Comparison of next generation diagnostic systems (NGDS) for the detection of SARS-CoV-2.

INTRODUCTION: The World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a pandemic in March 2020. Initially, supply chain disruptions and increased demand for testing led to shortages of critical laboratory reagents and inadequate testing capacity. Thus, alternative means of biosample collection and testing were essential to overcome these obstacles and reduce viral transmission. This study aimed to 1) compare the sensitivity and specificity of Cepheid GeneXpert® IV and BioFire® FilmArray® 2.0 next generation detection systems to detect SARS-CoV-2, 2) evaluate the performance of both platforms using different biospecimen types, and 3) assess saline as an alternative to viral transport media (VTM) for sample collection. METHODS: A total of 1,080 specimens consisting of nasopharyngeal (NP) swabs in VTM, NP swabs in saline, nasal swabs, oropharyngeal (OP) swabs, and saliva were collected from 216 enrollees. Limit of detection (LoD) assays, NP VTM and NP saline concordance, and saliva testing were performed on the BioFire® FilmArray® 2.0 Respiratory Panel 2.1 and Cepheid GeneXpert® Xpress SARS-CoV-2/Flu/RSV assays. RESULTS: LoD and comparative testing demonstrated increased sensitivity with the Cepheid compared with the BioFire® in detecting SARS-CoV-2 in NP VTM and saline, nasal, and OP swabs. Conversely, saliva testing on the Cepheid showed statistically significant lower sensitivity compared to the BioFire® . Finally, NP swabs in saline showed no significant difference compared with NP swabs in VTM on both platforms. CONCLUSION: The Cepheid and BioFire® NGDS are viable options to address a variety of public health needs providing rapid and reliable, point-of-care testing using a variety of clinical matrices.

Spectral Reflectance as a Unique Tissue Identifier in Healthy Humans and Inhalation Injury Subjects.

Tracheal intubation is the preferred method of airway management, a common emergency trauma medicine problem. Currently, methods for confirming tracheal tube placement are lacking, and we propose a novel technology, spectral reflectance, which may be incorporated into the tracheal tube for verification of placement. Previous work demonstrated a unique spectral profile in the trachea, which allowed differentiation from esophageal tissue in ex vivo swine, in vivo swine, and human cadavers. The goal of this study is to determine if spectral reflectance can differentiate between trachea and other airway tissues in living humans and whether the unique tracheal spectral profile persists in the presence of an inhalation injury. Reflectance spectra were captured using a custom fiber-optic probe from the buccal mucosa, posterior oropharynx, and trachea of healthy humans intubated for third molar extraction and from the trachea of patients admitted to a burn intensive care unit with and without inhalation injury. Using ratio comparisons, we found that the tracheal spectral profile was significantly different from buccal mucosa or posterior oropharynx, but the area under the curve values are not high enough to be used clinically. In addition, inhalation injury did not significantly alter the spectral reflectance of the trachea. Further studies are needed to determine the utility of this technology in a clinical setting and to develop an algorithm for tissue differentiation.

Spectral Reflectance Can Differentiate Tracheal and Esophageal Tissue in the Presence of Bodily Fluids and Soot.

Endotracheal intubation is a common life-saving procedure implemented in emergency care to ensure patient oxygenation, but it is difficult and often performed in suboptimal conditions leading to high rates of patient complications. Undetected misplacement in the esophagus is a preventable complication that can lead to fatalities in 5-10% of patients who undergo emergency intubation. End-tidal carbon dioxide monitoring and other proper placement detection methods are useful, yet the problem of misplacement persists. Our previous work demonstrated the utility of spectral reflectance sensors for differentiating esophageal and tracheal tissues, which can be used to confirm proper endotracheal tube placement. In this study, we examine the effectiveness of spectral characterization in the presence of saline, blood, "vomit", and soot in the trachea. Our results show that spectral properties of the trachea that differentiate it from the esophagus persist in the presence of these substances. This work further confirms the potential usefulness of this novel detection technology in field applications.

Contribution of Inbred Singletons to Variance Component Estimation of Heritability and Linkage.

OBJECTIVES: An interesting consequence of consanguinity is that the inbred singleton becomes informative for genetic variance. We determine the contribution of an inbred singleton to variance component analysis of heritability and linkage. METHODS: Statistical theory for the power of variance component analysis of quantitative traits is used to determine the expected contribution of an inbred singleton to likelihood-ratio tests of heritability and linkage. RESULTS: In variance component models, an inbred singleton contributes relatively little to a test of heritability but can contribute substantively to a test of linkage. For small-to-moderate quantitative trait locus (QTL) effects and a level of inbreeding comparable to matings between first cousins (the preferred form of union in many human populations), an inbred singleton can carry nearly 25% of the information of a non-inbred sib pair. In more highly inbred contexts available with experimental animal populations, nonhuman primate colonies, and some human subpopulations, the contribution of an inbred singleton relative to a sib pair can exceed 50%. CONCLUSIONS: Inbred individuals, even in isolation from other members of a sample, can contribute to variance component estimation and tests of heritability and linkage. Under certain conditions, the informativeness of the inbred singleton can approach that of a non-inbred sib pair.

Time to response and patient visibility during tonic-clonic seizures in the epilepsy monitoring unit.

OBJECTIVE: There is a high cost associated with recording quality video and electroencephalography (EEG) data in National Association of Epilepsy Center (NAEC) level IV epilepsy monitoring units (EMU). This study considers potential quality measures in EMUs for generalized tonic-clonic (GTC) seizures: types of safety signals, response time, and visibility of patient's limbs for semiology. These quality measures have been summarized across 12 EMUs to estimate response times to GTC seizures and the quality of video data that is captured during admissions. METHODS: Video electroencephalographies (vEEGs) from two prospective regulatory studies for the Brain Sentinel device were reviewed. A total of 232 subjects with a history of GTC seizures underwent routine clinical EMU stays. Fifty-four of the study subjects had 96 GTC seizures. The vEEG of events were reviewed for safety signal used, response time, and visibility of patient's limbs. RESULTS: The average response time from members of the hospital team was 22 s from electrographic generalization (minimum -37 s, maximum 111 s, two no response). For caregivers, average response was 11 s (minimum -15 s, maximum 33 s, 45 not present/no response). In 73% of events, the patient visibility was limited at seizure onset. In 55% of events with limited limb visibility, the visibility was improved (by removing sheets or improving camera angle) >30 s after start of the event. The primary safety signals were as follows: an alert from outside the patient room (54%), button press (23%), hospital team present at seizure start (14%), caregiver vocal alert (6%), and no response (2%). SIGNIFICANCE: The average response time of caregivers was twice as fast as the hospital team, underscoring the importance of having a person in the room during onset of a GTC seizure. Diagnostic yield could be improved with more timely removal of patient coverings. It was observed that when patients experienced a GTC seizure, 40% were fully or partially obscured for more than 30 s during the event, compromising the ability of epileptologists to evaluate semiology during seizure onset. Automated seizure alarms may help staff get to patients more quickly and improve diagnostic characterization.

Exome sequences of multiplex, multigenerational families reveal schizophrenia risk loci with potential implications for neurocognitive performance.

Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder. In total, 11,878 non-synonymous variants from 6,396 genes were tested for their association with schizophrenia spectrum disorders. Pathway enrichment analyses were conducted on gene-based test results, protein-protein interaction (PPI) networks, and epistatic effects. Using a significance threshold of FDR < 0.1, association was detected for rs10941112 (p = 2.1 × 10-5 ; q-value = 0.073) in AMACR, a gene involved in fatty acid metabolism and previously implicated in schizophrenia, with significant cis effects on gene expression (p = 5.5 × 10-4 ), including brain tissue data from the Genotype-Tissue Expression project (minimum p = 6.0 × 10-5 ). A second SNP, rs10378 located in TMEM176A, also shows risk effects in the exome data (p = 2.8 × 10-5 ; q-value = 0.073). PPIs among our top gene-based association results (p < 0.05; n = 359 genes) reveal significant enrichment of genes involved in NCAM-mediated neurite outgrowth (p = 3.0 × 10-5 ), while exome-wide SNP-SNP interaction effects for rs10941112 and rs10378 indicate a potential role for kinase-mediated signaling involved in memory and learning. In conclusion, these association results implicate AMACR and TMEM176A in schizophrenia risk, whose effects may be modulated by genes involved in synaptic plasticity and neurocognitive performance.

The Relationship Between Pre-Pandemic Comorbidities With SARS-CoV-2 Infections and Hospitalizations in Black Versus White Military Service Members: A Retrospective Study.

INTRODUCTION: Comorbidities such as hypertension, diabetes mellitus, asthma, and cardiovascular conditions have been reported to worsen the clinical progression of coronavirus disease 2019 (COVID-19) and related hospitalizations. Furthermore, the COVID-19 pandemic has disproportionately affected the historically marginalized groups, i.e., Black, Hispanic, and Asian individuals have substantially higher rates of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection, COVID-19 hospitalization, and death compared to White individuals. Despite these findings in civilian populations, the impact of comorbidities and race in SARS-CoV-2 infection and COVID-19 hospitalizations in military populations is unknown. We evaluated the relationship of pre-selected pre-pandemic comorbidities and race with SARS-CoV-2 infections and COVID-19 hospitalizations in U.S. military service members (SMs). MATERIALS AND METHODS: We conducted a systematic review of Military Health System beneficiaries' records by accessing the Defense Medical Epidemiological Database. Our inclusion criteria were being an active duty SM and having at least one pre-COVID-19 pandemic comorbidity. Retired as well as uninfected healthy active duty SMs and beneficiaries were excluded from the study. A total population of 1.334 million active duty SM records was drawn from Defense Medical Epidemiological Database. The data were stratified, by race (primary outcome), as well as gender, age, and military service branches (secondary outcomes). RESULTS: We found higher trends in SARS-CoV-2 infection and COVID-19 hospitalization rates in Black compared to White SMs. This seamless inequality was also seen in other viral infections affecting SMs including human immunodeficiency virus and viral hepatitis. We hypothesized this disparity to some extent be associated with the presence of pre-pandemic comorbidities that is affecting this military subpopulation. Supporting our hypothesis, we found trends toward the higher pre-pandemic prevalence of diabetes mellitus, asthma, hypertension, and ischemic heart disease, in Black compared to White military SMs, especially in Black older male adults. CONCLUSION: Our results highlight the role of pre-pandemic comorbidities and race likely enhancing the frequency of SARS-CoV-2 infections and COVID-19 hospitalizations in military SMs. These preliminary findings underscore the need for future retrospective studies using additional Military Health System data bases reporting data on this military subpopulation, especially in the setting of future pathogens outbreaks or pandemics affecting military populations.

A Baseline Model of PTSD From the ACES Cohort.

INTRODUCTION: Post-traumatic stress disorder (PTSD) is a primary military psychiatric condition with complex etiology including strong genetic and/or environmental influences. Environmental influences and demographics can play a role in supporting underlying genetic traits for clinical utility evaluation as risk modifying factors. We are undertaking an IRB approved study to evaluate polygenic scores of PTSD risk in the adverse childhood experience and serotonin (ACES) transporter cohort. MATERIALS AND METHODS: Baseline demographic characteristics and statistical modeling of 291 active duty service members from ACES cohort were used and excluded individuals with traumatic brain injury-induced loss of consciousness, pre-deployment PTSD or anxiety disorder, and pre-deployment prescription of antidepressants or psychoactive medications. Summary of categorical and numerical variables were evaluated using chi-square and t-test, respectively. We model PTSD risk and associated scores using linear and logistic regressions. RESULTS: The ACES subset was 79.1% males, multi-ancestry, and mean age of 38.3 years. Most PTSD individuals received behavioral therapy (89.6%) and/or prescribed antidepressants (67%) had higher scores in ACES, combat exposure scales, PTSD checklist military version, neurobehavioral symptom inventory, Pittsburg sleep quality index, insomnia severity index, and composite autonomic symptom score surveys and were less likely to expect future deployment. A positive correlation between age, total months deployed, ACES, CES, PCL-M, and positive-PTSD diagnosis were consistent but not in older individuals, who were more likely and frequently deployed although increasing risk for combat exposure. CONCLUSION: Demographic characteristics of the ACES cohort fit a coherent model of risk for PTSD to evaluate polygenic scores. Additional research is merited to understand PTSD effects on these confounding factors.

Evaluating sensitivity and specificity of the Biomeme Franklin™ three9 real-time PCR device and SARS-CoV-2 go-strips assay using clinical samples.

We evaluated the sensitivity and specificity of the Biomeme Franklin™ three9 Real-Time PCR Thermocycler and Biomeme SARS-CoV-2 Go-Strips in the detection of SARS-CoV-2. The Biomeme Franklin™ three9 platform is a portable, battery-operated system that could be used in remote settings. We assessed performance of the Biomeme SARS-CoV-2 detection system at a wide range of viral concentrations, examined cross-reactivity of the SARS-CoV-2 Go-Strips against several near-neighbor respiratory pathogens, and evaluated agreement against the BioFire® Respiratory Panel 2.1 in four clinical sample types. Our data indicate the Biomeme Go-Strips can reliably detect SARS-CoV-2 at a concentration of 4.2 × 103 copies/mL. No cross reactivity of the Go-Strips targets was detected against any of the tested near-neighbor respiratory pathogens. Cohen's kappa statistics ranged from 0.68 to 0.92 between results from the Biomeme SARS-CoV-2 Go-Strips and the BioFire® Respiratory Panel 2.1 in all the different sample types. Compared to the BioFire® Respiratory Panel 2.1, the Biomeme SARS-CoV-2 Go-Strips demonstrated statistically significantly lower sensitivity in 3 out of 5 sample types. Overall, our study demonstrates the Biomeme Franklin™ three9 used with the SARS-CoV-2 Go-Strips is an effective system for the detection of SARS-CoV-2 that could potentially be used in a remote or austere environment.

Genotype phasing in pedigrees using whole-genome sequence data.

Phasing is the process of inferring haplotypes from genotype data. Efficient algorithms and associated software for accurate phasing in pedigrees are needed, especially for populations lacking reference panels of sequenced individuals. We present a novel method for phasing genotypes from whole-genome sequence data in pedigrees, called PULSAR (Phasing Using Lineage Specific Alleles/Rare variants). The method is based on the property that alleles specific to a single founding chromosome within a pedigree are highly informative for identifying haplotypes that are shared identical by descent. Simulation studies are used to assess the performance of PULSAR with various pedigree sizes and structures, and the effect of genotyping errors and the presence of nonsequenced individuals is investigated. In pedigrees with complete sequencing and realistic genotyping error rates, PULSAR correctly phases >99.9% of heterozygous genotypes, excluding sites at which all individuals are heterozygous, and does so with a switch error rate frequently below 10-4. PULSAR is highly accurate, capable of genotype error correction and imputation, and computationally competitive with alternative phasing software applicable to pedigrees. Our method has the significant advantage of not requiring reference panels that are essential for other population-based phasing algorithms. A software implementation of PULSAR is freely available.

Prehospital airway procedures performed in trauma patients by ground forces in Afghanistan.

BACKGROUND: Airway management is of critical importance in combat trauma patients. Airway compromise is the second leading cause of potentially survivable death on the battlefield and accounts for approximately 1 in 10 preventable deaths. Reports from the Iraq and Afghanistan wars indicate 4% to 7% incidence of airway interventions on casualties transported to combat hospitals. The goal of this study was to describe airway management in the prehospital combat setting and document airway devices used on the battlefield. METHODS: This study is a retrospective review of casualties that required a prehospital lifesaving airway intervention during combat operations in Afghanistan. We obtained data from the Prehospital Trauma Registry that was linked to the Department of Defense Trauma Registry for outcome data for the time period between January 2013 and September 2014. RESULTS: Seven hundred five total trauma patients were included, 16.9% required a prehospital airway management procedure. There were 132 total airway procedures performed, including 83 (63.4%) endotracheal intubations and 26 (19.8%) nasopharyngeal airway placements. Combat medics were involved in 48 (36.4%) of airway cases and medical officers in 73 (55.3%). Most (94.2%) patients underwent airway procedures due to battle injuries caused by explosion or gunshot wounds. Casualties requiring airway management were more severely injured and less likely to survive as indicated by Injury Severity Score, responsiveness level, Glascow Coma Scale, and outcome. CONCLUSION: Percentages of airway interventions more than tripled from previous reports from the wars in Afghanistan and Iraq. These changes are significant, and further study is needed to determine the causes. Casualties requiring airway interventions sustained more severe injuries and experienced lower survival than patients who did not undergo an airway procedure, findings suggested in previous reports. LEVEL OF EVIDENCE: Prognostic and epidemiological study, level III.

Exome Sequence Data From Multigenerational Families Implicate AMPA Receptor Trafficking in Neurocognitive Impairment and Schizophrenia Risk.

Schizophrenia is a mental disorder characterized by impairments in behavior, thought, and neurocognitive performance. We searched for susceptibility loci at a quantitative trait locus (QTL) previously reported for abstraction and mental flexibility (ABF), a cognitive function often compromised in schizophrenia patients and their unaffected relatives. Exome sequences were determined for 134 samples in 8 European American families from the original linkage study, including 25 individuals with schizophrenia or schizoaffective disorder. At chromosome 5q32-35.3, we analyzed 407 protein-altering variants for association with ABF and schizophrenia status. For replication, significant, Bonferroni-corrected findings were tested against cognitive traits in Mexican American families (n = 959), as well as interrogated for schizophrenia risk using GWAS results from the Psychiatric Genomics Consortium (PGC). From the gene SYNPO, rs6579797 (MAF = 0.032) shows significant associations with ABF (P = .015) and schizophrenia (P = .040), as well as jointly (P = .0027). In the Mexican American pedigrees, rs6579797 exhibits significant associations with IQ (P = .011), indicating more global effects on neurocognition. From the PGC results, other SYNPO variants were identified with near significant effects on schizophrenia risk, with a local linkage disequilibrium block displaying signatures of positive selection. A second missense variant within the QTL, rs17551608 (MAF = 0.19) in the gene WWC1, also displays a significant effect on schizophrenia in our exome sequences (P = .038). Remarkably, the protein products of SYNPO and WWC1 are interaction partners involved in AMPA receptor trafficking, a brain process implicated in synaptic plasticity. Our study reveals variants in these genes with significant effects on neurocognition and schizophrenia risk, identifying a potential pathogenic mechanism for schizophrenia spectrum disorders.

Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.

Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease.

Imputation in families using a heuristic phasing approach.

Whole genome sequencing (WGS) remains prohibitively expensive, which has encouraged the development of methods to impute WGS data into nonsequenced individuals using a framework of single nucleotide polymorphisms genotyped for genome-wide association studies (GWAS). Although successful methods have been developed for cohorts of unrelated individuals, current imputation methods in related individuals are limited by pedigree size, by the distance of relationships, or by computation time. In this article, we describe a method for imputation in arbitrarily shaped multigenerational pedigrees that can impute genotypes across distantly related individuals based on identity by descent. We evaluate this approach using GWAS data and apply this approach to WGS data distributed for Genetic Analysis Workshop 18.

Validation of copy number variants associated with prostate cancer risk and prognosis.

OBJECTIVE: Two recent studies have reported novel heritable copy number variants on chromosomes 2p, 15q, and 12q to be associated with prostate cancer (PCa) risk in non-Hispanic Caucasians. The goal of this study was to determine whether these findings could be independently confirmed in the Caucasian population from the South Texas area. METHODS AND MATERIALS: The study subjects consisted of participants of the San Antonio Biomarkers of Risk for PCa cohort and additional cases ascertained in the same metropolitan area. We genotyped all 7 of the reported copy number variants using real-time quantitative polymerase chain reaction in 1,536 (317 cases and 1,219 controls) non-Hispanic Caucasian men, and additionally, we genotyped 632 (191 cases and 441 controls) Hispanic Caucasian men for one of these variants, a deletion on 2p24.3. RESULTS: Association of the deletion on 2p24.3 with overall PCa risk did not meet our significance criteria but was consistent with previous reports (odds ratio, 1.40; 95% confidence interval 0.99-2.00; P = 0.06). Among Hispanic Caucasians, this deletion is much less prevalent (minor allele frequencies of 0.059 and 0.024 in non-Hispanic and Hispanic Caucasians, respectively) and did not show evidence of association with risk for PCa. Interestingly, among non-Hispanic Caucasians, carrying a homozygous deletion of 2p24.3 was significantly associated with high-grade PCa as defined by Gleason score sum ≥8 (odds ratio, 27.99; 95% confidence interval 1.99-392.6; P = 0.007 [the Fisher exact test]). The remaining 6 copy number variable regions either were not polymorphic in our cohort of non-Hispanic Caucasians or showed no evidence of association. CONCLUSIONS: Our findings are consistent with the reported observation that a heritable deletion on 2p24.3 is associated with PCa risk in non-Hispanic Caucasians. Additionally, our observations indicate that the 2p24.3 variant is associated with risk for high-grade PCa in a recessive manner. We were unable to replicate any association with PCa for the variants on chromosomes 15q and 12q, which may be explained by regional population differences in low frequency variants and disease heterogeneity.

Utilizing extended pedigree information for discovery and confirmation of copy number variable regions among Mexican Americans.

Copy number variation (CNV) remains poorly defined in many populations, including Mexican Americans. We report the discovery and genetic confirmation of copy number variable regions (CNVRs) in subjects of the San Antonio Family Heart and the San Antonio Family Diabetes Gallbladder Studies, both comprised of multigenerational pedigrees of Mexican American descent. In a discovery group of 1677 participants genotyped using Illumina Infinium Beadchips, we identified 2937 unique CNVRs, some with observation frequencies as low as 0.002, using a process that integrates pedigree information with CNV calls made by PennCNV and/or QuantiSNP. Quantitative copy number values had statistically significant (P ≤ 1.792e-5) heritability estimates ranging from 0.139 to 0.863 for 2776 CNVRs. Additionally, 920 CNVRs showed evidence of linkage to their genomic location, providing strong genetic confirmation. Linked CNVRs were enriched in a set of independently identified CNVRs from a second group of 380 samples, confirming that these CNVRs can be used as predefined CNVRs of high confidence. Interestingly, we identified 765 putatively novel variants that do not overlap with the Database of Genomic Variants. This study is the first to use linkage and heritability in multigenerational pedigrees as a confirmation approach for the discovery of CNVRs, and the largest study to date investigating copy number variation on a genome-wide scale in individuals of Mexican American descent. These results provide insight to the structural variation present in Mexican Americans and show the strength of multigenerational pedigrees to elucidate structural variation in the human genome.