Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human host cells via angiotensin-converting enzyme 2 (ACE2) and causes coronavirus disease 2019 (COVID-19). Here, through a genome-wide association study, we identify a variant (rs190509934, minor allele frequency 0.2-2%) that downregulates ACE2 expression by 37% (P = 2.7 × 10-8) and reduces the risk of SARS-CoV-2 infection by 40% (odds ratio = 0.60, P = 4.5 × 10-13), providing human genetic evidence that ACE2 expression levels influence COVID-19 risk. We also replicate the associations of six previously reported risk variants, of which four were further associated with worse outcomes in individuals infected with the virus (in/near LZTFL1, MHC, DPP9 and IFNAR2). Lastly, we show that common variants define a risk score that is strongly associated with severe disease among cases and modestly improves the prediction of disease severity relative to demographic and clinical factors alone.

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. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.

Analysis of Healthcare Cost and Utilization in the First Two Years of the Medicare Shared Savings Program Using Big Data from the CMS Enclave.

The Medicare Shared Savings Program (MSSP) is the larger of the first two Accountable Care Organization (ACO) programs by the Centers for Medicare and Medicaid Services (CMS). In this study we assessed healthcare cost and utilization of 1.71 million Medicare beneficiaries assigned to the 333 MSSP ACOs in the calendar years of 2013 and 2014, in comparison to years 2010 and 2011, using the official CMS data. We employed doubly robust estimation (propensity score weighting followed by generalized linear regression) to adjust the analyses to beneficiary personal traits, history of chronic conditions, previous healthcare utilization, ACO administrative region, and ZIP code socioeconomic factors. In comparison to the care delivered to the control cohort of 17.7 million non-ACO beneficiaries, we found that the care patterns for ACO beneficiaries shifted away from some costly types of care, but at the expense of increased utilization of other types, increased imaging and testing expenditures, and increased medication use, with overall net greater increase in cost instead of smaller increase.

Identifying Repetitive Institutional Review Board Stipulations by Natural Language Processing and Network Analysis.

The corrections ("stipulations") to a proposed research study protocol produced by an institutional review board (IRB) can often be repetitive across many studies; however, there is no standard set of stipulations that could be used, for example, by researchers wishing to anticipate and correct problems in their research proposals prior to submitting to an IRB. The objective of the research was to computationally identify the most repetitive types of stipulations generated in the course of IRB deliberations. The text of each stipulation was normalized using the natural language processing techniques. An undirected weighted network was constructed in which each stipulation was represented by a node, and each link, if present, had weight corresponding to the TF-IDF Cosine Similarity of the stipulations. Network analysis software was then used to identify clusters in the network representing similar stipulations. The final results were correlated with additional data to produce further insights about the IRB workflow. From a corpus of 18,582 stipulations we identified 31 types of repetitive stipulations. Those types accounted for 3,870 stipulations (20.8% of the corpus) produced for 697 (88.7%) of all protocols in 392 (also 88.7%) of all the CNS IRB meetings with stipulations entered in our data source. A notable peroportion of the corrections produced by the IRB can be considered highly repetitive. Our shareable method relied on a minimal manual analysis and provides an intuitive exploration with theoretically unbounded granularity. Finer granularity allowed for the insight that is anticipated to prevent the need for identifying the IRB panel expertise or any human supervision.

Computationally Comparing and Analyzing All Published Scoring Systems for Diagnosis of Disseminated Intravascular Coagulation.

The clinical literature presents four different scoring systems (SS) for the diagnosis of disseminated intravascular coagulation (DIC) by four institutions: ISTH, JMHLW, JAAM and KSTH. In this study a Java program was written to retrieve medical records from the MIMIC-II database and apply the criteria of all four. The program then quantified the agreement of each DIC SS with each other and demonstrated notorious dissent. Furthermore, the average internal composition of each score was also quantified. All source code produced is available for download at https://github.com/fabkury/hedicim.

Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II.

In this paper we sought to reproduce, as a computational retrospective study in an EHR database (MIMIC-II), a recent large prospective clinical study: the 2013 publication, by the Japanese Association for Acute Medicine (JAAM), about disseminated intravascular coagulation, in the journal Critical Care (PMID: 23787004). We designed in SQL and Java a set of electronic phenotypes that reproduced the study's data sampling, and used R to perform the same statistical inference procedures. All produced source code is available online at https://github.com/fabkury/paamia2015. Our program identified 2,257 eligible patients in MIMIC-II, and the results remarkably agreed with the prospective study. A minority of the needed data elements was not found in MIMIC-II, and statistically significant inferences were possible in the majority of the cases.