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Methods Mol Biol. 2012;823:89-105. doi: 10.1007/978-1-60327-216-2_7.

Genomic profiling: cDNA arrays and oligoarrays.

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  • 1Genetics and Biomarkers-Exploratory Medicine, Merck Serono Ivrea, Colleretto Giacosa-TO, Italy.


The introduction of microarray technology, which is a multiplexed hybridization-based process, allows simultaneous analysis of a large number of nucleic acid transcripts. This massively parallel analysis of a cellular genome will become essential for guiding disease diagnosis and molecular profiling of an individual patient's tumor. Nucleic acid based microarrays can be used for: gene expression profiling, single-nucleotide polymorphisms (SNPs) detection, array-comparative genomic hybridizations, comparisons of DNA-methylation status, and microRNA evaluation.A multitude of commercial platforms are available to construct and analyze the microarrays. Typical workflow for a microarray experiment is: preparation of cDNA or gDNA, array construction, hybridization, fluorescent detection, and analysis. Since many sources of variability can affect the outcome of one experiment and there is a multitide of microarray platforms available, microarray standards have been developed to provide industry-wide quality control and information related to each microarray. In this chapter, we review array construction, methodologies, and applications relevant to molecular profiling.

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