Functional genomics: High-density oligonucleotide arrays

Abstract

As the Human Genome Project and related efforts identify and determine the DNA sequences of human genes, it is important that highly reliable and efficient mechanisms be found to assess individual genetic variation. Three methods for obtaining genome-wide mRNA expression data–oligonucleotide “chips,”’ serial analysis of gene expression (SAGE), and DNA microarrays4,5–are particularly powerful in the context of knowing the entire genome sequence. Present array formats can be categorized into the following four groups: macroarray, microarrays, high-density oligonucleotide arrays (gene chips), and microelectronic arrays. The chapter focuses on high-density oligonucleotide arrays. The leading arrays in the category of high-density oligonucleotide arrays are manufactured by Affymetrix and utilize the combinatorial synthesis principle. The arrays are designed by using a light-directed chemical synthesis process that creates a series of photolithographic masks to define chip exposure sites, followed by specific chemical synthesis steps. This process constructs high-density arrays of oligonucleotides.