title: Genomic profiling: cDNA arrays and oligoarrays.
abstract: 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.
authors.affiliation: Genetics and Biomarkers-Exploratory Medicine, Merck Serono Ivrea, Colleretto Giacosa-TO, Italy. francesco.gorreta@merckserono.net
authors.forename: Francesco
authors.initials: F
authors.lastname: Gorreta
authors.forename: Walter
authors.initials: W
authors.lastname: Carbone
authors.forename: Dagania
authors.initials: D
authors.lastname: Barzaghi
mesh_terms: D055028:Comparative Genomic Hybridization; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D015203:Reproducibility of Results