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access icon free Correcting estimates of DNA CNAs using improved confidence masks tuned to gold standard

© The Institution of Engineering and Technology
Received 24/02/2018, Accepted 04/02/2019, Revised 09/01/2019, Published 05/02/2019

Copy number alterations (CNAs) are hallmarks of cancer, which are now been routinely measured by different techniques and used for diagnostic and prognostic purpose. Efficient and accurate detection of the breakpoint positions in heterogeneous cancer sample measured with intrinsic random noise and subjected to technical and biological biases is a challenging practical and methodological problem. To improve the CNA estimates, the authors present the probabilistic approach for breakpoints detection that gives confidence masks (the system of local segmentation profiles with confidence probabilities) tuned using experts estimates. The authors show that the asymmetric exponential power distribution matches well the uncertainties (jitter) in the breakpoint locations. The confidence upper and lower boundary masks for the breakpoint location are built using this function. The confidence masks are then tuned based on the medical expert annotations of the training set of the breakpoints obtained by the standard circular binary segmentation (CBS) algorithm. Comparison of modified confidence masks and experts annotations on the testing set of CNA profiles of neuroblastoma showed improvement of the CNA estimates.

Inspec keywords: cancer; patient diagnosis; molecular biophysics; DNA; random noise; probability

Other keywords: accurate detection; technical biases; confidence probabilities; heterogeneous cancer sample; standard circular binary segmentation algorithm; local segmentation profiles; gold standard; neuroblastoma; modified confidence masks; confidence upper; intrinsic random noise; prognostic purpose; CNA estimates; breakpoint positions; correcting estimates; improved confidence masks; breakpoint location; breakpoint detection; DNA CNAs; lower boundary masks; methodological problem; probabilistic approach; diagnostic purpose; asymmetric exponential power distribution; medical expert annotations; copy number alterations; biological biases

Subjects: Probability theory, stochastic processes, and statistics; Biomedical measurement and imaging; Molecular biophysics; Patient diagnostic methods and instrumentation; Other topics in statistics

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