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This article is part of the supplement: IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School

Open Access Research

Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain

Heng Huang1*, Nha Nguyen2, Soontorn Oraintara2 and An Vo2

Author affiliations

1 Department of Computer Science and Engineering, University of Texas at Arlington, TX, USA

2 Department of Electrical Engineering, University of Texas at Arlington, Texas, USA

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Citation and License

BMC Genomics 2008, 9(Suppl 2):S17  doi:10.1186/1471-2164-9-S2-S17

Published: 16 September 2008

Abstract

Background

Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable detection of local one-copy-level variations. Characterization of these DNA copy number changes is important for both the basic understanding of cancer and its diagnosis. In order to develop effective methods to identify aberration regions from array CGH data, many recent research work focus on both smoothing-based and segmentation-based data processing. In this paper, we propose stationary packet wavelet transform based approach to smooth array CGH data. Our purpose is to remove CGH noise in whole frequency while keeping true signal by using bivariate model.

Results

In both synthetic and real CGH data, Stationary Wavelet Packet Transform (SWPT) is the best wavelet transform to analyze CGH signal in whole frequency. We also introduce a new bivariate shrinkage model which shows the relationship of CGH noisy coefficients of two scales in SWPT. Before smoothing, the symmetric extension is considered as a preprocessing step to save information at the border.

Conclusion

We have designed the SWTP and the SWPT-Bi which are using the stationary wavelet packet transform with the hard thresholding and the new bivariate shrinkage estimator respectively to smooth the array CGH data. We demonstrate the effectiveness of our approach through theoretical and experimental exploration of a set of array CGH data, including both synthetic data and real data. The comparison results show that our method outperforms the previous approaches.