Title
Algorithm for DNA copy number variation detection with read depth and paramorphism information
Campus Units
Agronomy, Electrical and Computer Engineering, Bioinformatics and Computational Biology, Molecular, Cellular and Developmental Biology, Plant Biology, Center for Plant Genomics, Plant Sciences Institute
Document Type
Conference Proceeding
Conference
IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
Publication Version
Published Version
Publication Date
2016
Journal or Book Title
2015 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
First Page
869
Last Page
873
DOI
10.1109/ICASSP.2016.7471799
Conference Title
IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
Conference Date
March 20-25, 2016
City
Shanghai, China
Abstract
Next-generation sequencing (NGS) has revolutionized the detection of structural variation in genome. Among NGS strategies, read depth is widely used and paramorphism information contained inside is generally ignored. We develop an algorithm that can fully exploit both read depth and paramorphism information. We embed mutation procedure in our system model for estimating prior likelihood of single nucleotide base. Hidden Markov model (HMM) is used to connect single base into segments and belief propagation algorithm is performed for the optimal solution of the HMM model. Simulations show promising results in detecting important types of structural variation. We have applied the algorithm on the maize B73 and MO17 genome data and compared the results with those obtained from array CGH method based micro-array data. Inconsistency between the two sets of data is discussed.
Rights
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.
Language
en
File Format
application/pdf
Recommended Citation
Shen, Rong; Ying, Kai; Wang, Zhengdao; and Schnable, Patrick, "Algorithm for DNA copy number variation detection with read depth and paramorphism information" (2016). Electrical and Computer Engineering Conference Papers, Posters and Presentations. 102.
https://lib.dr.iastate.edu/ece_conf/102
Included in
Agronomy and Crop Sciences Commons, Computational Biology Commons, Signal Processing Commons
Comments
This proceeding is published as Shen, Rong, Kai Ying, Zhengdao Wang, and Patrick S. Schnable. "Algorithm for DNA copy number variation detection with read depth and paramorphism information." In 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). (2016): 869-873. DOI: 10.1109/ICASSP.2016.7471799.