Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group.

The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results. The Association for Molecular Pathology Electronic Health Record Working Group was convened to assess the challenges and opportunities and to recommend solutions on ways to resolve current problems associated with the display and use of genomic data in electronic health records.

Evaluation of Radioactivity in Patient Specimens Received in the Core Laboratory at a National Cancer Institute (NCI) Designated Cancer Center.

BACKGROUND: Biological specimens from patients who have received radiopharmaceuticals are often collected for diagnostic testing and sent to clinical laboratories. Residual radiation has long been assumed to be minimal. However, literature is sparse and may not represent the specimen volumes or spectrum of radionuclides currently seen at National Cancer Institute (NCI)-designated cancer centers. This study examined the radiopharmaceuticals associated with patient specimens received in the hospital core laboratory and assessed the potential risk of external radiation exposure to laboratory personnel. METHODS: The types and amounts of radiopharmaceuticals administered in a large metropolitan hospital system were retrospectively examined over a 20-month study period. The associated biological specimens sent to the largest core laboratory in the system for testing were evaluated. In addition, manual survey meter assessment of random clinical specimens and weekly wipe tests were performed for 44 weeks, and wearable and environmental dosimeters were placed for 6 months. RESULTS: Over 11 000 specimens, collected within 5 physical half-lives of radiopharmaceutical administration, were processed by our laboratory. Manual survey meter assessment of random clinical specimens routinely identified radioactive specimens. If held in a closed palm for >2 min, many samples could potentially deliver a 0.02 mSv effective dose of radiation. CONCLUSIONS: The laboratory regularly receives radioactive patient specimens without radioactive labels. Although the vast majority of these are blood specimens associated with low-dose diagnostic radiopharmaceuticals, some samples may be capable of delivering a significant amount of radiation. Recommendations for laboratories associated with NCI cancer centers are given.

Herpes Simplex Virus-1 qPCR in the Diagnosis of Lower Respiratory Tract Infections in Organ Transplant Recipients and Critically Ill Patients.

OBJECTIVES: To determine a quantitative herpes simplex virus (HSV) DNA threshold in lower respiratory tract specimens that correlates with positive viral culture and clinical outcomes. METHODS: Bronchoalveolar lavage and bronchial wash samples from 53 HSV culture-positive and 61 culture-negative matched controls were tested using HSV-1 and HSV-2 quantitative polymerase chain reaction (qPCR). RESULTS: Median viral culture turnaround time was 21.8 days and 9.9 days for culture-negative and culture-positive specimens, respectively. Using an HSV-1 viral load threshold of 1.62 × 103 copies/mL, there was 93% agreement with viral culture. An HSV-1 viral load ≥1.3 × 104 copies/mL was associated with worse clinical outcome compared to a viral load <1.3 × 104 copies/mL (hazard ratio [HR] = 4.27, P = .017), and there was a trend of worse outcome compared to patients with undetectable HSV-1 DNA (HR = 1.60, P = .056). CONCLUSIONS: qPCR has clinical utility for rapid accurate identification of HSV-1 in lower respiratory tract specimens.

Behavioral and physiological effects of RDX on adult zebrafish.

1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) is a nitroamine explosive, with common toxic effects including seizures. Here, we explore the behavioral effects of acute RDX exposure in adult zebrafish Danio rerio, a rapidly developing model in neuroscience and neurotoxicology research. Overall, a 30-min exposure to RDX low dose of 0.1 mM evoked behavioral activation in zebrafish, while a higher dose of 1 mM markedly reduced exploration, increased freezing and evoked seizure-like responses (i.e., bouts of hyperactivity, spasms, and corkscrew swimming). Likewise, whole-body cortisol levels were also significantly elevated in fish exposed to 1 mM (but not 0.1 mM) RDX. In line with clinical and animal data, our study demonstrates the dose-dependent behavioral activation and pro-convulsant effects of RDX in zebrafish-based models.

Measuring behavioral and endocrine responses to novelty stress in adult zebrafish.

Several behavioral assays are currently used for high-throughput neurophenotyping and screening of genetic mutations and psychotropic drugs in zebrafish (Danio rerio). In this protocol, we describe a battery of two assays to characterize anxiety-related behavioral and endocrine phenotypes in adult zebrafish. Here, we detail how to use the 'novel tank' test to assess behavioral indices of anxiety (including reduced exploration, increased freezing behavior and erratic movement), which are quantifiable using manual registration and computer-aided video-tracking analyses. In addition, we describe how to analyze whole-body zebrafish cortisol concentrations that correspond to their behavior in the novel tank test. This protocol is an easy, inexpensive and effective alternative to other methods of measuring stress responses in zebrafish, thus enabling the rapid acquisition and analysis of large amounts of data. As will be shown here, fish anxiety-like behavior can be either attenuated or exaggerated depending on stress or drug exposure, with cortisol levels generally expected to parallel anxiety behaviors. This protocol can be completed over the course of 2 d, with a variable testing duration depending on the number of fish used.

Characterization of behavioral and endocrine effects of LSD on zebrafish.

Lysergic acid diethylamide (LSD) is a potent hallucinogenic drug that strongly affects animal and human behavior. Although adult zebrafish (Danio rerio) are emerging as a promising neurobehavioral model, the effects of LSD on zebrafish have not been investigated previously. Several behavioral paradigms (the novel tank, observation cylinder, light-dark box, open field, T-maze, social preference and shoaling tests), as well as modern video-tracking tools and whole-body cortisol assay were used to characterize the effects of acute LSD in zebrafish. While lower doses (5-100 microg/L) did not affect zebrafish behavior, 250 microg/L LSD increased top dwelling and reduced freezing in the novel tank and observation cylinder tests, also affecting spatiotemporal patterns of activity (as assessed by 3D reconstruction of zebrafish traces and ethograms). LSD evoked mild thigmotaxis in the open field test, increased light behavior in the light-dark test, reduced the number of arm entries and freezing in the T-maze and social preference test, without affecting social preference. In contrast, LSD affected zebrafish shoaling (increasing the inter-fish distance in a group), and elevated whole-body cortisol levels. Overall, our findings show sensitivity of zebrafish to LSD action, and support the use of zebrafish models to study hallucinogenic drugs of abuse.

Modeling seizure-related behavioral and endocrine phenotypes in adult zebrafish.

Larval zebrafish (Danio rerio) have recently been suggested as a high-throughput experimental model of epilepsy-related pathogenetic states. Here we use adult zebrafish to study behavioral symptoms associated with drug-evoked seizures. Experimental epilepsy-like states were evoked in zebrafish by exposure for 20min to three chemoconvulsant drugs: caffeine (250mg/L; 1.3mM), pentylenetetrazole (1.5g/L; 11.0mM) and picrotoxin (100mg/L; 0.17mM). Fish behavior was analyzed using manual and video-tracking methods (Noldus Ethovision XT7). Compared to their respective controls, all three drug-treated groups showed robust seizure-like responses (hyperactivity bouts, spasms, circular and corkscrew swimming) accompanied by elevated whole-body cortisol levels (assessed by ELISA). In contrast, control fish did not display seizure-like behaviors and had significantly lower cortisol levels. Paralleling behavioral and endocrine phenotypes observed in clinical and rodent studies, our data implicates adult zebrafish as an emerging experimental model for epilepsy research.

The effects of chronic social defeat stress on mouse self-grooming behavior and its patterning.

Stress induced by social defeat is a strong modifier of animal anxiety and depression-like phenotypes. Self-grooming is a common rodent behavior, and has an ordered cephalo-caudal progression from licking of the paws to head, body, genitals and tail. Acute stress is known to alter grooming activity levels and disrupt its patterning. Following 15-17 days of chronic social defeat stress, grooming behavior was analyzed in adult male C57BL/6J mice exhibiting either dominant or subordinate behavior. Our study showed that subordinate mice experience higher levels of anxiety and display disorganized patterning of their grooming behaviors, which emerges as a behavioral marker of chronic social stress. These findings indicate that chronic social stress modulates grooming behavior in mice, thus illustrating the importance of grooming phenotypes for neurobehavioral stress research.

Modeling withdrawal syndrome in zebrafish.

The zebrafish (Danio rerio) is rapidly becoming a popular model species in behavioral neuroscience research. Zebrafish behavior is robustly affected by environmental and pharmacological manipulations, and can be examined using exploration-based paradigms, paralleled by analysis of endocrine (cortisol) stress responses. Discontinuation of various psychotropic drugs evokes withdrawal in both humans and rodents, characterized by increased anxiety. Sensitivity of zebrafish to drugs of abuse has been recently reported in the literature. Here we examine the effects of ethanol, diazepam, morphine and caffeine withdrawal on zebrafish behavior. Overall, discontinuation of ethanol, diazepam and morphine produced anxiogenic-like behavioral or endocrine responses, demonstrating the utility of zebrafish in translational research of withdrawal syndrome.