Comparison of two microarray CGH platforms for genomewide copy number profilings: Oligo-based arrays versus bacterial artificial chromosome arrays

Abstract

Array-based comparative genomic hybridization (array CGH) is a powerful and high-resolution approach for detection of DNA copy number gains and losses, associated to chromosomal abnormalities, many of which are below the detection limit of the routine cytogenetic analysis. Technological improvements to acquire higher resolution have led to generation of novel microarray platforms harboring larger numbers of shorter DNA sequences (oligonucleotides). Two main technologies are currently used for DNA copy number genome profiling - the Bacterial Artificial Chromosome and the oligo-based CGH arrays. In this study we present a comparison of two array-based platforms for genome-wide copy number screening in a group of six patients with idiopathic congenital anomalies and mental retardation or developmental delay. Each of our patients was studied separately with BAC and oligo-based microarray and the imbalances found were FISH confirmed. Our results indicated that the oligo-based platform had higher sensitivity than the BAC arrays, which allowed more precise detection of microdeletion/microduplication changes and could also improve the quality of array CGH analysis for the purpose of clinical diagnosis.