Common and rare variant associations with clonal haematopoiesis phenotypes.

Clonal haematopoiesis involves the expansion of certain blood cell lineages and has been associated with ageing and adverse health outcomes. Here we use exome sequence data on 628,388 individuals to identify 40,208 carriers of clonal haematopoiesis of indeterminate potential (CHIP). Using genome-wide and exome-wide association analyses, we identify 24 loci (21 of which are novel) where germline genetic variation influences predisposition to CHIP, including missense variants in the lymphocytic antigen coding gene LY75, which are associated with reduced incidence of CHIP.

ANGPTL7, a therapeutic target for increased intraocular pressure and glaucoma.

Glaucoma is a leading cause of blindness. Current glaucoma medications work by lowering intraocular pressure (IOP), a risk factor for glaucoma, but most treatments do not directly target the pathological changes leading to increased IOP, which can manifest as medication resistance as disease progresses. To identify physiological modulators of IOP, we performed genome- and exome-wide association analysis in >129,000 individuals with IOP measurements and extended these findings to an analysis of glaucoma risk.

Germline Mutations in and Protection against Liver Disease.

Background: Exome sequencing in hundreds of thousands of persons may enable the identification of rare protein-coding genetic variants associated with protection from human diseases like liver cirrhosis, providing a strategy for the discovery of new therapeutic targets.

Methods: We performed a multistage exome sequencing and genetic association analysis to identify genes in which rare protein-coding variants were associated with liver phenotypes. We conducted in vitro experiments to further characterize associations.

Exome sequencing and analysis of 454,787 UK Biobank participants.

A major goal in human genetics is to use natural variation to understand the phenotypic consequences of altering each protein-coding gene in the genome. Here we used exome sequencing to explore protein-altering variants and their consequences in 454,787 participants in the UK Biobank study. We identified 12 million coding variants, including around 1 million loss-of-function and around 1.

Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential.

Comparing Clinical Characteristics of Influenza and Common Coronavirus Infections Using Electronic Health Records.

Background: We compared outcomes in inpatients and outpatients, pre-COVID-19, who were infected with either coronavirus or influenza.

Methods: Using deidentified electronic health records data from the Geisinger-Regeneron partnership, we compared patients with RT-PCR-positive tests for the 4 common coronaviruses (229E, HKU1, NL63, OC43) or influenza (A and B) from June 2016 to February 2019.

Results: Overall, 52 833 patients were tested for coronaviruses and influenza.

Implementation and early adaptation of patient-reported outcome measures into an electronic health record: A technical report.

We integrated and optimized patient-reported outcome measures into the electronic health record to provide quantitative, objective data regarding patients' health status, which is important for patient care, payer contracts, and research. With a multidisciplinary team from information technology, clinical informatics, population health, and physician champions, we used formal human-computer interaction techniques and user-centered design to integrate several technology platforms and computerized adaptive testing for the National Institutes of Health Patient-Reported Outcomes Measurement Information System. The patient-reported outcome measure system leverages software frequently used by health systems and provides data for research and clinical care via a mobile-responsive web application using Symfony, with REDCap for configuring assessments and de-identified data storage.

Measuring Patient and Staff Satisfaction Before and After Implementation of a Paperless Registration System.

While many aspects of patient care have transitioned to digital technology, the patient registration process often is still paper based. Several studies have examined the effects of changes in clinic workflows and appointment scheduling on patient satisfaction, but few have investigated changes from a paper-based to a paperless registration process. The authors measured patient and staff satisfaction before and after implementation of a new, tablet-based registration process at NYU Langone Health's Center for Women's Health in New York City.

Integrating Data On Social Determinants Of Health Into Electronic Health Records.

As population health becomes more of a focus of health care, providers are realizing that data outside of traditional clinical findings can provide a broader perspective on potential drivers of a patient's health status and can identify approaches to improving the effectiveness of care. However, many challenges remain before data related to the social determinants of health, such as environmental conditions and education levels, are as readily accessible and actionable as medical data are. Key challenges are a lack of consensus on standards for capturing or representing social determinants of health in electronic health records and insufficient evidence that once information on them has been collected, social determinants can be effectively addressed through referrals or other action tools.

FACETS: using open data to measure community social determinants of health.

Objective: To develop a dataset based on open data sources reflective of community-level social determinants of health (SDH).

Materials And Methods: We created FACETS (Factors Affecting Communities and Enabling Targeted Services), an architecture that incorporates open data related to SDH into a single dataset mapped at the census-tract level for New York City.

Results: FACETS (https://github.

Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.

Marinobacter sp. strain MCTG268 was isolated from the cosmopolitan marine diatom Skeletonema costatum and can degrade oil hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 4,449,396 bp with 4,157 genes and an average G+C content of 57.

Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.

Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the ability to utilize polycyclic aromatic hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 5,550,230 bp with 4,722 genes and an average G+C content of 39.7%.

Repurposing historical control clinical trial data to provide safety context.

Billions of dollars spent, millions of subject-hours of clinical trial experience and an abundance of archived study-level data, yet why are historical data underutilized? We propose that historical data can be aggregated to provide safety, background incidence rate and context to improve the evaluation of new medicinal products. Here, we describe the development and application of the eControls database, which is derived from the control arms of studies of licensed products, and discuss the challenges and potential solutions to the proper application of historical data to help interpret product safety.