Timing for the Introduction of Cycled Light for Extremely Preterm Infants: A Randomized Controlled Trial

Day‐night cycled light improves health outcomes in preterm infants, yet the best time to institute cycled light is unclear. The hypothesis of this study was that extremely preterm infants receiving early cycled light would have better health and developmental outcomes than infants receiving late cycled light. Infants born at ≤28 weeks gestation were randomly assigned to early cycled light (ECL) starting at 28 weeks postmenstrual age [PMA] or late cycled light (LCL), starting at 36 weeks PMA. Daylight was 200–600 lux and night was 5–30 lux. Primary outcomes were weight over time and length of hospitalization. Secondary outcomes were hospital costs, sleep development, and neurodevelopment at 9, 18, and 24 months corrected age. Of 121 infants randomized, 118 were included in analysis. Weight gain in the two groups did not differ significantly but increased across time in both groups. In PMA weeks 36–44, the mean weight gain was 193.8 grams in the ECL group compared to 176.3 grams in the LCL group. Effect sizes for weight were Cohen d = 0.26 and 0.36 for 36 and 44 weeks PMA. Infants in the ECL group went home an average of 5.5 days earlier than the LCL group, but this difference was not statistically significant. There were no group differences on neurodevelopmental outcomes. Although statistically non‐significant, clinically important differences of improved weight gain and decreased hospital stay were observed with ECL. The small observed effect sizes on weight during hospitalization should be considered in future cycled light research with extremely preterm infants. © 2017 Wiley Periodicals, Inc.     

Safety,risk, and aggression: Health professionals’ experiences of caring for people affected by methamphetamine when presenting for emergency care

The crystalline form of methamphetamine, commonly known as crystal meth (crystal methamphetamine) or ICE, is a highly‐addictive and powerful stimulant. Users of crystal meth often require emergency care, and are associated with a substantial burden of care by emergency care providers. The aim of the present qualitative study was to explore health professionals’ experiences of providing care for patients affected by ICE who presented to the emergency department (ED). Nine semistructured interviews were conducted. The major theme, ‘staying safe’, was revealed, in which participants described their experiences of being exposed to potentially unsafe situations, and their responses to challenging behaviours, including aggression. The findings highlight the need for ED staff to understand the nature of ICE use and its adverse impact on the mental and physical health of users. Furthermore, it is clear that establishing and maintaining safety in the emergency care setting is of utmost importance, and should be a priority for health‐care managers.     

Association between early returns and frequent ED visits at a rural academic medical center

The objective of this study was to examine the influence of frequent emergency department (ED) use on early returns to the ED at a large rural academic medical center. An analysis was done of all 35,440 visits by 22,442 individuals to a large rural academic medical center ED during calendar year 2000. Of 35,440 ED visits, there were 1,992 (5.62%) return visits within 72 hours (early return). Frequent ED visits (visits made by individuals making 4 or more visits per year) was a predictor of early return visits (odds ratio [OR] 3.21, 95% confidence interval [CI] 2.93-3.52; Wald chi(2), P <.0001). Of 22,442 individuals who came to the ED during the study period, 1,601 (7.13%) returned within 72 hours. Frequency of ED use by a particular individual (4 or more visits per year) was also a predictor of early return for that individual (OR 14.55, 95% CI 12.84-16.48; Wald chi(2), P <.000001). The high rate of early returns to this rural academic ED was significantly associated with frequent visits (4 or more times per year) to the ED by particular individual.     

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung,Melanoma, and Gastrointestinal Malignancies

We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines.In modern oncologic practice, patients with advanced-stage non-small cell lung cancer (NSCLC),^{1, 2} melanoma,^{3, 4} and colorectal adenocarcinoma^{5, 6} are often treated with targeted therapies as standard of care or after enrollment in clinical trials. Molecular mutation analysis is the preferred testing modality to guide therapeutic decision making and/or eligibility for biological studies. Therefore, laboratory-developed mutation assays require robust workflows that produce high-quality sequence information from routine clinical specimens, namely formalin-fixed, paraffin-embedded (FFPE) samples. As molecular testing transitions from an ancillary tool to a seminal requirement for optimal oncologic patient management, multiplex sequencing assays with clearly defined content and bioinformatics workflows are essential for accurate and consistent results, reporting, and patient management.Published guidelines endorse which genes to test in a particular tumor type and provide timeframes for receipt of actionable results, but they also grant individual laboratories autonomy to perform mutation testing using any suitable validated method.² Historically at our institution, single-gene mutation analysis for clinically relevant genes was performed either in-house or at a Clinical Laboratory improvement Amendment–certified reference laboratory. Depending on the result, reflex testing was performed for additional genes per mutation frequency or designated algorithms. Unfortunately, this approach introduced considerable turn-around time delays and unnecessary cost, particularly when send-out testing was required. Therefore, we sought testing modalities that could analyze multiple clinically relevant mutations simultaneously, accurately, and expeditiously.Next-generation sequencing (NGS) technologies have revolutionized genomic medicine by allowing high-throughput, parallel sequencing of the human genome.⁷ Currently, however, a large proportion of clinical NGS endeavors are supported by larger academic institutions with shared access to established genomic and bioinformatics research infrastructures, and routine clinical implementation of NGS is complicated by mitigating factors, such as clinical performance, laboratory expertise, lengthy turn-around times, and cost.⁸ Thus, we investigated affordable methods to detect clinically relevant somatic mutations in NSCLC, melanoma, and gastrointestinal (GI) malignancies that generated high-quality sequencing data from FFPE samples, and offered manageable turn-around times. Targeted amplicon-based library preparation methods combined with parallel sequencing offered a practical solution, and recent studies have demonstrated the utility of this approach.^{9, 10}Reversible terminal dideoxynucleotide sequencing chemistry by Illumina (San Diego, CA) consistently generates accurate and reproducible sequencing data.^{11, 12} To use this chemistry for clinical testing, we purchased the bench-top NGS sequencer, the Illumina MiSeq, and paired it with the MiSeq-compatible Illumina TruSight tumor (TST) 26-target amplicon-based library preparation kit. TST targets 26 genes and 174 amplicons selected from College of American Pathologists/National Comprehensive Cancer Network guidelines, relevant publications, and late-phase pharmaceutical clinical trials (Supplemental Table S1). TST offered several advantages over other commercially available mutation testing kits, such as bidirectional targeting of the positive and negative DNA strands, full-exon coverage as opposed to hotspot analysis, and robust vendor-supplied bioinformatics techniques optimized for somatic variant detection. More important, TST library preparation is optimized for FFPE samples, multiple safeguards exist to detect FFPE variant artifacts, and deep sequencing of TST libraries consistently yields high depths of coverage of targeted regions.Somatic mutation testing for many of the TST genes has clinical utility in a wide variety of solid tumors. For example, testing for CTNNB1 exon 3 is performed clinically for diagnostic and prognostic purposes in pediatric desmoid tumors, select PIK3CA hotspot mutations are positive prognostic factors for breast carcinoma, and multiple exons in PDGFRA and KIT are routinely tested in GI stromal tumors to predict response to targeted therapies. More important for our intended validation purposes, all of the clinically relevant genes and regions mutated in NSCLC, melanoma, and colonic adenocarcinoma that were tested in our routine clinical practice were represented. In addition, we could easily incorporate the TST NGS into a 5 business day workflow model, and a cost-analysis demonstrated a reasonable cost per test.Last, TST NGS data are processed from raw sequence (FASTQ) to called variants with on-board MiSeq Reporter software version 2.3, and variant annotations can be performed with Illumina''s VariantStudio software version 2.1 software using standard desktop and laptop computers. The ease of library preparation, sequencing, and data analysis with tools provided by a single vendor best fit our clinical priorities and the resources available at our academic molecular pathology laboratory.Herein, we present our results from the clinical validation of TST NGS using 80 sequenced samples that were selected from 100 FFPE patient samples (40 NSCLCs, 30 melanomas, and 30 GI malignancies). During our validation, we achieved high depths of coverage for multiple clinically relevant variants when multiplexing 8 to 12 samples on a single MiSeq flow cell. TST NGS consistently demonstrated sensitivities comparable to reference assays, showed 100% concordance with known variants, detected novel variants in many samples, and uncovered variants missed by less-sensitive testing modalities. The TST variant-calling pipeline was robust and showed high concordance when compared with an alternative analysis pipeline, and we used an in-house custom Java program to assess laboratory-defined quality control (QC) metrics and streamline clinical reporting (developed by G.H.S., Emory University, http://github.com/ghsmith/coverageQc). More important, although the results detailed herein represent the experience of a single institution, the data and validation strategies shown herein are broadly applicable to most clinical molecular laboratories interested in offering NGS for NSCLCs, melanomas, and GI malignancies as well as many other solid tumors.