Core Concepts in Pharmacoepidemiology: Principled Use of Artificial Intelligence and Machine Learning in Pharmacoepidemiology and Healthcare Research.

Artificial intelligence (AI) and machine learning (ML) are important tools across many fields of health and medical research. Pharmacoepidemiologists can bring essential methodological rigor and study design expertise to the design and use of these technologies within healthcare settings. AI/ML-based tools also play a role in pharmacoepidemiology research, as we may apply them to answer our own research questions, take responsibility for evaluating medical devices with AI/ML components, or participate in interdisciplinary research to create new AI/ML algorithms.

Low antibody levels associated with significantly increased rate of SARS-CoV-2 infection in a highly vaccinated population from the US National Basketball Association.

SARS-CoV-2 antibody levels may serve as a correlate for immunity and could inform optimal booster timing. The relationship between antibody levels and protection from infection was evaluated in vaccinated individuals from the US National Basketball Association who had antibody levels measured at a single time point from September 12, 2021, to December 31, 2021. Cox proportional hazards models were used to estimate the risk of infection within 90 days of serologic testing by antibody level (<250, 250-800, and >800 AU/mL ), adjusting for age, time since last vaccine dose, and history of SARS-CoV-2 infection.

The "Bubble": What Can Be Learned from the National Basketball Association (NBA)'s 2019-20 Season Restart in Orlando during the COVID-19 Pandemic.

Background: The National Basketball Association (NBA) suspended operations in response to the COVID-19 pandemic in March 2020. To safely complete the 2019-20 season, the NBA created a closed campus in Orlando, Florida, known as the NBA "Bubble." More than 5000 individuals lived, worked, and played basketball at a time of high local prevalence of SARS-CoV-2.

Viral kinetics of sequential SARS-CoV-2 infections.

The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we identified 71 individuals with two well-sampled SARS-CoV-2 infections between March 11, 2020, and July 28, 2022. We compared the SARS-CoV-2 viral kinetics of first vs.

Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study.

Background: The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear.

Methods: We characterized 1,280 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic viral RNA kinetics models were used to quantify the effect of age, variant, symptom status, infection history, vaccination status and antibody titer to the founder SARS-CoV-2 strain on the duration of potential infectiousness and overall viral kinetics.

Association Between COVID-19 Booster Vaccination and Omicron Infection in a Highly Vaccinated Cohort of Players and Staff in the National Basketball Association.

This study compares the incidence of SARS-CoV-2 infection in players and staff of the National Basketball Association (NBA) who did vs those who did not receive a COVID-19 vaccine booster dose.

SARS-CoV-2 Transmission Risk Among National Basketball Association Players, Staff, and Vendors Exposed to Individuals With Positive Test Results After COVID-19 Recovery During the 2020 Regular and Postseason.

Importance: Clinical data are lacking regarding the risk of viral transmission from individuals who have positive reverse-transcription-polymerase chain reaction (RT-PCR) SARS-CoV-2 test results after recovery from COVID-19.

Objective: To describe case characteristics, including viral dynamics and transmission of infection, for individuals who have clinically recovered from SARS-CoV-2 infection but continued to have positive test results following discontinuation of isolation precautions.

Design, Setting, And Participants: This retrospective cohort study used data collected from June 11, 2020, to October 19, 2020, as part of the National Basketball Association (NBA) closed campus occupational health program in Orlando, Florida, which required daily RT-PCR testing and ad hoc serological testing for SARS-CoV-2 IgG antibodies.

Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts.

Even distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types.

A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility.

To identify rare variants associated with prostate cancer susceptibility and better characterize the mechanisms and cumulative disease risk associated with common risk variants, we conducted an integrated study of prostate cancer genetic etiology in two cohorts using custom genotyping microarrays, large imputation reference panels, and functional annotation approaches. Specifically, 11,984 men (6,196 prostate cancer cases and 5,788 controls) of European ancestry from Northern California Kaiser Permanente were genotyped and meta-analyzed with 196,269 men of European ancestry (7,917 prostate cancer cases and 188,352 controls) from the UK Biobank. Three novel loci, including two rare variants (European ancestry minor allele frequency < 0.

Multiple Stakeholder Views on Data Sharing in a Biobank in an Integrated Healthcare Delivery System: Implications for Biobank Governance.

Background: Beginning in 2005, researchers at Kaiser Permanente Northern California (KPNC) Division of Research developed the Research Program on Genes, Environment, and Health (RPGEH), a research resource of linked biospecimens, health surveys, and electronic health records on more than 200,000 adult KPNC members. This study examined multiple stakeholders' values and preferences regarding protection of participants' privacy and wide sharing of participant data by RPGEH.

Methods: We conducted 45 semi-structured interviews in person or via phone and two focus groups with seven stakeholder groups, including RPGEH participants and decliners who are KPNC members, KPNC research scientists, external scientists, leadership, Human Subjects Research Protection Program staff, and RPGEH Community Advisory Panel members.

Update on the State of the Science for Analytical Methods for Gene-Environment Interactions.

The analysis of gene-environment interaction (G×E) may hold the key for further understanding the etiology of many complex traits. The current availability of high-volume genetic data, the wide range in types of environmental data that can be measured, and the formation of consortiums of multiple studies provide new opportunities to identify G×E but also new analytical challenges. In this article, we summarize several statistical approaches that can be used to test for G×E in a genome-wide association study.

The Population Burden of Cancer: Research Driven by the Catchment Area of a Cancer Center.

Cancer centers, particularly those supported by the National Cancer Institute, are charged with reducing the cancer burden in their catchment area. However, methods to define both the catchment area and the cancer burden are diverse and range in complexity often based on data availability, staff resources, or confusion about what is required. This article presents a review of the current literature identifying 4 studies that have defined various aspects of the cancer burden in a defined geographical area and highlights examples of how some cancer centers and other health institutions have defined their catchment area and characterized the cancer burden within it.

Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk.

Breast cancer is the most common solid organ malignancy and the most frequent cause of cancer death among women worldwide. Previous research has yielded insights into its genetic etiology, but there remains a gap in the understanding of genetic factors that contribute to risk, and particularly in the biological mechanisms by which genetic variation modulates risk. The National Cancer Institute's "Up for a Challenge" (U4C) competition provided an opportunity to further elucidate the genetic basis of the disease.

Detecting gene-environment interactions in human birth defects: Study designs and statistical methods.

Background: The National Birth Defects Prevention Study (NBDPS) contains a wealth of information on affected and unaffected family triads, and thus provides numerous opportunities to study gene-environment interactions (G×E) in the etiology of birth defect outcomes. Depending on the research objective, several analytic options exist to estimate G×E effects that use varying combinations of individuals drawn from available triads.

Methods: In this study, we discuss important considerations in the collection of genetic data and environmental exposures.

Leveraging state cancer registries to measure and improve the quality of cancer care: a potential strategy for California and beyond.

Despite recent increased attention to healthcare performance and the burden of disease from cancer, measures of quality of cancer care are not readily available. In 2013, the California HealthCare Foundation convened an expert workgroup to explore the potential for leveraging data in the California Cancer Registry (CCR), one of the world's largest population-based cancer registries, for measuring and improving the quality of cancer care. The workgroup assessed current registry operations, the value to be gained by linking CCR data with health insurance claims or encounter data and clinical data contained in health system electronic health records, and potential barriers to these linkages.

Video-based educational tool improves patient comprehension of common prostate health terminology.

Background: Health care providers often counsel prostate cancer patients about treatment options with medical terminology. However, studies have demonstrated a severe lack of comprehension of these terms, particularly in underserved populations. It was hypothesized that a video-based educational tool would significantly improve the understanding of key terms related to prostate health in a predominantly lower literacy population.

External validation of the modified Glasgow prognostic score for renal cancer.

Purpose: The modified Glasgow prognostic Score (mGPS) incorporates C-reactive protein and albumin as a clinically useful marker of tumor behavior. The ability of the mGPS to predict metastasis in localized renal cell carcinoma (RCC) remains unknown in an external validation cohort.

Patients And Methods: Patients with clinically localized clear cell RCC were followed for 1 year post-operatively.

Severe lack of comprehension of common prostate health terms among low-income inner-city men.

Background: Patients diagnosed with prostate cancer are often counseled about treatment options with the use of terms that are part of the "core vocabulary" of prostate cancer. It is hypothesized that predominantly lower literacy patients would demonstrate a severe lack of comprehension of prostate cancer terms, thus validating the findings of a previous single-institution study.

Methods: A previously developed survey was used to evaluate understanding of terms related to urinary, bowel, and sexual function.