Dataset Information

FuSpot: a web-based tool for visual evaluation of fusion candidates.

ABSTRACT: Gene fusions often occur in cancer cells and in some cases are the main driver of oncogenesis. Correct identification of oncogenic gene fusions thus has implications for targeted cancer therapy. Recognition of this potential has led to the development of a myriad of sequencing-based fusion detection tools. However, given the same input, many of these detectors will find different fusion points or claim different sets of supporting data. Furthermore, the rate at which these tools falsely detect fusion events in data varies greatly. This discrepancy between tools underscores the fact that computation algorithms still cannot perfectly evaluate evidence; especially when provided with small amounts of supporting data as is typical in fusion detection. We assert that when evidence is provided in an easily digestible form, humans are more proficient in identifying true positives from false positives.We have developed a web tool that, given the genomic coordinates of a candidate fusion breakpoint, will extract fusion and non-fusion reads adjacent to the fusion point from partner transcripts, and color code reads by transcript origin and read orientation for ease of intuitive inspection by the user. Fusion partner transcript read alignments are performed using a novel variant of the Smith-Waterman algorithm.Combined with dynamic filtering parameters, the visualization provided by our tool introduces a powerful new investigative step that allows researchers to comprehensively evaluate fusion evidence. Additionally, this allows quick identification of false positives that may deceive most fusion detectors, thus eliminating unnecessary gene fusion validation. We apply our visualization tool to publicly available datasets and provide examples of true as well as false positives reported by open source fusion detection tools.

SUBMITTER: Killian JA

PROVIDER: S-EPMC5812216 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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FuSpot: a web-based tool for visual evaluation of fusion candidates.

Killian Jackson A JA Topiwala Taha M TM Pelletier Alex R AR Frankhouser David E DE Yan Pearlly S PS Bundschuh Ralf R

BMC genomics 20180213 1

<h4>Background</h4>Gene fusions often occur in cancer cells and in some cases are the main driver of oncogenesis. Correct identification of oncogenic gene fusions thus has implications for targeted cancer therapy. Recognition of this potential has led to the development of a myriad of sequencing-based fusion detection tools. However, given the same input, many of these detectors will find different fusion points or claim different sets of supporting data. Furthermore, the rate at which these too ...[more]

PMID: 29439649

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Project description:This article describes the evaluation of an open-access web-based respiratory protective equipment selector tool (RPE-Select, accessible at http://www.healthyworkinglives.com/rpe-selector). This tool is based on the principles of the COSHH-Essentials (C-E) control banding (CB) tool, which was developed for the exposure risk management of hazardous chemicals in the workplace by small and medium sized enterprises (SMEs) and general practice H&S professionals. RPE-Select can be used for identifying adequate and suitable RPE for dusts, fibres, mist (solvent, water, and oil based), sprays, volatile solids, fumes, gases, vapours, and actual or potential oxygen deficiency. It can be applied for substances and products with safety data sheets as well as for a large number of commonly encountered process-generated substances (PGS), such as poultry house dusts or welding fume. Potential international usability has been built-in by using the Hazard Statements developed for the Globally Harmonised System (GHS) and providing recommended RPE in picture form as well as with a written specification. Illustration helps to compensate for the variabilities in assigned protection factors across the world. RPE-Select uses easily understandable descriptions/explanations and an interactive stepwise flow for providing input/answers at each step. The output of the selection process is a report summarising the user input data and a selection of RPE, including types of filters where applicable, from which the user can select the appropriate one for each wearer. In addition, each report includes 'Dos' and 'Don'ts' for the recommended RPE. RPE-Select outcomes, based on up to 20 hypothetical use scenarios, were evaluated in comparison with other available RPE selection processes and tools, and by 32 independent users with a broad range of familiarities with industrial use scenarios in general and respiratory protection in particular. For scenarios involving substances having safety data sheets, 87% of RPE-Select outcomes resulted in a 'safe' RPE selection, while 98% 'safe' outcomes were achieved for scenarios involving process-generated substances. Reasons for the outliers were examined. User comments and opinions on the mechanics and usability of RPE-Select are also presented.

Project description:PurposeTo evaluate the outcome of a web-based digital assessment of visual acuity and refractive error, compared to a conventional supervised assessment, in keratoconus patients with complex refractive errors.Material and methodsKeratoconus patients, aged 18 to 40, with a refractive error between -6 and +4 diopters were considered eligible. An uncorrected visual acuity and an assessment of refractive error was taken web-based (index test) and by manifest refraction (reference test) by an optometrist. Corrected visual acuity was assessed with the prescription derived from both the web-based tool and the manifest refraction. Non-inferiority was defined as the 95% limits-of-agreement (95%LoA) of the differences in spherical equivalent between the index and reference test not exceeding +/- 0.5 diopters. Agreement was assessed by a Bland-Altman analyses.ResultsA total of 100 eyes of 50 patients were examined. The overall mean difference of the uncorrected visual acuity measured -0.01 LogMAR (95%LoA:-0.63-0.60). The variability of the differences decreased in the better uncorrected visual acuity subgroup (95%LoA:-0.25-0.55). The overall mean difference in spherical equivalent between the index and reference test exceeded the non-inferiority margin: -0.58D (95%LoA:-4.49-3.33, P = 0.008). The mean differences for myopic and hyperopic subjects were 0.09 diopters (P = 0.675) and -2.06 diopters (P<0.001), respectively. The corrected visual acuities attained with the web-based derived prescription underachieved significantly (0.22±0.32 logMAR vs. -0.01±0.13 LogMAR, P <0.001).ConclusionsRegarding visual acuity, the web-based tool shows promising results for remotely assessing visual acuity in keratoconus patients, particularly for subjects within a better visual acuity range. This could provide physicians with a quantifiable outcome to enhance teleconsultations, especially relevant when access to health care is limited. Regarding the assessment of the refractive error, the web-based tool was found to be inferior to the manifest refraction in keratoconus patients. This study underlines the importance of validating digital tools and could serve to increase overall safety of the web-based assessments by better identification of outlier cases.

Project description:BACKGROUND:Digital tools provide a unique opportunity to increase access to eye care. We developed a Web-based test that measures visual acuity and both spherical and cylindrical refractive errors. This test is Conformité Européenne marked and available on the Easee website. The purpose of this study was to compare the efficacy of this Web-based tool with traditional subjective manifest refraction in a prospective open-label noninferiority clinical trial. OBJECTIVE:The aim of this study was to evaluate the outcome of a Web-based refraction compared with a manifest refraction (golden standard). METHODS:Healthy volunteers from 18 to 40 years of age, with a refraction error between -6 and +4 diopter (D), were eligible. Each participant performed the Web-based test, and the reference test was performed by an optometrist. An absolute difference in refractive error of <0.5 D was considered noninferior. Reliability was assessed by using an intraclass correlation coefficient (ICC). Both uncorrected and corrected visual acuity were measured. RESULTS:A total of 200 eyes in 100 healthy volunteers were examined. The Web-based assessment of refractive error had excellent correlation with the reference test (ICC=0.92) and was considered noninferior to the reference test. Uncorrected visual acuity was similar with the Web-based test and the reference test (P=.21). Visual acuity was significantly improved using the prescription obtained by using the Web-based tool (P<.01). The Web-based test provided the best results in participants with mild myopia (ie, <3 D), with a mean difference of 0.02 (SD 0.49) D (P=.48) and yielding a corrected visual acuity of >1.0 in 90% (n=77) of participants. CONCLUSIONS:Our results indicate that Web-based eye testing is a valid and safe method for measuring visual acuity and refractive error in healthy eyes, particularly for mild myopia. This tool can be used for screening purposes, and it is an easily accessible alternative to the subjective manifest refraction test. TRIAL REGISTRATION:Clinicaltrials.gov NCT03313921; https://clinicaltrials.gov/ct2/show/NCT03313921.

Dataset Information

FuSpot: a web-based tool for visual evaluation of fusion candidates.

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FuSpot: a web-based tool for visual evaluation of fusion candidates.

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