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Denoising array-based comparative genomic hybridization data using wavelets. (English) Zbl 1071.62104
Summary: Array-based comparative genomic hybridization (array-CGH) provides a high-resolution, high-throughput method to measure relative changes in DNA copy number simultaneously at thousands of genomic loci. Typically, these measurements are reported and displayed linearly on chromosome maps, and gains and losses are detected as deviations from normal diploid cells. We propose that one may consider denoising the data to uncover the true copy number changes before drawing inferences on the patterns of aberrations in the samples. Nonparametric techniques are particularly suitable for data denoising as they do not impose a parametric model in finding structures in the data.
We employ wavelets to denoise the data as wavelets have sound theoretical properties and a fast computational algorithm, and are particularly well suited for handling the abrupt changes seen in array-CGH data. A simulation study shows that denoising data prior to testing can achieve greater power in detecting the aberrant spot than using the raw data without denoising. Finally, we illustrate the method on two array-CGH data sets.

MSC:
62P10 Applications of statistics to biology and medical sciences; meta analysis
42C40 Nontrigonometric harmonic analysis involving wavelets and other special systems
92C40 Biochemistry, molecular biology
62G99 Nonparametric inference
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