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VarSight: prioritizing clinically reported variants with binary classification algorithms.
BackgroundWhen applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.MethodsWe tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.ResultsWe treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.ConclusionsWe demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets
Moving forward with combinatorial interaction testing
Combinatorial interaction testing (CIT) is an efficient and effective method of detecting failures that are caused by the interactions of various system input parameters. In this paper, we discuss CIT, point out some of the difficulties of applying it in practice, and highlight some recent advances that have improved CITâs applicability to modern systems. We also provide a roadmap for future research and directions; one that we hope will lead to new CIT research and to higher quality testing of industrial systems
Requirements Prioritization Based on Benefit and Cost Prediction: A Method Classification Framework
In early phases of the software development process, requirements prioritization necessarily relies on the specified requirements and on predictions of benefit and cost of individual requirements. This paper induces a conceptual model of requirements prioritization based on benefit and cost. For this purpose, it uses Grounded Theory. We provide a detailed account of the procedures and rationale of (i) how we obtained our results and (ii) how we used them to form the basis for a framework for classifying requirements prioritization methods
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