ABO blood type may influence cancer development and progression, and if such associations can be exploited for risk prediction or cancer prevention is warranted.

Citation Format: Alicia Beeghly-Fadiel, Ayush Giri, Lisa Bastarache, Jill Pulley, Jeremy Warner, Josh Denny. ABO blood type and cancer risk: preliminary findings from a phenome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1293. doi:10.1158/1538-7445.AM2017-1293

Practical considerations in genomic decision support: The eMERGE experience

BACKGROUND

Genomic medicine has the potential to improve care by tailoring treatments to the individual. There is consensus in the literature that pharmacogenomics (PGx) may be an ideal starting point for real-world implementation, due to the presence of well-characterized drug-gene interactions. Clinical Decision Support (CDS) is an ideal avenue by which to implement PGx at the bedside. Previous literature has established theoretical models for PGx CDS implementation and discussed a number of anticipated real-world challenges. However, work detailing actual PGx CDS implementation experiences has been limited. Anticipated challenges include data storage and management, system integration, physician acceptance, and more.

METHODS

In this study, we analyzed the experiences of ten members of the Electronic Medical Records and Genomics (eMERGE) Network, and one affiliate, in their attempts to implement PGx CDS. We examined the resulting PGx CDS system characteristics and conducted a survey to understand the unanticipated implementation challenges sites encountered.

RESULTS

Ten sites have successfully implemented at least one PGx CDS rule in the clinical setting. The majority of sites elected to create an Omic Ancillary System (OAS) to manage genetic and genomic data. All sites were able to adapt their existing CDS tools for PGx knowledge. The most common and impactful delays were not PGx-specific issues. Instead, they were general IT implementation problems, with top challenges including team coordination/communication and staffing. The challenges encountered caused a median total delay in system go-live of approximately two months.

CONCLUSIONS

These results suggest that barriers to PGx CDS implementations are generally surmountable. Moreover, PGx CDS implementation may not be any more difficult than other healthcare IT projects of similar scope, as the most significant delays encountered were not unique to genomic medicine. These are encouraging results for any institution considering implementing a PGx CDS tool, and for the advancement of genomic medicine.

A conceptual model for translating omic data into clinical action

Genomic, proteomic, epigenomic, and other “omic” data have the potential to enable precision medicine, also commonly referred to as personalized medicine. The volume and complexity of omic data are rapidly overwhelming human cognitive capacity, requiring innovative approaches to translate such data into patient care. Here, we outline a conceptual model for the application of omic data in the clinical context, called “the omic funnel.” This model parallels the classic “Data, Information, Knowledge, Wisdom pyramid” and adds context for how to move between each successive layer. Its goal is to allow informaticians, researchers, and clinicians to approach the problem of translating omic data from bench to bedside, by using discrete steps with clearly defined needs. Such an approach can facilitate the development of modular and interoperable software that can bring precision medicine into widespread practice.

The Mid-South clinical Data Research Network

The Mid-South Clinical Data Research Network (CDRN) encompasses three large health systems: (1) Vanderbilt Health System (VU) with electronic medical records for over 2 million patients, (2) the Vanderbilt Healthcare Affiliated Network (VHAN) which currently includes over 40 hospitals, hundreds of ambulatory practices, and over 3 million patients in the Mid-South, and (3) Greenway Medical Technologies, with access to 24 million patients nationally. Initial goals of the Mid-South CDRN include: (1) expansion of our VU data network to include the VHAN and Greenway systems, (2) developing data integration/interoperability across the three systems, (3) improving our current tools for extracting clinical data, (4) optimization of tools for collection of patient-reported data, and (5) expansion of clinical decision support. By 18 months, we anticipate our CDRN will robustly support projects in comparative effectiveness research, pragmatic clinical trials, and other key research areas and have the capacity to share data and health information technology tools nationally.

The CTSA Consortium's Catalog of Assets for Translational and Clinical Health Research (CATCHR)

The 61 CTSA Consortium sites are home to valuable programs and infrastructure supporting translational science and all are charged with ensuring that such investments translate quickly to improved clinical care. Catalog of Assets for Translational and Clinical Health Research (CATCHR) is the Consortium's effort to collect and make available information on programs and resources to maximize efficiency and facilitate collaborations. By capturing information on a broad range of assets supporting the entire clinical and translational research spectrum, CATCHR aims to provide the necessary infrastructure and processes to establish and maintain an open-access, searchable database of consortium resources to support multisite clinical and translational research studies. Data are collected using rigorous, defined methods, with the resulting information made visible through an integrated, searchable Web-based tool. Additional easy-to-use Web tools assist resource owners in validating and updating resource information over time. In this paper, we discuss the design and scope of the project, data collection methods, current results, and future plans for development and sustainability. With increasing pressure on research programs to avoid redundancy, CATCHR aims to make available information on programs and core facilities to maximize efficient use of resources.

Models of interinstitutional partnerships between research intensive universities and minority serving institutions (MSI) across the Clinical Translational Science Award (CTSA) consortium

Health disparities are an immense challenge to American society. Clinical and Translational Science Awards (CTSAs) housed within the National Center for Advancing Translational Science (NCATS) are designed to accelerate the translation of experimental findings into clinically meaningful practices and bring new therapies to the doorsteps of all patients. Research Centers at Minority Institutions (RCMI) program at the National Institute on Minority Health and Health Disparities (NIMHD) are designed to build capacity for biomedical research and training at minority serving institutions. The CTSA created a mechanism fostering formal collaborations between research intensive universities and minority serving institutions (MSI) supported by the RCMI program. These consortium-level collaborations activate unique translational research approaches to reduce health disparities with credence to each academic institutions history and unique characteristics. Five formal partnerships between research intensive universities and MSI have formed as a result of the CTSA and RCMI programs. These partnerships present a multifocal approach; shifting cultural change and consciousness toward addressing health disparities, and training the next generation of minority scientists. This collaborative model is based on the respective strengths and contributions of the partnering institutions, allowing bidirectional interchange and leveraging NIH and institutional investments providing measurable benchmarks toward the elimination of health disparities.

Ethical and practical challenges to studying patients who opt out of large-scale biorepository research

Large-scale biorepositories that couple biologic specimens with electronic health records containing documentation of phenotypic expression can accelerate scientific research and discovery. However, differences between those subjects who participate in biorepository-based research and the population from which they are drawn may influence research validity. While an opt-out approach to biorepository-based research enhances inclusiveness, empirical research evaluating voluntariness, risk, and the feasibility of an opt-out approach is sparse, and factors influencing patients' decisions to opt out are understudied. Determining why patients choose to opt out may help to improve voluntariness, however there may be ethical and logistical challenges to studying those who opt out. In this perspective paper, the authors explore what is known about research based on the opt-out model, describe a large-scale biorepository that leverages the opt-out model, and review specific ethical and logistical challenges to bridging the research gaps that remain.

Preparedness of the CTSA's structural and scientific assets to support the mission of the National Center for Advancing Translational Sciences (NCATS)

The formation of the National Center for Advancing Translational Sciences (NCATS) brings new promise for moving basic science discoveries to clinical practice, ultimately improving the health of the nation. The Clinical and Translational Science Award (CTSA) sites, now housed with NCATS, are organized and prepared to support in this endeavor. The CTSAs provide a foundation for capitalizing on such promise through provision of a disease-agnostic infrastructure devoted to clinical and translational (C&T) science, maintenance of training programs designed for C&T investigators of the future, by incentivizing institutional reorganization and by cultivating institutional support.

ResearchMatch: a national registry to recruit volunteers for clinical research

The authors designed ResearchMatch, a disease-neutral, Web-based recruitment registry to help match individuals who wish to participate in clinical research studies with researchers actively searching for volunteers throughout the United States. In this article, they describe ResearchMatch's stakeholders, workflow model, technical infrastructure, and, for the registry's first 19 months of operation, utilization metrics. Having launched volunteer registration tools in November 2009 and researcher registration tools in March 2010, ResearchMatch had, as of June 2011, registered 15,871 volunteer participants from all 50 states. The registry was created as a collaborative project for institutions in the Clinical and Translational Science Awards (CTSA) consortium. Also as of June 2011, a total of 751 researchers from 61 participating CTSA institutions had registered to use the tool to recruit participants into 540 active studies and trials. ResearchMatch has proven successful in connecting volunteers with researchers, and the authors are currently evaluating regulatory and workflow options to open access to researchers at non-CTSA institutions.

Community engagement in biobanking: Experiences from the eMERGE Network

Advances in genomic technologies and the promise of "personalised medicine" have spurred the interest of researchers, healthcare systems, and the general public. However, the success of population-based genetic studies depends on the willingness of large numbers of individuals and diverse communities to grant researchers access to detailed medical and genetic information. Certain features of this kind of research - such as the establishment of biobanks and prospective data collection from participants' electronic medical records - make the potential risks and benefits to participants difficult to specify in advance. Therefore, community input into biobank processes is essential. In this report, we describe community engagement efforts undertaken by six United States biobanks, various outcomes from these engagements, and lessons learned. Our aim is to provide useful insights and potential strategies for the various disciplines that work with communities involved in biobank-based genomic research.

Principles of human subjects protections applied in an opt-out, de-identified biobank

BioVU, the Vanderbilt DNA Databank, is one of few biobanks that qualifies as non-human subjects research as determined by the local IRB and the federal Office of Human Research Protections (OHRP). BioVU accrues DNA samples extracted from leftover blood remaining from routine clinical testing. The resource is linked to a de-identified version of data extracted from an Electronic Medical Record (EMR) system, termed the Synthetic Device (SD), in which all personal identifiers have been removed. Thus, there is no identifiable private information attached to the records. The Belmont Report enumerates the importance of the boundary between practice and research, and three principles: Respect for Persons, Beneficence, and Justice, which constitute the essential ethical framework by which IRBs and ethics committees judge the risks and benefits of research involving human subjects. BioVU was developed by designing and implementing new procedures, for which there were no previously established methods, which are consistent with the principles of the Belmont Report. These included special oversight and governance, new informatics technologies, provisions to accommodate patients' preferences, as well as an extensive public education and communications component. Considerations of core principles and protections in the practical implementation of BioVU is the focus of this paper.

Identifying unpredicted drug benefit through query of patient experiential knowledge: a proof of concept web-based system

Information necessary to recognize unexpected drug efficacy is not routinely collected. Once a drug is approved, opportunities for understanding these phenomena are usually lost within clinical care. We propose that patients are willing to provide a wide range of experiential knowledge about the effects of therapies that is seldom solicited. Experience with various drug therapies might be solicited directly from patients in both structured and unstructured formats. Although the signal to noise ratio is expected to be low, these data, if organized in a constructive manner, could provide a useful hypothesis generation resource for areas of further pharmacologic inquiry. A pilot study was conducted for 18 months; 1,065 individuals using the MyHealthAtVanderbilt.com patient portal clicked on a research link to find more information about the study; 375 completed the survey (response rate of 37%). Of those, 218 patients reported that they were currently taking at least one prescription. Statistical methods applied detected known associations between drugs and their intended effects. This validated the type and frequency of effects being reported by patients and provided evidence for the potential for using patient-supplied information to generate hypotheses related to unexpected positive benefits associated with medications. Improved data filtering and mining methods will be needed to expand this concept.

A personnel time-motion study of intranasal influenza vaccination in healthy children

Vaccinating millions of Americans depends, in part, on short vaccination times. During two intranasal influenza vaccine trials, times for six vaccination steps were recorded for 497 children. The total of mean times for the steps was 115 s, almost half spent explaining the vaccine and intranasal delivery. Intranasal influenza vaccination time showed little variation by patient age, was comparable to reported intramuscular vaccination times, and was a small fraction of the visit time. Total family visit time decreased by 64 s if the youngest child was receiving a second dose. Alternative delivery systems (e.g., group visits) are needed to take advantage of short vaccination times.