Getting Started in Tiling Microarray Analysis

The availability of sequenced eukaryotic genomes and commercial oligonucleotide tiling microarrays has enabled many genomics applications. Different from expression microarrays, tiling microarrays have probes that cover the entire genome or contigs of the genome in an unbiased fashion. Currently three commercial sources provide tiling microarrays with different probe lengths and spacing, and array design characteristics. Affymetrix tiles 6 million 25-mer probes per array, which offers the lowest price per probe and the highest resolution (chromosomal distance between neighboring probe centers). Its arrays use one-color assays, so individual samples are hybridized to different arrays. NimbleGen can tile 385,000 50to 75-mer probes, and Agilent can tile 244,000 60-mer probes per array. The latter two platforms, with longer oligonucleotide probes and two-color assays for which treatment and control samples are differentially labeled and put on the same array for competitive hybridization, have slightly better sensitivity. They are also flexible for custom array design, especially Agilent’s multiplex arrays, which allow multiple samples to hybridize on different subareas of the same array. These tiling arrays offer diverse genomic applications, each with its own data analysis challenges.