Med Biol Eng Comput - A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH.

Tópicos

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Resumo

Array comparative genomic hybridization (aCGH) provides a genome-wide technique for identifying chromosomal aberrations in human diseases, including cancer. Chromosomal aberrations in cancers are defined as regions that contain an increased or decreased DNA copy number, relative to normal samples. The identification of genomic regions associated with systematic aberrations provides insights into initiation and progression of cancer, and improves diagnosis, prognosis, and therapy strategies. The McNemar test can be used to detect differentially expressed genes after discretization of gene expressions in a microarray experiment for the matched dataset. In this study, we propose a method to detect significantly altered DNA regions, shifted McNemar test, which is based on the standard McNemar test and takes into account changes in copy number variations and the region size throughout the whole genome. In addition, this novel method can be used to detect genomic regions associated with the progress of oral squamous cell carcinoma (OSCC). The performance of the proposed method was evaluated based on the homogeneity within the selected regions and the classification accuracies of the selected regions. This method might be useful for identifying new candidate genes that neighbor known genes based on the whole-genomic variation because it detects significant chromosomal regions, not independent probes.

Resumo Limpo

array compar genom hybrid acgh provid genomewid techniqu identifi chromosom aberr human diseas includ cancer chromosom aberr cancer defin region contain increas decreas dna copi number relat normal sampl identif genom region associ systemat aberr provid insight initi progress cancer improv diagnosi prognosi therapi strategi mcnemar test can use detect differenti express gene discret gene express microarray experi match dataset studi propos method detect signific alter dna region shift mcnemar test base standard mcnemar test take account chang copi number variat region size throughout whole genom addit novel method can use detect genom region associ progress oral squamous cell carcinoma oscc perform propos method evalu base homogen within select region classif accuraci select region method might use identifi new candid gene neighbor known gene base wholegenom variat detect signific chromosom region independ probe

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