Search Results (6)

Background: In clinical practice, various methods are used to identify ALK gene rearrangements in tumor samples, ranging from “classic” techniques, such as IHC, FISH, and RT-qPCR, to more advanced highly multiplexed approaches, such as NanoString technology and NGS panels. Each of these methods has its own advantages and disadvantages, but they share the drawback of detecting only a restricted (although sometimes quite extensive) set of preselected biomarkers. At the same time, whole transcriptome sequencing (WTS, RNAseq) can, in principle, be used to detect gene fusions while simultaneously analyzing an incomparably wide range of tumor characteristics. However, WTS is not widely used in practice due to purely analytical limitations and the high complexity of bioinformatic analysis, which requires considerable expertise. In particular, methods to detect gene fusions in RNAseq data rely on the identification of chimeric reads. However, the typically low number of true fusion reads in RNAseq limits its sensitivity. In a previous study, we observed asymmetry in the RNAseq exon coverage of the 3′ partners of some fusion transcripts. In this study, we conducted a comprehensive evaluation of the accuracy of ALK fusion detection through an analysis of differences in the coverage of its tyrosine kinase exons. Methods: A total of 906 human cancer biosamples were subjected to analysis using experimental RNAseq data, with the objective of determining the extent of asymmetry in ALK coverage. A total of 50 samples were analyzed, comprising 13 samples with predicted ALK fusions and 37 samples without predicted ALK fusions. These samples were assessed by targeted sequencing with two NGS panels that were specifically designed to detect fusion transcripts (the TruSight RNA Fusion Panel and the OncoFu Elite panel). Results: ALK fusions were confirmed in 11 out of the 13 predicted cases, with an overall accuracy of 96% (sensitivity 100%, specificity 94.9%). Two discordant cases exhibited low ALK coverage depth, which could be addressed algorithmically to enhance the accuracy of the results. It was also important to consider read strand specificity due to the presence of antisense transcripts involving parts of ALK. In a limited patient sample undergoing ALK-targeted therapy, the algorithm successfully predicted treatment efficacy. Conclusions: RNAseq exon coverage analysis can effectively detect ALK rearrangements. Full article

This study examines short-term improvement of music performances and oculomotor behaviour during four successive executions of a brief musical piece composed by Bartók, “Slovak Boys’ Dance”. Pianists (n = 22) were allowed to practice for two minutes between each trial. Eye-tracking data were collected as well as MIDI information from pianists’ performances. Cognitive skills were assessed by a spatial memory test and a reading span test. Principal component analysis (PCA) enabled us to distinguish two axes, one associated with anticipation and the other with dependence/independence on written code. The effect of musical structure, determined by the emergence of different sections in the score, was observed in all the dependent variables selected from the PCA; we also observed the effect of practice on the number of fixations, the number of glances at the keyboard (GAK) and the awareness span. Pianist expertise was associated with fewer fixations and GAK, better anticipation capacities and more effective strategies for visual monitoring of motor movements. The significant correlations observed between the reading span test and GAK duration highlight the challenge of working memory involvement during music reading. Full article

In a sight-reading task, the position of the eyes on the score is generally further ahead than the note being produced by the instrument. This anticipation allows musicians to identify the upcoming notes and possible difficulties and to plan their gestures accordingly. The eye-hand span (EHS) corresponds to this offset between the eye and the hand and measures the distance or latency between an eye fixation on the score and the production of the note on the instrument. While EHS is mostly quite short, the variation in its size can depend on multiple factors. EHS increases in line with the musician's expertise level, diminishes as a function of the complexity of the score and can vary depending on the context in which it is played. By summarizing the main factors that affect EHS and the methodologies used in this field of study, the present review of the literature highlights the fact that a) to ensure effective sight reading, the EHS must be adaptable and optimized in size (neither too long not too short), with the best sight readers exhibiting a high level of perceptual flexibility in adapting their span to the complexity of the score; b) it is important to interpret EHS in the light of the specificities of the score, given that it varies so much both within and between scores; and c) the flexibility of EHS can be a good indicator of the perceptual and cognitive capacities of musicians, showing that a musician's gaze can be attracted early by a complexity in a still distant part of the score. These various points are discussed in the light of the literature on music-reading expertise. Promising avenues of research using the eye tracking method are proposed in order to further our knowledge of the construction of an expertise that requires multisensory integration. Full article

The ability to sight-read traditional staff notation is an important skill for all classically trained musicians. Up until now, however, most research has focused on pianists, by comparing experts and novices. Eye movement studies are a niche area of sight-reading research, focusing on eye-hand span and perceptual span of musicians, mostly pianists. Research into eye movement of non-piano sight-reading is limited. Studies into eye movement of woodwind sight-reading were conducted in the 1980s and early 2000s, highlighting the need for new research using modern equipment. This pilot study examined the eye movements of six woodwind (flute, clarinet) undergraduates of intermediate-to-advanced skill level during sight-reading of scores of increased difficulty. The data was analysed in relation to expertise level and task difficulty, focusing on numbers of fixations and fixation durations. The results show that as music examples became more difficult the numbers of fixations increased and fixation durations decreased; more experienced players with better sight-reading skills required less time to process musical notation; and participants with better sight-reading skills utilised fewer fixations to acquire information visually. The findings confirm that the efficiency of eye movements is related to instrumental and sight-reading expertise, and that task difficulty affects eye movement strategies. Full article

In this review, we focus on the methodological aspects of eye-tracking research in the domain of music, published and/or available between 1994 and 2017, and we identify potentially fruitful next steps to increase coherence and systematicity within this emerging field. We review and discuss choices of musical stimuli, the conditions under which these were performed (i.e., control of performance tempo and music-reading protocols), performer’s level of musical expertise, and handling of performance errors and eye-movement data. We propose that despite a lack of methodological coherence in research to date, careful reflection on earlier methodological choices can help in formulating future research questions and in positioning new work. These steps would represent progress towards a cumulative research tradition, where joint understanding is built by systematic and consistent use of stimuli, research settings and methods of analysis. Full article

Previous studies have shown that performance at a defined level of music sight-reading for pianists (6th Grade) is predictive of eye movement patterns (Waters, Townsend, & Underwood, 1998) and that such patterns resemble those of text reading experts (Furneaux & Land, 1999, Sloboda, 1974, Truitt, Clifton, Pollatsek, & Rayner, 1997; Wolf, 1976). These patterns include fewer fixations of shorter duration and fewer regressive saccades that allows for more efficient processing of visual information per fixation. However, little is known about how expertise might affect eye movement patterns when the score has been visually disrupted using notational features that are unexpected or outside conventional presentation. The current project examined the effect of altering features of the music score on eye movement patterns of expert and non-expert music sight-readers. Participants read, by sight, specifically composed musical excerpts. These pieces were then re-presented with the bar-lines removed, disrupted spacing and unpredictable beaming directions. Fixation and saccade characteristics were measured and compared between the two performances. It was expected that expert music sight-readers would be most affected when the score was disrupted as they would be less capable of grouping notes into familiar, single units for efficient visual processing. Expert sight-readers performed significantly faster than non-experts in both conditions: p < 0.0001. Saccadic latency increased significantly for experts in the disrupted condition: p = 0.03. Non-experts increased slightly, but not significantly. This suggests that the disruption of visual expectation was sufficient to cause a lengthening of saccade programming in the experts—an indication of interference with the ‘chunking’ process. The resultant EM patterns for the non-experts demonstrated heightened non-expert behaviours: increased fixations of shorter duration. Full article