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.

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.

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

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