Comparing Anesthesia and Surgery Controlled Time for Primary Total Knee and Hip Arthroplasty Between an Academic Medical Center and a Community Hospital: Retrospective Cohort Study

BACKGROUND

Osteoarthritis is a significant cause of disability, resulting in increased joint replacement surgeries and health care costs. Establishing benchmarks that more accurately predict surgical duration could help to decrease costs, maximize efficiency, and improve patient experience. We compared the anesthesia-controlled time (ACT) and surgery-controlled time (SCT) of primary total knee (TKA) and total hip arthroplasties (THA) between an academic medical center (AMC) and a community hospital (CH) for 2 orthopedic surgeons.

OBJECTIVE

This study aims to validate and compare benchmarking times for ACT and SCT in a single patient population at both an AMC and a CH.

METHODS

This retrospective 2-center observational cohort study was conducted at the University of Colorado Hospital (AMC) and UCHealth Broomfield Hospital (CH). Cases with current procedural terminology codes for THA and TKA between January 1, 2019, and December 31, 2020, were assessed. Cases with missing data were excluded. The primary outcomes were ACT and SCT. Primary outcomes were tested for association with covariates of interest. The primary covariate of interest was the location of the procedure (CH vs AMC); secondary covariates of interest included the American Society of Anesthesiologists (ASA) classification and anesthetic type. Linear regression models were used to assess the relationships.

RESULTS

Two surgeons performed 1256 cases at the AMC and CH. A total of 10 THA cases and 12 TKA cases were excluded due to missing data. After controlling for surgeon, the ACT was greater at the AMC for THA by 3.77 minutes and for TKA by 3.58 minutes (P<.001). SCT was greater at the AMC for THA by 11.14 minutes and for TKA by 14.04 minutes (P<.001). ASA III/IV classification increased ACT for THA by 3.76 minutes (P<.001) and increased SCT for THA by 6.33 minutes after controlling for surgeon and location (P=.008). General anesthesia use was higher at the AMC for both THA (29.2% vs 7.3%) and TKA (23.8% vs 4.2%). No statistically significant association was observed between either ACT or SCT and anesthetic type (neuraxial or general) after adjusting for surgeon and location (all P>.05).

CONCLUSIONS

We observed lower ACT and SCT at the CH for both TKA and THA after controlling for the surgeon of record and ASA classification. These findings underscore the efficiency advantages of performing primary joint replacements at the CH, showcasing an average reduction of 16 minutes in SCT and 4 minutes in ACT per case. Overall, establishing more accurate benchmarks to improve the prediction of surgical duration for THA and TKA in different perioperative environments can increase the reliability of surgical duration predictions and optimize scheduling. Future studies with study populations at multiple community hospitals and academic medical centers are needed before extrapolating these findings.

Operational outcomes of propofol sedation versus fentanyl, midazolam and diphenhydramine sedation for endoscopies and colonoscopies at an academic medical center

BACKGROUND

On July 1st, 2021, the University of Colorado Hospital (UCH) implemented new sedation protocols in the luminal gastrointestinal (GI) suite. GI proceduralist supervised, Nurse Administered Sedation with fentanyl, midazolam, and diphenhydramine (NAS) sedation was transitioned to Monitored Anesthesia Care with propofol under physician anesthesiologist supervision (MAC).

OBJECTIVE

To determine if there are statistically significant reductions in Sedation-Start to Scope-In time (SSSI) when using Monitored Anesthesia Care with propofol (MAC) versus Nurse Administered Sedation with fentanyl, midazolam, and diphenhydramine (NAS). Secondary objectives were to determine if statistically significant improvements to other operational times, quality measures, and satisfaction metrics were present.

METHOD

This study was a retrospective analysis of a natural experiment resultant of a change from NAS to MAC sedation protocols. Outcomes for NAS protocols from 1/1/21-6/30/21 were compared to outcomes of MAC protocols from the dates 8/1/21-10/31/21. Results were analyzed using Quasi-Poisson regression analysis and stratified based on upper GI, lower GI, and combined procedures. Patient demographic data including age, biological sex, comorbidities, and BMI, were adjusted for in the analysis. ASA matching was not performed as nursing sedation does not use ASA classifications. Pre-anesthesia co-morbidities were assessed via evaluation of a strict set of comorbidities abstracted from the electronic medical record. Perioperative operational outcomes include Sedation Start to Scope-In (SSSI), In-Room to Scope-In Time (IRSI), Scope Out to Out of Room (SOOR), Total Case Length (TCL), and Post Anesthesia Care Unit Length of Stay (PACU LOS). Quality outcomes include PACU Administered Medications (PAM), and Clinician Satisfaction Scores (CSS).

RESULTS

A total of 5,582 gastrointestinal (GI) endoscopic cases (upper, lower, and combined endoscopies) were observed. Statistically significant decreases in SSSI of 2.5, 2.1, and 2.2 minutes for upper, lower, and dual GI procedures were observed when using MAC protocols. A statistically significant increase in satisfaction scores of 47.0 and 19.6 points were observed for nurses and proceduralists, respectively, when using MAC.

CONCLUSION

MAC protocols for endoscopic GI procedures at UCH led to statistically significant decreases in the time required to complete procedures thus increasing operational efficiency.

Factors Predictive of Treatment Success in CT-Guided Fibrin Occlusion of CSF-Venous Fistulas: A Multicenter Retrospective Cross-Sectional Study

BACKGROUND AND PURPOSE

CSF-to-venous fistulas contribute to spontaneous intracranial hypotension. CT-guided fibrin occlusion has been described as a minimally invasive treatment strategy; however, its reproducibility across different institutions remains unclear. This multi-institution study evaluated the clinical and radiologic outcomes of CT-guided fibrin occlusion, hypothesizing a correlation among cure rates, fibrin injectate spread, and drainage patterns.

MATERIALS AND METHODS

A retrospective evaluation was conducted on CT-guided fibrin glue treatment in patients with CSF-to-venous fistulas from 6 US and UK institutions from 2020 to 2023. Patient information, procedural characteristics, and injectate spread and drainage patterns were examined. Clinical improvement assessed through medical records served as the primary outcome.

RESULTS

Of 119 patients at a mean follow-up of 5.0 months, fibrin occlusion resulted in complete clinical improvement in 59.7%, partial improvement in 34.5%, and no improvement in 5.9% of patients. Complications were reported in 4% of cases. Significant associations were observed between clinical improvement and concordant injectate spread with the fistula drainage pattern (P = .0089) and pretreatment symptom duration (P < .001). No associations were found between clinical improvement and cyst puncture, intravascular extension, rebound headache, body mass index, age, or number of treatment attempts.

CONCLUSIONS

Fibrin occlusion performed across various institutions shows cure when associated with injectate spread matching the CVF drainage pattern and shorter pretreatment symptom duration, emphasizing the importance of accurate injectate placement and early intervention.

Prenatal exposures to per- and polyfluoroalkyl substances and epigenetic aging in umbilical cord blood: The Healthy Start study

BACKGROUND

Per- and polyfluoroalkyl substances (PFAS) are ubiquitous, environmentally persistent chemicals, and prenatal exposures have been associated with adverse child health outcomes. Prenatal PFAS exposure may lead to epigenetic age acceleration (EAA), defined as the discrepancy between an individual's chronologic and epigenetic or biological age.

OBJECTIVES

We estimated associations of maternal serum PFAS concentrations with EAA in umbilical cord blood DNA methylation using linear regression, and a multivariable exposure-response function of the PFAS mixture using Bayesian kernel machine regression.

METHODS

Five PFAS were quantified in maternal serum (median: 27 weeks of gestation) among 577 mother-infant dyads from a prospective cohort. Cord blood DNA methylation data were assessed with the Illumina HumanMethylation450 array. EAA was calculated as the residuals from regressing gestational age on epigenetic age, calculated using a cord-blood specific epigenetic clock. Linear regression tested for associations between each maternal PFAS concentration with EAA. Bayesian kernel machine regression with hierarchical selection estimated an exposure-response function for the PFAS mixture.

RESULTS

In single pollutant models we observed an inverse relationship between perfluorodecanoate (PFDA) and EAA (-0.148 weeks per log-unit increase, 95% CI: -0.283, -0.013). Mixture analysis with hierarchical selection between perfluoroalkyl carboxylates and sulfonates indicated the carboxylates had the highest group posterior inclusion probability (PIP), or relative importance. Within this group, PFDA had the highest conditional PIP. Univariate predictor-response functions indicated PFDA and perfluorononanoate were inversely associated with EAA, while perfluorohexane sulfonate had a positive association with EAA.

CONCLUSIONS

Maternal mid-pregnancy serum concentrations of PFDA were negatively associated with EAA in cord blood, suggesting a pathway by which prenatal PFAS exposures may affect infant development. No significant associations were observed with other PFAS. Mixture models suggested opposite directions of association between perfluoroalkyl sulfonates and carboxylates. Future studies are needed to determine the importance of neonatal EAA for later child health outcomes.

Prophylactic Administration of Vasopressors Prior to Emergency Intubation in Critically Ill Patients: A Secondary Analysis of Two Multicenter Clinical Trials

Hypotension affects approximately 40% of critically ill patients undergoing emergency intubation and is associated with an increased risk of death. The objective of this study was to examine the association between prophylactic vasopressor administration and the incidence of peri-intubation hypotension and other clinical outcomes.

DESIGN

A secondary analysis of two multicenter randomized clinical trials. The clinical effect of prophylactic vasopressor administration was estimated using a one-to-one propensity-matched cohort of patients with and without prophylactic vasopressors.

SETTING

Seven emergency departments and 17 ICUs across the United States.

PATIENTS

One thousand seven hundred ninety-eight critically ill patients who underwent emergency intubation at the study sites between February 1, 2019, and May 24, 2021.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

The primary outcome was peri-intubation hypotension defined as a systolic blood pressure less than 90 mm Hg occurring between induction and 2 minutes after tracheal intubation. A total of 187 patients (10%) received prophylactic vasopressors prior to intubation. Compared with patients who did not receive prophylactic vasopressors, those who did were older, had higher Acute Physiology and Chronic Health Evaluation II scores, were more likely to have a diagnosis of sepsis, had lower pre-induction systolic blood pressures, and were more likely to be on continuous vasopressor infusions prior to intubation. In our propensity-matched cohort, prophylactic vasopressor administration was not associated with reduced risk of peri-intubation hypotension (41% vs 32%; p = 0.08) or change in systolic blood pressure from baseline (-12 vs -11 mm Hg; p = 0.66).

CONCLUSIONS

The administration of prophylactic vasopressors was not associated with a lower incidence of peri-intubation hypotension in our propensity-matched analysis. To address potential residual confounding, randomized clinical trials should examine the effect of prophylactic vasopressor administration on peri-intubation outcomes.

A Multi-Omic Mosaic Model of Acetaminophen Induced Alanine Aminotransferase Elevation

BACKGROUND

Acetaminophen (APAP) is the most common cause liver injury following alcohol in US patients. Predicting liver injury and subsequent hepatic regeneration in patients taking therapeutic doses of APAP may be possible using new 'omic methods such as metabolomics and genomics. Multi'omic techniques increase our ability to find new mechanisms of injury and regeneration.

METHODS

We used metabolomic and genomic data from a randomized controlled trial of patients administered 4 g of APAP per day for 14 days or longer with blood samples obtained at 0 (baseline), 4, 7, 10, 13 and 16 days. We used the highest ALT as the clinical outcome to be predicted in our integrated analysis. We used penalized regression to model the relationship between genetic variants and day 0 metabolite level, and then performed a metabolite-wide colocalization scan to associate the genetically regulated component of metabolite expression with ALT elevation. Genome-wide association study (GWAS) analyses were conducted for ALT elevation and metabolite level using linear regression, with age, sex, and the first five principal components included as covariates. Colocalization was tested via a weighted sum test.

RESULTS

Out of the 164 metabolites modeled, 120 met the criteria for predictive accuracy and were retained for genetic analyses. After genomic examination, eight metabolites were found to be under genetic control and predictive of ALT elevation due to therapeutic acetaminophen. The metabolites were: 3-oxalomalate, allantoate, diphosphate, L-carnitine, L-proline, maltose, and ornithine. These genes are important in the tricarboxylic acid cycle (TCA), urea breakdown pathway, glutathione production, mitochondrial energy production, and maltose metabolism.

CONCLUSIONS

This multi'omic approach can be used to integrate metabolomic and genomic data allowing identification of genes that control downstream metabolites. These findings confirm prior work that have identified mitochondrial energy production as critical to APAP induced liver injury and have confirmed our prior work that demonstrate the importance of the urea cycle in therapeutic APAP liver injury.

Relationship of Bern Score, Spinal Elastance, and Opening Pressure in Patients With Spontaneous Intracranial Hypotension

BACKGROUND AND OBJECTIVES

Existing tools to diagnose spontaneous intracranial hypotension (SIH), namely spinal opening pressure (OP) and brain MRI, have limited sensitivity. We investigated whether evaluation of brain MRI using the Bern Score, combined with calculated craniospinal elastance, would aid in diagnosing SIH and provide insight into its pathophysiology.

METHODS

A retrospective chart review was performed of patients who underwent brain MRI and pressure-augmented dynamic CT myelography (dCTM) for suspicion of SIH. Two blinded Neuroradiologists assigned Bern Scores for each brain MRI. OP and incremental pressure changes after intrathecal saline infusion were recorded to calculate craniospinal elastance. The relationship between Bern Score, OP, elastance, and whether a leak was found were analyzed.

RESULTS

72 consecutive dCTMs were performed in 53 patients. 12 CSF-venous fistulae, two ruptured meningeal diverticula, two dural defects, and one dural bleb were found (17/53=32%). Among patients with imaging proven CSF leak/fistula, OP was normal in all but one patient, and was not significantly different in those with a leak compared to those without (15.1 vs 13.6 cm H2O, p = 0.24, A=0.40). Average Bern Score in individuals with a leak was significantly higher than in those without (5.35 vs 1.85, p < 0.001, A=0.85), even when excluding pachymeningeal enhancement from the score (3.77 vs 1.57, p = 0.001, A=0.78). Average elastance in those with a leak was higher than in those without, but this difference was not statistically significant (2.05 vs 1.20 mL/cm H2O, p = 0.19, A=0.40). Increased elastance was significantly associated with an increased Bern Score (p < 0.01, 95% CI -0.55, 0.12), and was significantly associated with venous distention, pachymeningeal enhancement, prepontine narrowing, and subdural collections, but not a narrowed mamillopontine or suprasellar distance.

DISCUSSION

OP is not an effective predictor for diagnosing CSF leak, and if used in isolation would result in misdiagnosis of 94% of patients in our cohort. The Bern Score was associated with a higher diagnostic yield of dCTM. Elastance was significantly associated with certain components of the Bern Score.

Ordering Characteristics Predictive of Noncontrast CT Head Positivity in the Emergency Department

RATIONALE AND OBJECTIVES

Recent decades have seen a steady increase in noncontrast head CT utilization in the emergency department with a concurrent rise in the practice of physician assistants (PAs) and nurse practitioners (NPs). The goal of this study was to identify ordering and patient characteristics predictive of positive noncontrast head CTs in the ED. We hypothesized NP/PAs would have lower positivity rates compared to physicians, suggestive of relative overutilization.

MATERIALS AND METHODS

We retrospectively identified ED patients who underwent noncontrast head CTs at a single institution: a nonlevel 1 trauma center, during a 7-year period, recording examination positivity, ordering provider training/experience, and multiple additional ordering/patient attributes. Exam positivity was defined as any intracranial abnormality necessitating a change in acute management, such as acute hemorrhage, hydrocephalus, herniation, or worsening prior findings.

RESULTS

6624 patients met inclusion criteria. 4.6% (280/6107) of physician exams were positive while 3.7% (19/517) of NP/PA exams were positive; however, differences were not significant. Increasing provider experience was not associated with positivity. Attributes with increased positivity were patient age (p < 0.001), daytime exam (p < 0.05), and indications regarding malignancy (p < 0.001) or focal neurologic deficit (p = 0.001). Attributes with decreased positivity were indications of trauma (p < 0.001) or vertigo/dizziness (p < 0.05).

CONCLUSION

We found no significant difference in rates of exam positivity between physicians and NP/PAs, even accounting for years of experience. This suggests increasing utilization of head CTs in the ED is not due to the increasing presence of NP/PAs, and may be reflective of general practice trends and clear diagnostic algorithms leading to head CT.

Evaluation of Cerebrovascular Reactivity and Vessel Wall Imaging in Patients With Prior COVID-19: A Prospective Case-Control MRI Study

BACKGROUND. SARS-CoV-2 infection is associated with acute stroke, possibly caused by viral tropism to the vascular endothelium. Whether cerebrovascular endothelial dysfunction and inflammation persist after acute infection is poorly understood. OBJECTIVE. The purposes of this study were to assess the association between prior SARS-CoV-2 infection and cerebrovascular reactivity (CVR) and vessel wall imaging (VWI) abnormalities and to explore the association between CVR impairment and post-COVID neurologic conditions. METHODS. This prospective study included 15 participants with prior SARS-CoV-2 infection (11 women, four men; mean age, 43 years; mean time since infection, 238 days; three with prior critical illness, 12 with prior mild illness; seven with post-COVID neurologic conditions) and 10 control participants who had never had SARS-CoV-2 infection (two women, two men; mean age, 44 years) from July 1, 2021, to February 9, 2022. Participants underwent research MRI that included arterial spin labeling perfusion imaging with acetazolamide stimulus to measure cerebral blood flow (CBF) and calculate CVR. Examinations also included VWI, performed with a contrast-enhanced black-blood 3D T1-weighted sequence. An age- and sex-adjusted linear model was used to assess associations between CVR and prior infection. A t test was used to assess associations between CVR and post-COVID neurologic conditions in participants with previous infection. A difference of proportions test was used to assess associations between VWI abnormalities and infection status. RESULTS. Mean whole-cortex CBF after acetazolamide administration was greater in participants without previous infection than in participants with previous infection (73.8 ± 13.2 [SD] vs 60.5 ± 15.8 mL/100 gm/min; p = .04). Whole-brain CVR was lower in participants with previous infection than those without previous infection (difference, -8.9 mL/100 g/min; p < .001); significantly lower CVR was also observed in participants with previous infection after exclusion of those with prior critical illness. Among participants with previous infection, CVR was lower in those with than those without post-COVID neurologic conditions, although this difference was not significant (16.9 vs 21.0 mL/100 g/min; p = .22). Six of 15 (40%) participants with previous infection versus 1 of 10 (10%) participants without previous infection had at least one VWI abnormality (p = .18). All VWI abnormalities were consistent with atherosclerosis. CONCLUSION. SARS-CoV-2 infection is associated with chronic impairment of CVR. The mechanism is unknown from this study. CLINICAL IMPACT. Future studies are needed to determine the clinical implications of SARS-CoV-2-associated CVR impairment.

Genetic variants associated with ALT elevation from therapeutic acetaminophen

BACKGROUND

Several studies have suggested genetic variants associated with acetaminophen induced liver injury (DILI) following overdose. Genetic variation associated with acetaminophen-induced alanine aminotransferase elevation during therapeutic dosing has not been examined.

METHODS

We performed genetic analyses on patients that ingested therapeutic doses of 4 grams of acetaminophen for up to 16 days. We examined 20 genes previously implicated in the metabolism of acetaminophen or the development of immune-mediated DILI using the Illumina Multi-Ethnic Global Array 2. Autosomes were aligned and imputed using TOPMed. A candidate gene region analysis was performed by testing each gene individually using linkage disequilibrium (LD) pruned variants with the adaptive sum of powered scores (aSPU) test from the aSPU R package. The highest measured ALT during therapy, the maximum ALT, was used as the outcome.

RESULTS

192 subjects taking therapeutic APAP were included in the genetic analysis. 136 (70.8%) were female, 133 (69.2%) were Caucasian race, and the median age was 34 years (IQR: 26, 46). Age > 50 years was the only clinical factor associated with maximum ALT increase. Variants in SULT1E1, the gene responsible for Sulfotransferase Family 1E Member 1 enzyme production, were associated with maximum ALT. No single variant drove this association, but rather the association was due to the additive effects of numerous variants within the gene. No other genes were associated with maximum ALT increase in this cohort.

CONCLUSION

Acetaminophen induced ALT elevation at therapeutic doses was not associated with variation in most genes associated with acetaminophen metabolism or immune-induced DILI in this cohort. The role of SULT1E1 polymorphism in acetaminophen-induced elevated ALT needs further examination.

Time-of-day dependent effects of midazolam administration on myocardial injury in non-cardiac surgery

Background

Animal studies have shown that midazolam can increase vulnerability to cardiac ischemia, potentially via circadian-mediated mechanisms. We hypothesized that perioperative midazolam administration is associated with an increased incidence of myocardial injury in patients undergoing non-cardiac surgery (MINS) and that circadian biology may underlie this relationship.

Methods

We analyzed intraoperative data from the Multicenter Perioperative Outcomes Group for the occurrence of MINS across 50 institutions from 2014 to 2019. The primary outcome was the occurrence of MINS. MINS was defined as having at least one troponin-I lab value ≥0.03 ng/ml from anesthesia start to 72 h after anesthesia end. To account for bias, propensity scores and inverse probability of treatment weighting were applied.

Results

A total of 1,773,118 cases were available for analysis. Of these subjects, 951,345 (53.7%) received midazolam perioperatively, and 16,404 (0.93%) met criteria for perioperative MINS. There was no association between perioperative midazolam administration and risk of MINS in the study population as a whole (odds ratio (OR) 0.98, confidence interval (CI) [0.94, 1.01]). However, we found a strong association between midazolam administration and risk of MINS when surgery occurred overnight (OR 3.52, CI [3.10, 4.00]) or when surgery occurred in ASA 1 or 2 patients (OR 1.25, CI [1.13, 1.39]).

Conclusion

Perioperative midazolam administration may not pose a significant risk for MINS occurrence. However, midazolam administration at night and in healthier patients could increase MINS, which warrants further clinical investigation with an emphasis on circadian biology.

Non-contrast free-breathing whole-heart 3D cine cardiovascular magnetic resonance with a novel 3D radial leaf trajectory

PURPOSE

To develop and validate a non-contrast free-breathing whole-heart 3D cine steady-state free precession (SSFP) sequence with a novel 3D radial leaf trajectory.

METHODS

We used a respiratory navigator to trigger acquisition of 3D cine data at end-expiration to minimize respiratory motion in our 3D cine SSFP sequence. We developed a novel 3D radial leaf trajectory to reduce gradient jumps and associated eddy-current artifacts. We then reconstructed the 3D cine images with a resolution of 2.0mm³ using an iterative nonlinear optimization algorithm. Prospective validation was performed by comparing ventricular volumetric measurements from a conventional breath-hold 2D cine ventricular short-axis stack against the non-contrast free-breathing whole-heart 3D cine dataset in each patient (n = 13).

RESULTS

All 3D cine SSFP acquisitions were successful and mean scan time was 07:09 ± 01:31 min. End-diastolic ventricular volumes for left ventricle (LV) and right ventricle (RV) measured from the 3D datasets were smaller than those from 2D (LV: 159.99 ± 42.99 vs. 173.16 ± 47.42; RV: 180.35 ± 46.08 vs. 193.13 ± 49.38; p-value≤0.044; bias<8%), whereas ventricular end-systolic volumes were more comparable (LV: 79.12 ± 26.78 vs. 78.46 ± 25.35; RV: 97.18 ± 32.35 vs. 102.42 ± 32.53; p-value≥0.190, bias<6%). The 3D cine data had a lower subjective image quality score.

CONCLUSION

Our non-contrast free-breathing whole-heart 3D cine sequence with novel leaf trajectory was robust and yielded smaller ventricular end-diastolic volumes compared to 2D cine imaging. It has the potential to make examinations easier and more comfortable for patients.

Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel

The Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of four plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. In particular, we investigate three approaches based on genome-wide mixed model analysis, and one approach based on ordinary least squares linear regression. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power. In simulation of eQTL data in the HRDP, we find that a mixed model approach that leverages leave-one-chromosome-out kinship estimation attains the highest power while controlling type I error.

A Multi-center, Prospective, Observational-cohort controlled study of Clinical Outcomes following COVID-19 Convalescent plasma therapy in hospitalized COVID-19 patients

BACKGROUND

The SARS-CoV2 pandemic has caused high inpatient mortality and morbidity throughout the world. COVID19 convalescent plasma has been utilized as a potential therapy for patients hospitalized with COVID19 pneumonia. This study evaluated the outcomes of hospitalized COVID19 patients treated with COVID19 convalescent plasma in a prospective, observational multicenter trial.

METHODS

From April 2020 through August 2020, hospitalized COVID19 patients at 16 participating hospitals in Colorado were enrolled and treated with COVID19 convalescent plasma (CCP) and compared to hospitalized patients with COVID19 who were not treated with convalescent plasma. Plasma antibody levels were determined following the trial given that antibody tests were not approved at the initiation of the trial. CCP-treated and untreated COVID19 hospitalized patients were matched using propensity scores followed by analysis for length of hospitalization and inpatient mortality.

RESULTS

542 total hospitalized COVID19 patients were enrolled at 16 hospitals across the region. A total of 468 hospitalized COVID19 patients were entered into propensity score matching with 188 patients matched for analysis in the CCP-treatment and control arms. Fine-Gray models revealed increased length of hospital stay in CCP-treated patients and no change in inpatient mortality compared to controls. In subgroup analysis of CCP-treated patients within 7 days of admission, there was no difference in length of hospitalization and inpatient mortality.

CONCLUSIONS

These data show that treatment of hospitalized COVID19 patients with CCP did not significantly improve patient hospitalization length of stay or inpatient mortality.

FGL1 as a modulator of plasma D-dimer levels: Exome-wide marker analysis of plasma tPA, PAI-1, and D-dimer

BACKGROUND

Use of targeted exome-arrays with common, rare variants and functionally enriched variation has led to discovery of new genes contributing to population variation in risk factors. Plasminogen activator-inhibitor 1 (PAI-1), tissue plasminogen activator (tPA), and the plasma product D-dimer are important components of the fibrinolytic system. There have been few large-scale genome-wide or exome-wide studies of PAI-1, tPA, and D-dimer.

OBJECTIVES

We sought to discover new genetic loci contributing to variation in these traits using an exome-array approach.

METHODS

Cohort-level analyses and fixed effects meta-analyses of PAI-1 (n = 15 603), tPA (n = 6876,) and D-dimer (n = 19 306) from 12 cohorts of European ancestry with diverse study design were conducted, including single-variant analyses and gene-based burden testing.

RESULTS

Five variants located in NME7, FGL1, and the fibrinogen locus, all associated with D-dimer levels, achieved genome-wide significance (P < 5 × 10-8 ). Replication was sought for these 5 variants, as well as 45 well-imputed variants with P < 1 × 10-4 in the discovery using an independent cohort. Replication was observed for three out of the five significant associations, including a novel and uncommon (0.013 allele frequency) coding variant p.Trp256Leu in FGL1 (fibrinogen-like-1) with increased plasma D-dimer levels. Additionally, a candidate-gene approach revealed a suggestive association for a coding variant (rs143202684-C) in SERPINB2, and suggestive associations with consistent effect in the replication analysis include an intronic variant (rs11057830-A) in SCARB1 associated with increased D-dimer levels.

CONCLUSION

This work provides new evidence for a role of FGL1 in hemostasis.

Penalized regression and model selection methods for polygenic scores on summary statistics

Polygenic scores quantify the genetic risk associated with a given phenotype and are widely used to predict the risk of complex diseases. There has been recent interest in developing methods to construct polygenic risk scores using summary statistic data. We propose a method to construct polygenic risk scores via penalized regression using summary statistic data and publicly available reference data. Our method bears similarity to existing method LassoSum, extending their framework to the Truncated Lasso Penalty (TLP) and the elastic net. We show via simulation and real data application that the TLP improves predictive accuracy as compared to the LASSO while imposing additional sparsity where appropriate. To facilitate model selection in the absence of validation data, we propose methods for estimating model fitting criteria AIC and BIC. These methods approximate the AIC and BIC in the case where we have a polygenic risk score estimated on summary statistic data and no validation data. Additionally, we propose the so-called quasi-correlation metric, which quantifies the predictive accuracy of a polygenic risk score applied to out-of-sample data for which we have only summary statistic information. In total, these methods facilitate estimation and model selection of polygenic risk scores on summary statistic data, and the application of these polygenic risk scores to out-of-sample data for which we have only summary statistic information. We demonstrate the utility of these methods by applying them to GWA studies of lipids, height, and lung cancer.

Polygenic risk scores use genetic data to predict the genetic risk associated with a given phenotype. Often, due to privacy concerns, genetic data is provided in a limited format called summary statistics. This means that we have limited data with which to estimate polygenic risk scores and cannot apply many standard modelling techniques. We provide novel methods for the estimation of polygenic risk scores via penalized regression using summary statistics, and make software available to do this estimation. We also provide novel methods for model selection and the assessment of model performance in the summary statistic framework. In total, this enables us to use summary statistic data to estimate polygenic risk scores, select a polygenic risk score from among a set of candidate models, and assess the performance of these models. This allows us to leverage summary statistic data to better understand genetic risk. We establish the usefulness of our novel methods via simulation, and apply them to genetic analyses of height, blood lipid levels, and lung cancer.

Abnormal Endothelial Gene Expression Associated With Early Coronary Atherosclerosis

Background We examined feasibility of a unique approach towards gaining insight into heritable risk for early atherosclerosis: surveying gene expression by endothelial cells from living subjects. Methods and Results Subjects aged <50 years (mean age, 37; range, 22-49) without obstructive coronary artery disease underwent coronary reactivity testing that identified them as having normal or abnormal coronary endothelial function. Cultures of Blood Outgrowth Endothelial Cells (BOEC) from 6 normal and 13 abnormal subjects passed rigorous quality control and were used for microarray assessment of gene expression. Of 9 genes differentially expressed at false discovery rate <0.1%, we here focus upon abnormal subjects having elevated expression of HMGB1 (high mobility group box 1) which we unexpectedly found to be linked to low LAMC1 (laminin gamma 1) expression. This linkage was corroborated by 3 of our past studies and confirmed bio-functionally. Compared with normal BOEC, abnormal BOEC released 13±3-fold more HMGB1 in response to lipopolysaccharide; and they deposited one tenth as much LAMC1 into collagen subendothelial matrix during culture. Clinical follow-up data are provided for 4 normal subjects (followed 13.4±0.1 year) and for 12 abnormal subjects (followed 9.1±4.5 years). Conclusions The known pathogenic effects of high-HMGB1 and low-LAMC1 predict that the combination would biologically converge upon the focal adhesion complex, to the detriment of endothelial shear responsiveness. This gene expression pattern may comprise a heritable risk state that promotes early coronary atherosclerosis. If so, the testing could be applied even in childhood, enabling early intervention. This approach offers a way to bridge the information gap between genetics and clinical phenotype.

Replication of Newly Identified Genetic Associations Between Abdominal Aortic Aneurysm and SMYD2, LINC00540, PCIF1/MMP9/ZNF335, and ERG

OBJECTIVE

A recently published genome wide association study of abdominal aortic aneurysms (AAA), based on pooled case control data of European ancestry, identified four new loci for AAA: SMYD2 (top single nucleotide polymorphism [SNP] rs1795061), LINC00540 (rs9316871), PCIF1/MMP9/ZNF335 (rs3827066), and ERG (rs2836411). Of the four, rs1795061 and rs2836411 showed significant heterogeneity across studies and the p value for rs9316871 did not reach the genome wide significance threshold until discovery and replication data were pooled together in that study. The objective of this study was to replicate these newly identified genetic associations for AAA in a US based prospective cohort study, the Atherosclerosis Risk in Communities (ARIC) Study, and a Greece based case control study.

METHODS

ARIC identified 408 clinically diagnosed AAAs among 8 962 individuals of European ancestry during a median of 22 years of follow up. The Greek case control study included 341 AAAs of European ancestry recruited in a tertiary referral centre and 292 geographically and ethnically matched controls recruited from the same institution. A Cox proportional hazards model was used to analyse the ARIC data and logistic regression to analyse the Greek data.

RESULTS

In ARIC, rs9316871 and rs3827066 were significantly associated with AAA risk (HR [p] was 0.77 [.004] and 1.22 [.03], respectively), rs2836411 was associated at borderline significance (1.13 [.08]), whereas rs1795061 was not associated (p = .55). In the Greek case control study, rs1795061 and rs2836411 were significantly associated with AAA (OR [p] was 1.66 [< .001] and 1.29 [.04], respectively), whereas rs9316871 was not (p = .81). Genotyping of rs3827066 did not succeed. In the meta-analysis of the two studies, the association for rs9316871and rs2836411 was statistically significant and consistent between the two studies: p = .02 and .007, respectively.

CONCLUSIONS

Associations between rs9316871and rs2836411 and AAA risk were replicated in the meta-analysis of the two independent cohorts, providing further support for the importance of these loci in the aetiology of AAA.

Integrating germline and somatic genetics to identify genes associated with lung cancer

Genome-wide association studies (GWAS) have successfully identified many genetic variants associated with complex traits. However, GWAS experience power issues, resulting in the failure to detect certain associated variants. Additionally, GWAS are often unable to parse the biological mechanisms of driving associations. An existing gene-based association test framework, Transcriptome-Wide Association Studies (TWAS), leverages expression quantitative trait loci data to increase the power of association tests and illuminate the biological mechanisms by which genetic variants modulate complex traits. We extend the TWAS methodology to incorporate somatic information from tumors. By integrating germline and somatic data we are able to leverage information from the nuanced somatic landscape of tumors. Thus we can augment the power of TWAS-type tests to detect germline genetic variants associated with cancer phenotypes. We use somatic and germline data on lung adenocarcinomas from The Cancer Genome Atlas in conjunction with a meta-analyzed lung cancer GWAS to identify novel genes associated with lung cancer.

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.