Clinical Performance of a Gene-Based Machine Learning Classifier in Assessing Risk of Developing OUD in Subjects Taking Oral Opioids: A Prospective Observational Study.

OBJECTIVE: To reduce the incidence of Opioid Use Disorder (OUD), multiple guidelines recommend assessing the risk of OUD prior to prescribing oral opioids. Although subjective risk assessments are available to help classify subjects at risk for OUD, we are aware of no clinically validated objective risk assessment tools. An objective risk assessment based on genetics may help inform shared decision-making prior to prescribing short-duration oral opioids. METHODS: A multicenter, observational cohort of adults exposed to prescription oral opioids for 4-30 days was conducted to determine the performance of an OUD classifier derived from machine learning (ML). From this cohort, the demographics of the U.S. adult opioid-prescribed population were used to create a blinded, random, representative group of subjects (n=385) for analysis to accurately estimate the performance characteristics in the intended use population. Genotyping was performed via a qualitative SNP microarray on DNA extracted from buccal samples. RESULTS: In the study subjects, the classifier demonstrated 82.5% sensitivity (95% confidence intervals: 76.1%-87.8%) and 79.9% specificity (73.7-85.2%), with no statistically significant differences in clinical performance observed based on gender, age, length of follow-up from opioid exposure, race, or ethnicity. CONCLUSION: This study demonstrates an ML classifier may provide additional objective information regarding a patient's risk of developing OUD. This information may enable subjects and healthcare providers to make more informed decisions when considering the use of oral opioids.

Effectiveness of Practices to Support Appropriate Laboratory Test Utilization: A Laboratory Medicine Best Practices Systematic Review and Meta-Analysis.

OBJECTIVES: To evaluate the effectiveness of practices used to support appropriate clinical laboratory test utilization. METHODS: This review followed the Centers for Disease Control and Prevention (CDC) Laboratory Medicine Best Practices A6 cycle method. Eligible studies assessed one of the following practices for effect on outcomes relating to over- or underutilization: computerized provider order entry (CPOE), clinical decision support systems/tools (CDSS/CDST), education, feedback, test review, reflex testing, laboratory test utilization (LTU) teams, and any combination of these practices. Eligible outcomes included intermediate, systems outcomes (eg, number of tests ordered/performed and cost of tests), as well as patient-related outcomes (eg, length of hospital stay, readmission rates, morbidity, and mortality). RESULTS: Eighty-three studies met inclusion criteria. Fifty-one of these studies could be meta-analyzed. Strength of evidence ratings for each practice ranged from high to insufficient. CONCLUSION: Practice recommendations are made for CPOE (specifically, modifications to existing CPOE), reflex testing, and combined practices. No recommendation for or against could be made for CDSS/CDST, education, feedback, test review, and LTU. Findings from this review serve to inform guidance for future studies.

The Accuracy of the Sysmex UF-1000i in Urine Bacterial Detection Compared With the Standard Urine Analysis and Culture.

CONTEXT: - Urinary tract infections are characterized by the presence of microbial pathogens within the urinary tract. They represent one of the most common infections in hospitalized and clinic patients. OBJECTIVES: - To model the parameters of the Sysmex UF-1000i to the gold standard, urine culture, and to compare the detection of dipstick leukocyte esterase and nitrates to urine cultures and UF-1000i results. DESIGN: - Data were compared from urine samples collected in sterile containers for bacterial culture and microscopic analysis. One sample was used to inoculate a 5% sheep blood agar and MacConkey agar plate using a 0.001-mL calibrated loop. The second sample was analyzed by urinalysis-associated microscopy. The media plates were investigated for growth after 18 to 24 hours of aerobic incubation at 37°C. The second sample was analyzed for bacteria and leukocytes with the Sysmex UF-1000i according to the manufacturer's guidelines. Three definitions for culture results, sensitivity, and specificity at different cutoff values were calculated for the UF-1000i. RESULTS: - The negative predictive value for any positive culture in the adult population included in the study was 95.5%, and the negative predictive value for positive cultures containing growth of 100 000 or more colony-forming units was 99.3% using the Sysmex UF-1000i. CONCLUSIONS: - Sysmex UF-1000i showed 98% sensitivity and 93.7% specificity with a 95.5% negative predictive value. Thus, a negative screen with the UF-1000i using defined thresholds for white blood cell counts and bacteria was likely to be a true negative, decreasing the need for presumptive antibiotics.

Multi-variant Genetic Panel for Genetic Risk of Opioid Addiction.

Over 116 million people worldwide have chronic pain and prescription dependence. In the US, opioids account for the majority of overdose deaths, and in 2014, almost 2 million Americans abused or were dependent on prescription opioids. Genetic factors may play a key role in opioid prescription addiction. Herein, we describe genetic variations between opioid addicted and non-addicted populations and derive a predictive model determining risk of opioid addiction. This case cohort study compares the frequency of 16 single nucleotide polymorphisms involved in the brain reward pathways in patients with and without opioid addiction. Data from 37 patients with prescription opioid or heroin addiction and 30 age and gender matched controls were used to design the predictive score. The predictive score was then tested on an additional 138 samples to determine generalizabilty. Results for Method Derivation of Observed data: ROC statistic=0.92, sensitivity=82% (95% CI: 66-90), specificity=75% (95% CI:56-87). TreeNet "learn" data: ROC statistic=0.92, sensitivity=92%, specificity=90%, precision=92%, and overall correct=91%. Results of Generalizability data: Sensitivity=97% (95% CI: 90 to 100), specificity=87% (95% CI: 86 to 93), positive likelihood ratio=7.3 (95% CI: 4.0 to 13.5), and negative likelihood ratio=0.03 (95% CI: 0.01 to 0.13). This negative likelihood ratio can be used as an evidence based measure to exclude patients with a high risk of opioid addicition or substance use disorder. By identifying patients with a lower risk for opioid addiction, our model may inform therapeutic decisions.

Anemia and the Need for Intravenous Iron Infusion after Roux-en-Y Gastric Bypass.

The frequency of anemia, iron deficiency, and the long-term need for IV iron following Roux-en-y gastric bypass (RYGB) surgery has not been well characterized. Three-hundred and nineteen out of 904 consecutive subjects who underwent RYGB at Penn State Hershey Medical Center from 1999 to 2006 met the inclusion criteria for a preoperative complete blood count (CBC) and at least one CBC >6 months following surgery. Cumulative incidence of anemia 7 years post procedure was 58%. Menstruation status and presence of preoperative anemia were predictive of anemia by univariate analysis and multivariable Cox regression (P = 0.0014 and 0.044, respectively). Twenty-seven subjects, primarily premenopausal women, representing 8.5% of the cohort and 22% of the 122 anemic subjects, needed intravenous (IV) iron a mean of 51 months postoperatively for anemia unresponsive or refractory to oral iron. The risk for development of anemia necessitating IV iron therapy following RYGB is highest in menstruating women and continues to increase for many years, even in post-menopausal women. Well-designed prospective studies are needed to identify the incidence of iron deficiency anemia and the patient populations at increased risk for requiring IV iron replacement after RYGB surgery.

Default settings of computerized physician order entry system order sets drive ordering habits.

BACKGROUND: Computerized physician order entry (CPOE) systems are quickly becoming ubiquitous, and groups of orders ("order sets") to allow for easy order input are a common feature. This provides a streamlined mechanism to view, modify, and place groups of related orders. This often serves as an electronic equivalent of a specialty requisition. A characteristic, of these order sets is that specific orders can be predetermined to be "preselected" or "defaulted-on" whenever the order set is used while others are "optional" or "defaulted-off" (though there is typically the option is to "deselect" defaulted-on tests in a given situation). While it seems intuitive that the defaults in an order set are often accepted, additional study is required to understand the impact of these "default" settings in an order set on ordering habits. This study set out to quantify the effect of changing the default settings of an order set. METHODS: For quality improvement purposes, order sets dealing with transfusions were recently reviewed and modified to improve monitoring of outcome. Initially, the order for posttransfusion hematocrits and platelet count had the default setting changed from "optional" to "preselected." The default settings for platelet count was later changed back to "optional," allowing for a natural experiment to study the effect of the default selections of an order set on clinician ordering habits. RESULTS: Posttransfusion hematocrit values were ordered for 8.3% of red cell transfusions when the default order set selection was "off" and for 57.4% of transfusions when the default selection was "preselected" (P < 0.0001). Posttransfusion platelet counts were ordered for 7.0% of platelet transfusions when the initial default order set selection was "optional," increased to 59.4% when the default was changed to "preselected" (P < 0.0001), and then decreased to 7.5% when the default selection was returned to "optional." The posttransfusion platelet count rates during the two "optional" periods: 7.0% versus 7.5% - were not statistically different (P = 0.620). DISCUSSION: Default settings in CPOE order sets can significantly influence physician selection of laboratory tests. Careful consideration by all stakeholders, including clinicians and pathologists, should be obtained when establishing default settings in order sets.

BRAF mutation testing in solid tumors: a methodological comparison.

Solid tumor genotyping has become standard of care for the characterization of proto-oncogene mutational status, which has traditionally been accomplished with Sanger sequencing. However, companion diagnostic assays and comparable laboratory-developed tests are becoming increasingly popular, such as the cobas 4800 BRAF V600 Mutation Test and the INFINITI KRAS-BRAF assay, respectively. This study evaluates and validates the analytical performance of the INFINITI KRAS-BRAF assay and compares concordance of BRAF status with two reference assays, the cobas test and Sanger sequencing. DNA extraction from FFPE tissue specimens was performed followed by multiplex PCR amplification and fluorescent label incorporation using allele-specific primer extension. Hybridization to a microarray, signal detection, and analysis were then performed. The limits of detection were determined by testing dilutions of mutant BRAF alleles within wild-type background DNA, and accuracy was calculated based on these results. The INFINITI KRAS-BRAF assay produced 100% concordance with the cobas test and Sanger sequencing and had sensitivity equivalent to the cobas assay. The INFINITI assay is repeatable with at least 95% accuracy in the detection of mutant and wild-type BRAF alleles. These results confirm that the INFINITI KRAS-BRAF assay is comparable to traditional sequencing and the Food and Drug Administration-approved companion diagnostic assay for the detection of BRAF mutations.

First North American case of Hemoglobin Shepherds Bush (ß 74[E18] Gly → Asp) in a central Pennsylvania family.

BACKGROUND: Hemoglobin Shepherds Bush (Human Genome Variation Society name: HBB:c.224G > A) is an unstable hemoglobin variant resulting from a ß 74 GGC to GAC mutation (Gly to Asp) that manifests clinically as hemolytic anemia or gall bladder disease due to chronic subclinical hemolysis. CASE PRESENTATION: We report a Pennsylvania family of English descent with this condition, first noticed in a 6-year-old female. The proband presented with splenomegaly, fatigue, dark urine and an elevated indirect bilirubin. Hemoglobin identification studies and subsequent genetic testing performed according to a systematic algorithm elucidated the diagnosis of Hb Shepherds Bush. CONCLUSIONS: This is the first case of this rare hemoglobin variant identified in North America to our knowledge. It was identified using a systematic algorithm of diagnostic tests that should be followed whenever considering a rare hemoglobinopathy as part of the differential diagnosis.

A rare soft tissue tumor masquerading as a parathyroid adenoma in a patient with birt-hogg-dubé syndrome and multiple cervical endocrinopathies.

Birt-Hogg-Dubé (BHD) syndrome is an autosomal dominant disorder that presents with renal tumors, pulmonary cysts with spontaneous pneumothoraces, and skin hamartomas. We present a case of a 67-year-old female with multiple endocrinopathies and a history of BHD syndrome. In 2011, a thyroidectomy with a four-gland parathyroidectomy was performed for toxic multinodular goiter (TMNG) and parathyroid hyperplasia. On frozen section, a tumor was identified next to a hypercellular parathyroid. After being worked up, this tumor was determined to be an adult rhabdomyoma. This represents the first time that both TMNG and parathyroid hyperplasia have been present in a BHD patient. Additionally, this is the first adult rhabdomyoma reported in a patient with BHD syndrome. Adult rhabdomyomas have no reported associations; however, potential colocation of the mutation in BHD syndrome and translocation in adult rhabdomyomas on chromosome 17p suggests a possible connection. Further work is needed to better understand this connection.

Interference with the Jaffé method for creatinine following 5-aminolevulinic acid administration.

BACKGROUND: The photosensitizer pro-drug 5-aminolevulinic acid (5-ALA) has been administered systemically for photodynamic therapy. Although several toxicities have been reported, nephrotoxicity has never been observed. MATERIALS AND METHODS: Patients with head and neck mucosal dysplasia have been treated on a phase 1 study of escalating light doses in combination with 60mg/kg of oral 5-ALA. Serum creatinine was measured with the modified Jaffe method or an enzymatic method in the first 24h after 5-ALA. Interference by 5-ALA, as well as by its photosensitizing product protoporphyrin IX, was assessed. RESULTS: Among 11 subjects enrolled to date, 9 of 11 had blood chemistries collected within the first 5h with 7 demonstrating significant grade 3 creatinine elevations (p=0.030). There was no additional evidence of compromised renal function or increased PDT-induced mucositis. Creatinine levels measured by the Jaffe assay increased linearly as a function of the ex vivo addition of ALA (p<0.0001). The exogenous addition of PpIX did not alter creatinine levels. ALA did not interfere with creatinine levels as measured by an enzymatic assay. A total of 4 of the 11 subjects had creatinine levels prospectively measured by both the Jaffe and the enzymatic assays. Only the Jaffe method demonstrated significant elevations as a function of time after ALA administration. CONCLUSIONS: The transient increase in creatinine after systematic ALA can be attributed, in part, if not entirely, to interference of ALA in the Jaffe reaction. Alternative assays should be employed in situations calling for monitoring of kidney function after systemic ALA.

Quantitation of tacrolimus in whole blood using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS).

We describe a multiple reaction monitoring positive ion HPLC/tandem mass spectrometric method for quantification of tacrolimus in human whole blood with online extraction and cleanup. Included in this procedure: API 2000 triple quadrupole mass spectrometer with turbo-ion spray source (Applied Biosystems, Foster City, CA); 10-port diverter/switching valve (Valco, Houston, TX); HPLC system (Agilent Technologies series 1100, Wilmington, DE); 10 mm (C(18)) guard cartridge (Perkin Elmer, Norwalk, CT) used as an extraction column; a Nova-Pak C18 analytical column (2.1 x 150 mm I.D., 4 microm, Waters Corp, Milford, MA); washing solution, methanol: 30 mM ammonium acetate pH 5.1 (80:20); eluting solution, methanol:30 mM ammonium acetate pH 5.1 (97:3); flow rate 0.8 mL/min; and a run-time of 2.8 min. The first and third quadrupoles were set to detect the ammonium adduct ion and a high mass fragment of tacrolimus (m/z 821.5-->768.3), and of an internal standard (ascomycin) (m/z 901.8-->834.4). The lower limit of quantification of this method is 3.75 mg/L. The concentration of drug is determined by comparing peak-area ratios for tacrolimus and internal standard to a standard curve constructed using non-weighted linear through zero regression.

Development of a bidirectional caspase-3 expression system for the induction of apoptosis.

Caspase-3 is the executioner caspase of apoptosis whose activation in mammalian cells represents the last stage of the programmed cell death signaling pathway and the initiation of the lethal digestion of cell proteins. Active caspase-3 is a tetramer composed of two p12 and two p17 subunits derived from cleavage of procaspase-3 during activation. Here, we armed GFP-fusion proteins of both the caspase-3 p12 and p17 subunits with signals from Ig-kappa light chain that allows its efficient secretion from the cells (Sec) and from HIV-1 Tat that facilitates its uptake and nuclear translocation by other cells (NLS). We found that treatment of cells with conditioned media from cells expressing both Sec-GFP-p17-NLS and Sec-GFP-p12-NLS was able to transduce active caspase-3 with consequent cell death of treated cultures. Use of various combinations of constructs demonstrated that both subunits were required and that each one needed to possess both Sec and NLS. Our observations introduce a bidirectional protein transduction system with the ability to introduce active caspase-3 into cells and cause apoptosis. This system may have important therapeutic applications.