Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing

• Published in: PLoS computational biology Vol. 17; no. 9; p. e1009350
• Main Authors: Smith, Michael, Chan, Rachel, Khurram, Maaz, Gordon, Paul M. K.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.09.2021; Public Library of Science (PLoS)
• Subjects: Accuracy; Algorithms; Biology and Life Sciences; Biomolecules; Computational Biology; Computer Simulation; Consensus Sequence; Deoxyribonucleic acid; DNA; DNA sequencing; Engineering and Technology; Entropy; Epigenetics; Evaluation; Funding; Magnetic tape; Methods; Molecular motors; Nanopore Sequencing - statistics & numerical data; Nanotechnology; Neural networks; Nucleotide sequence; Nucleotide sequencing; Nucleotides; Phosphopyruvate hydratase; Phosphopyruvate Hydratase - genetics; Physical Sciences; Research and Analysis Methods; Ribonucleic acid; RNA; RNA - genetics; RNA sequencing; Signal processing; Signal-To-Noise Ratio; Software; Stochastic Processes; Stochasticity; Voting; Canada
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1009350

Nanopore sequencing device analysis systems simultaneously generate multiple picoamperage current signals representing the passage of DNA or RNA nucleotides ratcheted through a biomolecule nanopore array by motor proteins. Squiggles are a noisy and time-distorted representation of an underlying nucleotide sequence, “gold standard model”, due to experimental and algorithmic artefacts. Other research fields use dynamic time warped - space averaging (DTWA) algorithms to produce a consensus signal from multiple time-warped sources while preserving key features distorted by standard, linear-averaging approaches. We compared the ability of DTW Barycentre averaging ( DBA ), minimize mean ( MM ) and stochastic sub-gradient descent ( SSG) DTWA algorithms to generate a consensus signal from squiggle-space ensembles of RNA molecules Enolase , Sequin R1-71-1 and Sequin R2-55-3 without knowledge of their associated gold standard model. We propose techniques to identify the leader and distorted squiggle features prior to DTWA consensus generation. New visualization and warping-path metrics are introduced to compare consensus signals and the best estimate of the “true” consensus, the study’s gold standard model. The DBA consensus was the best match to the gold standard for both Sequin studies but was outperformed in the Enolase study. Given an underlying common characteristic across a squiggle ensemble, we objectively evaluate a novel “voting scheme” that improves the local similarity between the consensus signal and a given fraction of the squiggle ensemble. While the gold standard is not used during voting, the increase in the match of the final voted-on consensus to the underlying Enolase and Sequin gold standard sequences provides an indirect success measure for the proposed voting procedure in two ways: First is the decreased least squares warped distance between the final consensus and the gold model, and second, the voting generates a final consensus length closer to the known underlying RNA biomolecule length. The results suggest considerable potential in marrying squiggle analysis and voted-on DTWA consensus signals to provide low-noise, low-distortion signals. This will lead to improved accuracy in detecting nucleotides and their deviation model due to chemical modifications (a.k.a. epigenetic information). The proposed combination of ensemble voting and DTWA has application in other research fields involving time-distorted, high entropy signals.