Method for manufacturing whole‐genome microarrays by rolling circle amplification

Abstract

Comparative genomic hybridization (CGH) to metaphase chromosomes is a method for genome‐wide detection of chromosomal aberrations in DNA samples. Recent advances in microarray technology have improved CGH by replacing metaphase chromosomes with a collection of mapped genomic clones placed on glass slides. However, it is quite expensive and labor‐intensive to prepare DNA from the genomic clones for use in constructing genomic microarrays. Here we used strand‐displacement rolling circle amplification (RCA) to manufacture whole‐genome microarrays by using a collection of about 4,500 mapped RPCI‐11 BAC clones that cover the human genome at approximately a 1‐Mb resolution. These genomic microarrays detected all major chromosomal aberrations in cancer cells lines and in cell lines with aneuploidy. In this article, we discuss the advantages of using RCA for the manufacturing of large genomic microarrays.