Applications of DNA tiling arrays for whole-genome analysis

• Published in: Genomics (San Diego, Calif.) Vol. 85; no. 1; pp. 1 - 15
• Main Authors: Mockler, Todd C., Ecker, Joseph R.
• Format: Journal Article
• Language: English
• Published: San Diego, CA Elsevier Inc 2005; Elsevier
• Subjects: Animals; Biological and medical sciences; Chromatin Immunoprecipitation - methods; Chromatin Immunoprecipitation - trends; DNA Methylation; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Profiling - trends; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; Genome; Genotype; Humans; Molecular and cellular biology; Molecular genetics; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - trends; Polymorphism, Genetic - genetics; Genome; Analysis; DNA; Genomics
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2004.10.005

DNA microarrays are a well-established technology for measuring gene expression levels. Microarrays designed for this purpose use relatively few probes for each gene and are biased toward known and predicted gene structures. Recently, high-density oligonucleotide-based whole-genome microarrays have emerged as a preferred platform for genomic analysis beyond simple gene expression profiling. Potential uses for such whole-genome arrays include empirical annotation of the transcriptome, chromatin-immunoprecipitation-chip studies, analysis of alternative splicing, characterization of the methylome (the methylation state of the genome), polymorphism discovery and genotyping, comparative genome hybridization, and genome resequencing. Here we review different whole-genome microarray designs and applications of this technology to obtain a wide variety of genomic scale information.