Evaluation of Glove Performance after Decontamination.

Studies of healthcare providers doffing personal protective equipment, especially gloves, indicate that self-contamination does occur. Although generally this is not hazardous, working with particularly pathogenic organisms, such as Ebola virus and Clostridium difficile, can present a serious health risk. Decontaminating medical gloves before removal can reduce self-contamination and mitigate the spread of these types of pathogens. Also, in cases of extreme shortage, the Centers for Disease Control and Prevention (CDC) has specific recommendations for decontaminating gloves for extended use. Reuse of medical gloves is strongly discouraged by both the CDC and Food and Drug Administration. This work seeks to lay a foundation of testing to evaluate whether a decontamination method is compatible for a given glove type and material. Four potential methods of decontamination (commercial hand soap, alcohol-based hand sanitizer, commercial bleach, and quaternary ammonium solution) were tested on a variety of surgical and patient examination gloves. The method of barrier performance evaluation was ASTM D5151-19, Standard Test Method for Detection of Holes in Medical Gloves. Our results indicated that the performance of the gloves after treatment was highly dependent on the composition of the medical gloves. In general, the surgical gloves in this study performed better than the patient examination gloves, regardless of the material from which they were made. Specifically, vinyl examination gloves tended to have poorer performance. In this study, the number of gloves available to test were limited and therefore statistical significance is beyond the scope of this project.

Research: Comparing ASTM F1671 with a Modified Dot-Blot Method to Evaluate Personal Protective Materials.

Effective personal protective equipment (PPE) is critical in preventing the spread of infectious diseases. Appropriate test systems and test soils are needed to adequately evaluate PPE. ASTM test method F903, which specifies the test method setup also used in ASTM F1670 and F1671, has been used for decades to test liquid (ASTM F1670) or viral (ASTM F1671) penetration resistance of PPE fabrics. However, an alteration of the bacteriophage propagation method detailed in the standard was necessary to obtain consistent titers of virus. In this study, modification of the nutrient broth provided consistently higher titers of virus and the use of the top agar in smaller increments prevented premature solidification. This study then compared the standard ASTM F1671 (using bacteriophage ϕχ174) with a modified dot-blot method to assess viral penetration of PPE materials. The results indicated that ASTM F1671 and the dot-blot apparatus methods were equivalent. The dot-blot method described here is less labor intensive and faster than the ASTM F1671 method. However, using the dot-blot system, which uses antibodies to detect the bacteriophage and signal amplification, does not indicate if virus viability or infectivity is retained, whereas the ASTM F1671 method indicates both. Nonetheless, the method presented in this investigation is a substantial improvement of a standard method for viral challenge testing of PPE materials.

Global Transcriptional Response to CRISPR/Cas9-AAV6-Based Genome Editing in CD34+ Hematopoietic Stem and Progenitor Cells.

Genome-editing technologies are currently being translated to the clinic. However, cellular effects of the editing machinery have yet to be fully elucidated. Here, we performed global microarray-based gene expression measurements on human CD34+ hematopoietic stem and progenitor cells that underwent editing. We probed effects of the entire editing process as well as each component individually, including electroporation, Cas9 (mRNA or protein) with chemically modified sgRNA, and AAV6 transduction. We identified differentially expressed genes relative to control treatments, which displayed enrichment for particular biological processes. All editing machinery components elicited immune, stress, and apoptotic responses. Cas9 mRNA invoked the greatest amount of transcriptional change, eliciting a distinct viral response and global transcriptional downregulation, particularly of metabolic and cell cycle processes. Electroporation also induced significant transcriptional change, with notable downregulation of metabolic processes. Surprisingly, AAV6 evoked no detectable viral response. We also found Cas9/sgRNA ribonucleoprotein treatment to be well tolerated, in spite of eliciting a DNA damage signature. Overall, this data establishes a benchmark for cellular tolerance of CRISPR/Cas9-AAV6-based genome editing, ensuring that the clinical protocol is as safe and efficient as possible.

Research: Using Clinically Relevant Test Soils to Evaluate Personal Protective Materials.

Effective personal protective equipment (PPE) is critically important to preventing the spread of infectious diseases. Appropriate test systems and test soils are needed to adequately evaluate PPE. ASTM test method F903, which specifies the test method setup also used in ASTM F1670/F1670M-17a and ASTM F1671/F1671M-13, has been used for decades to test liquid penetration resistance of fabrics. All three standards require at least 60 mL of challenge liquid, such as synthetic blood solution (F1670) or bacteriophage in nutrient broth (F1671). The three ASTM test methods also are labor intensive and prone to exhibiting problems with leakage around the gaskets. Previous work comparing the F903 test apparatus with a modified dot-blot apparatus to evaluate the visual penetration of a blood test soil in series of commercially available gowns and drapes demonstrated that the methods are comparable and revealed that penetration through PPE material may depend on the test solution. The study described here evaluated a series of clinically relevant test soils (blood, vomit, urine, and feces) in penetration of PPE garments using the modified dot-blot apparatus. The results indicated that a vomit test soil penetrates PPE material more often than blood, urine, or fecal test soils and that the blood test soil has the least number of PPE failures. Incorporating clinically relevant, chemically defined test soils to evaluate PPE material should be considered to protect healthcare workers and reduce the spread of infectious material.

Evaluation of Apparatus Used to Test Liquid through Protective Materials: Comparison of a Modified Dot-Blot Apparatus to the ASTM Penetration Cell.

Personal protective equipment (PPE), such as gowns used in the latest Ebola outbreak in Western Africa, are critical in preventing the spread of deadly diseases. Appropriate test systems and test soils are needed to adequately evaluate PPE. ASTM F903, Standard Test Method for Resistance of Materials Used in Protective Clothing to Penetration by Liquid, has been used for decades to test fabrics' resistance to liquid penetration. However, this test apparatus requires at least 60 mL of test solutions, is labor intensive, and has problems with leakage around the gaskets. We compared the F903 test apparatus to a modified dot-blot apparatus to evaluate the visual penetration of a blood test soil. A series of commercially available gowns and drapes were tested in each apparatus. Using blood test soil at 2 psi, there was no statistically significant difference between the two methods except for in one gown. By comparing this gown in the ASTM test apparatus with and without a screen, the particular screen selected did not account for the difference between the dot-blot and F903 apparatuses; however, it is conceivable that a particular screen/fabric combination could account for this difference. The modified dot-blot apparatus was evaluated using three different test solutions: blood, vomit, and a labeled protein (goat anti-rabbit immunoglobulin G-horseradish peroxidase [GaR IgG-HRP]) in a blood test soil solution. This testing revealed significant difference in penetration for some of the PPE garments. The modified dot-blot had several large advantages over the ASTM apparatus-over six times less specimen volume and no edge or gasket leakage. In addition, nitrocellulose can be easily incorporated into the modified dot-blot apparatus, enabling the trapping of viruses and proteins that penetrate PPE-thus permitting the use of antibodies to quickly and sensitively detect penetration.

lincRNAs act in the circuitry controlling pluripotency and differentiation.

Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem (ES) cells and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ES cell regulators. Notably, lincRNAs primarily affect gene expression in trans. Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ES cells and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state.

Controlled initial surge despite high drug fraction and high solubility.

Potential connections between release profiles and solvent evaporation rates alongside polymer chemistry were elucidated for the release of tetracycline hydrochloride from two different poly (d, l-lactide-co-glycolide) (PLGA) film matrices containing high drug fractions (50%, 30%, and 15%), and prepared at two distinct solvent evaporation rates. At highest tetracycline concentrations (50%), (i) the early release rates were ≤0.5 µg/min in all cases; (ii) release was linear from systems fabricated with lower lactic content and slower solvent evaporation rate and bimodal from systems fabricated with higher lactic content and faster evaporation rate; (iii) surface fractions covered by the drug were similar at both evaporation rates for 85:15 PLGA but very different for 50:50 PLGA, leading to unexpectedly reduced early release from 50:50 PLGA than from 85:15 PLGA when both the matrices were fabricated using a slower evaporation rate. These features remained unaffected in case of low drug concentration. Results suggested that during the formation of the drug-polymer microstructure, the combined effect of polymer chemistry and solvent evaporation rate sets apart the surface characteristics and the initial release profiles of systems containing high drug fraction, and an appropriate combination of these parameters may be utilized to control the early stage of drug release.

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

BACKGROUND: Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background. RESULTS: ERCC pools were analyzed on four different microarray platforms: Agilent 1- and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate. CONCLUSIONS: The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.

Evaluating Device Design and Cleanability of Orthopedic Device Models Contaminated with a Clinically Relevant Bone Test Soil.

UNLABELLED: Reusable medical devices need to be cleaned prior to disinfection or sterilization and subsequent use to prevent infections. The cleanability of medical devices depends in part on the design of the device. This study examined how models of orthopedic medical devices of increasing complexity retain calcium phosphate bone cement, a relevant test soil for these devices. METHODS: The dye Alizarin Red S and micro-computed tomography (µCT) were used to assess the amount and location of bone cement debris in a series of model orthopedic devices. Testing was performed after soiling and cleaning once, and soiling and cleaning 10 times. RESULTS: The color change of the dye after reacting with the bone cement was useful for indicating the presence of bone cement in these models. High-resolution µCT analysis provided the volume and location of the bone cement. Models that were more complex retained significantly more bone debris than simpler designs. Model devices repeatedly soiled and cleaned 10 times retained significantly more bone debris than those soiled and cleaned once. CONCLUSION: Significantly more bone cement was retained in the more complex lumen structures. This information may be useful in designing reusable orthopedic devices, and other complex medical devices with lumens.

Lack of correlation between age and/or gender with the force utilized in cleaning an anesthesia machine.

Several human factors influence the cleaning of reusable medical devices and equipment. This study evaluated whether a correlation exists between age and/or gender of a person cleaning, with the force applied to remove artificial blood soil on the surface of an anesthesia machine. The findings from this study may be used to increase our understanding of human factors in the cleaning of reusable medical equipment and suggest improvements in equipment design to address issues of concern.

Evaluation of intraocular reactivity to metallic and ethylene oxide contaminants of medical devices in a rabbit model.

OBJECTIVE: To evaluate the intraocular reactivity to metallic and ethylene oxide (EO) contaminants of ophthalmic devices in rabbits. DESIGN: Two experimental animal studies. PARTICIPANTS: Thirty-five New Zealand white rabbits. METHODS: A metallic exposure study and an EO exposure study were performed. In the first study, both eyes of 25 rabbits were equally allocated to intracameral injections of alumina 0.2 µg, alumina 20 µg, copper sulfate 0.4 µg, copper sulfate 20 µg, or an aqueous control. In the second study, 10 rabbits were allocated (5 per group) to receive intracamerally an ophthalmic viscosurgical device (OVD) exposed to EO or not exposed to EO (control). All eyes were examined by slit lamp at baseline and 3, 6, 9, 24, 48, and 72 hours after exposure, with dilated indirect ophthalmoscopy being performed at 24 and 72 hours. Tonometry was performed only in the first study. MAIN OUTCOME MEASURES: Grade of corneal clouding, anterior chamber (AC) flare, AC cells, AC fibrin, iridal hyperemia, cell and fibrin on the lens surface, vitreous haze and cells, lens opacities, intraocular pressure, and onset time. RESULTS: For metallic compounds at the study's low doses, mean inflammatory grades were 0.2 or less above the control for all responses at all time points. For the high-dose alumina, mean inflammatory grades peaked at 6 to 9 hours at 0.5 to 0.7 above the control responses for conjunctival congestion, iris hyperemia, AC cells, flare, and fibrin and declined over the remaining time points. For the high-dose copper sulfate, mean inflammatory grades peaked between 3 and 24 hours at 1.2 to 1.8 above the control responses for conjunctival congestion, iris hyperemia, AC cells, flare, fibrin, and corneal clouding, then subsequently declined. The intraocular pressure changes appeared significant for only high-dose copper sulfate, with mean declines of 4.3 to 7.5 mmHg at 6 to 72 hours. No clinically meaningful differences in ocular inflammation were observed between the OVD exposed to EO and the OVD not exposed to EO. CONCLUSIONS: Alumina and copper sulfate did not cause clinically meaningful ocular inflammation at the low study levels (levels expected with ophthalmic devices). Ethylene oxide exposure of an OVD was not associated with inflammation.

The effects of contact lens materials on a multipurpose contact lens solution disinfection activity against Staphylococcus aureus.

OBJECTIVES: To determine the effect of 8 different lens materials on polyhexamethylene biguanide (PHMB) concentration in multipurpose solution (MPS) levels over time and to determine the effect of lenses on lens solution microbial efficacy over time. METHODS: Silicone hydrogel lenses and conventional hydrogel lenses were soaked in polypropylene lens cases filled with contact lens MPS containing 1 ppm PHMB for 6, 12, 24, 72, and 168 hours. Cases filled with the same solution without lenses were controls. After each time period, solutions from cases with the 8 types of lenses and controls were assayed for activity against Staphylococcus aureus according to International Organization for Standardization-14729 with modifications. Solutions were analyzed for PHMB concentration at each time point. RESULTS: Some of the different lens materials significantly affected the PHMB concentration (P<0.0001) and the biocidal efficacy. Etafilcon A lenses significantly decreased PHMB levels after only 6 hours of lens soak time. The product lot of MPS used was also significant (P<0.0001). Enfilcon A, senofilcon A, and lotrafilcon B lenses did not significantly decrease PHMB levels. CONCLUSIONS: The efficacy of MPS was affected by some lens materials and PHMB concentration. Lens materials differ in their effect on PHMB concentration and the subsequent efficacy of the MPS. Over time, some lens materials can significantly reduce the PHMB concentration and the MPS's microbial activity against S. aureus.

The effect of contact lens materials on disinfection activity of polyquaternium-1 and myristamidopropyl dimethylamine multipurpose solution against Staphylococcus aureus.

OBJECTIVES: This study examined the interaction of seven different lens materials with a multipurpose solution (MPS) containing the disinfectants polyquaternium-1 (0.001%) and myristamidopropyl dimethylamine (0.0005%). The objective of this study was to determine whether the different lens materials affect the concentration of a disinfectant in this commercially available MPS and the efficacy of the disinfectant against Staphylococcus aureus. METHODS: Silicone hydrogel lenses (galyfilcon A, senofilcon A, comfilcon A, enfilcon A, balafilcon A, and lotrafilcon B) and a conventional hydrogel lens (etafilcon A) were soaked in polypropylene lens cases filled with commercially available MPS containing 0.001% polyquaternium-1 and 0.0005% myristamidopropyl dimethylamine for 6, 12, 24, 72, and 168 hours. Empty lens cases were also filled with MPS. After each time point, solutions from cases containing the seven types of lenses and controls were assayed for activity against S. aureus according to International Standards Organization 14729 standard with modifications. Test solutions were analyzed for polyquaternium-1 and myristamidopropyl dimethylamine concentration at each time point. RESULTS: The concentration of polyquaternium-1 and myristamidopropyl dimethylamine remaining in the lens cases was reduced only slightly over time. Storage with the lenses did not adversely affect biocidal efficacy of the solution, and in some cases, it was significantly better (P=0.0029). CONCLUSION: The efficacy of this polyquaternium-1 and myristamidopropyl dimethylamine MPS to kill S. aureus was not adversely affected by the presence of lens materials soaking in the cases. Thus, current methods for performing solution antimicrobial testing should be reevaluated.

Impact of contact lens materials on multipurpose contact lens solution disinfection activity against Fusarium solani.

OBJECTIVE: To investigate the effects of eight different soft contact lenses on disinfection efficacy of a multipurpose solution (MPS) containing polyhexamethylene biguanide (PHMB) against Fusarium solani. METHODS: Six silicone hydrogel lenses (galyfilcon A, senofilcon A, comfilcon A, enfilcon A, balafilcon A, and lotrifilcon B) and two conventional hydrogel lenses (polymacon and etafilcon A) were placed in polypropylene lens cases filled with MPS containing 0.0001% PHMB and soaked for 6, 12, 24, 72, and 168 hours. After each interval, depleted MPS from lens cases were removed and assayed for activity against F. solani according to International Organization for Standardization (ISO) 14729 stand-alone procedure. A portion was aliquoted for chemical analysis. RESULTS: Soaking etafilcon A, balafilcon A, and polymacon lenses for 6 hours reduced the concentration of PHMB in MPS by more than half the stated labeled concentration, with concentrations below the limit of detection for etafilcon A-depleted and balafilcon A-depleted solutions after 12 and 72 hours of soaking, respectively. Except for comfilcon A-depleted solutions, all others failed to consistently obtain one log reduction of F. solani. The solutions soaked with etafilcon A, balafilcon A, and polymacon lenses for 24 hours or more lost all or almost all fungicidal activity against F. solani. CONCLUSIONS: Over time, the disinfectant uptake by some lenses can significantly reduce the PHMB concentration and the fungicidal activity of the MPS against F. solani. Current ISO methodology does not address the reduction in microbiocidal efficacy when lenses are soaked in MPS. The ISO committee should consider adding "soaking experiments" to quantify the effect that contact lens materials have on the performance of MPSs.

Material properties that predict preservative uptake for silicone hydrogel contact lenses.

OBJECTIVES: To assess material properties that affect preservative uptake by silicone hydrogel lenses. METHODS: We evaluated the water content (using differential scanning calorimetry), effective pore size (using probe penetration), and preservative uptake (using high-performance liquid chromatography with spectrophotometric detection) of silicone and conventional hydrogel soft contact lenses. RESULTS: Lenses grouped similarly based on freezable water content as they did based on total water content. Evaluation of the effective pore size highlighted potential differences between the surface-treated and non-surface-treated materials. The water content of the lens materials and ionic charge are associated with the degree of preservative uptake. CONCLUSIONS: The current grouping system for testing contact lens-solution interactions separates all silicone hydrogels from conventional hydrogel contact lenses. However, not all silicone hydrogel lenses interact similarly with the same contact lens solution. Based upon the results of our research, we propose that the same material characteristics used to group conventional hydrogel lenses, water content and ionic charge, can also be used to predict uptake of hydrophilic preservatives for silicone hydrogel lenses. In addition, the hydrophobicity of silicone hydrogel contact lenses, although not investigated here, is a unique contact lens material property that should be evaluated for the uptake of relatively hydrophobic preservatives and tear components.

Environmental fate of polyhexamethylene biguanide.

Polyhexamethylene biguanide (PHMB) is used as a bacteriocidal agent in a variety of applications from medical devices to pools, but is highly toxic to some aquatic species. The stability of PHMB in various environmental matrices was examined. 80% of PHMB was present in fortified creek samples after 20 days, but bound immediately to soils with the exception of sandy soil. PHMB was absorbed to below detectable levels by weathered concrete within 12 h. In addition, one over the counter wound care product containing PHMB was evaluated to assess environmental leaching; detectable levels (20 µg/mL) were still present after 1 week.

Comparison of test methods to screen for residual chemical contamination on medical device surfaces.

Reprocessing medical devices involves several steps including cleaning and disinfection or sterilization. Chemical residuals can occur at various stages of reprocessing. These residues could interfere with device function and potentially harm patients. These solutions are composed of a combination of various chemicals and their residues are highly diluted post rinsing, therefore, it is difficult to find a sensitive and rapid method to detect toxicity due to chemical residues. This study focused on (1) finding the levels of residues that are cytotoxic using two mammalian cell lines and Daphnia magna, and (2) evaluating two test methods, Total Organic Carbon (TOC) and the Luminescent Bacteria Test (LBT), to measure residual chemicals levels. The two mammalian cell lines were equal in their cytotoxicity responses. However, Daphnia were more sensitive to some chemical residue than the two mammalian cell lines. TOC and LBT were able to detect the presence of residue well below the levels that were determined to cause mammalian cytotoxicity. LBT was more sensitive for some chemicals and TOC for others, both in solution and in simulated cleaning and rinsing for the limited number of solutions tested in this study.

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.

Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.

Inappropriate dispatcher decision for emergency medical service users with acute myocardial infarction.

OBJECTIVES: Current guidelines recommend utilization of prehospital emergency medical services (EMSs) by patients with ST-elevation myocardial infarction (STEMI). The aims of this study were to estimate the percentage of inappropriate initial dispatcher decisions and determine their impact on delays in reperfusion therapy for EMS users with STEMI. METHODS: As part of a prospective regional registry of patients with STEMI, we analyzed the original data for 245 patients who called a university hospital-affiliated EMS call center in France. The primary study outcome was time to reperfusion therapy calculated from the documented date and time of the first patient call. RESULTS: The initial EMS dispatcher's decision was appropriate (ie, dispatching a mobile intensive care unit staffed by an emergency or critical care physician) for 171 (70%) patients and inappropriate for 74 (30%) patients. Inappropriate decisions included referring the patient to a family physician (n = 59), providing medical advice (n = 9), and dispatching an ambulance (n = 6). Inappropriate initial decisions resulted in increased median time to reperfusion for 140 patients receiving fibrinolysis (95 vs 53 minutes; P < .001) and 91 patients undergoing primary percutaneous coronary intervention (170 vs 107 minutes; P < .001). In-hospital mortality was not different between the 2 study groups (6.8% vs 9.9%; P = .42). CONCLUSION: The initial dispatcher's decision is inappropriate for 30% of EMS users with STEMI and results in substantial delays in time to reperfusion therapy. Accuracy of telephone triage should be improved for patients who activate EMSs in response to symptoms suggestive of acute coronary syndrome.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

BACKGROUND: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. RESULTS: All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. CONCLUSION: This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.