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

Heng Huang, Nha H. Nguyen, Soontorn Oraintara, An Vo

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberS17
JournalBMC Genomics
Volume9
Issue numberSUPPL. 2
DOIs
StatePublished - Sep 16 2008
Externally publishedYes

Fingerprint

Wavelet Analysis
Comparative Genomic Hybridization
DNA Copy Number Variations
Noise
DNA
Research
Neoplasms

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain. / Huang, Heng; Nguyen, Nha H.; Oraintara, Soontorn; Vo, An.

In: BMC Genomics, Vol. 9, No. SUPPL. 2, S17, 16.09.2008.

Research output: Contribution to journalArticle

Huang, Heng ; Nguyen, Nha H. ; Oraintara, Soontorn ; Vo, An. / Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain. In: BMC Genomics. 2008 ; Vol. 9, No. SUPPL. 2.
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