COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine: Observational Study

Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine

Precision medicine initiatives across the globe have led to a revolution of repositories linking large-scale genomic data with electronic health records, enabling genomic analyses across the entire phenome. Many of these initiatives focus solely on research insights, leading to limited direct benefit to patients. We describe the biobank at the Colorado Center for Personalized Medicine (CCPM Biobank) that was jointly developed by the University of Colorado Anschutz Medical Campus and UCHealth to serve as a unique, dual-purpose research and clinical resource accelerating personalized medicine. This living resource currently has more than 200,000 participants with ongoing recruitment. We highlight the clinical, laboratory, regulatory, and HIPAA-compliant informatics infrastructure along with our stakeholder engagement, consent, recontact, and participant engagement strategies. We characterize aspects of genetic and geographic diversity unique to the Rocky Mountain region, the primary catchment area for CCPM Biobank participants. We leverage linked health and demographic information of the CCPM Biobank participant population to demonstrate the utility of the CCPM Biobank to replicate complex trait associations in the first 33,674 genotyped individuals across multiple disease domains. Finally, we describe our current efforts toward return of clinical genetic test results, including high-impact pathogenic variants and pharmacogenetic information, and our broader goals as the CCPM Biobank continues to grow. Bringing clinical and research interests together fosters unique clinical and translational questions that can be addressed from the large EHR-linked CCPM Biobank resource within a HIPAA- and CLIA-certified environment.

COVID-19 Mortality in the Colorado Center for Personalized Medicine Biobank

Over 6.37 million people have died from COVID-19 worldwide, but factors influencing COVID-19-related mortality remain understudied. We aimed to describe and identify risk factors for COVID-19 mortality in the Colorado Center for Personalized Medicine (CCPM) Biobank using integrated data sources, including Electronic Health Records (EHRs). We calculated cause-specific mortality and case-fatality rates for COVID-19 and common pre-existing health conditions defined by diagnostic phecodes and encounters in EHRs. We performed multivariable logistic regression analyses of the association between each pre-existing condition and COVID-19 mortality. Of the 155,859 Biobank participants enrolled as of July 2022, 20,797 had been diagnosed with COVID-19. Of 5334 Biobank participants who had died, 190 were attributed to COVID-19. The case-fatality rate was 0.91% and the COVID-19 mortality rate was 122 per 100,000 persons. The odds of dying from COVID-19 were significantly increased among older men, and those with 14 of the 61 pre-existing conditions tested, including hypertensive chronic kidney disease (OR: 10.14, 95% CI: 5.48, 19.16) and type 2 diabetes with renal manifestations (OR: 5.59, 95% CI: 3.42, 8.97). Male patients who are older and have pre-existing kidney diseases may be at higher risk for death from COVID-19 and may require special care.

Population Health Metrics During the Early Stages of the COVID-19 Pandemic: Correlative Pilot Study

BACKGROUND

COVID-19 has caused nearly 1 million deaths in the United States, not to mention job losses, business and school closures, stay-at-home orders, and mask mandates. Many people have suffered increased anxiety and depression since the pandemic began. Not only have mental health symptoms become more prevalent, but alcohol consumption has also increased during this time. Helplines offer important insight into both physical and mental wellness of a population by offering immediate, anonymous, cheap, and accessible resources for health and substance use disorders (SUD) that was unobstructed by many of the mandates of the pandemic. Further, the pandemic also launched the use of wastewater surveillance, which has the potential for tracking not only population infections but also consumption of substances such as alcohol.

OBJECTIVE

This study assessed the feasibility of using multiple public surveillance metrics, such as helpline calls, COVID-19 cases, and alcohol metabolites in wastewater, to better understand the need for interventions or public health programs in the time of a public health emergency.

METHODS

Ethanol metabolites were analyzed from wastewater collected twice weekly from September 29 to December 4, 2020, in a Midwestern state. Calls made to the helpline regarding housing, health care, and mental health/SUD were correlated with ethanol metabolites analyzed from wastewater samples, as well as the number of COVID-19 cases during the sampling period.

RESULTS

Correlations were observed between COVID-19 cases and helpline calls regarding housing and health care needs. No correlation was observed between the number of COVID-19 cases and mental health/SUD calls. COVID-19 cases on Tuesdays were correlated with the alcohol metabolite ethyl glucuronide (EtG). Finally, EtG levels were negatively associated with mental health/SUD helpline calls.

CONCLUSIONS

Although helpline calls provided critical services for health care and housing-related concerns early in the pandemic, evidence suggests helpline calls for mental health/SUD-related concerns were unrelated to COVID-19 metrics. Instead, COVID metrics were associated with alcohol metabolites in wastewater. Although this research was formative, with continued and expanded monitoring of population metrics, such as helpline usage, COVID-19 metrics, and wastewater, strategies can be implemented to create precision programs to address the needs of the population.