Screening of deletions and duplications in 1500 genomic loci in a single assay. J. Fan¹, S.J. White², M. Bibikova¹, L. Zhou¹, J. Chen¹, E. Wickham-Garcia¹, M.E. Kalf², M. Kriek², G.J.B. van Ommen², M.H. Breuning², L. Guo³, S.-H. Lu³, Q. Zhan³, W. Jiang³, O. Chan⁴, J. Wang-Rodriguez⁴, D.L. Barker¹, J.T. den Dunnen². 1) Illumina, Inc, San Diego, CA, USA; 2) Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Nederland; 3) Cancer Institute, Chinese Academy of Medical Sciences, Beijing, China; 4) The VA Medical Center, UCSD, San Diego, CA, USA.
   Copy number variations (CNV), i.e. deletions and duplications of genomic DNA, are known to be involved in many genetic diseases. Recent genome-wide analyses revealed extensive CNV in the human genome, the vast majority of which have not been correlated directly with disease. We have developed a highly multiplexed genotyping assay (GoldenGate assay) coupled with a universal BeadArray readout for CNV testing of hundreds to thousands of genomic regions in hundreds to thousands of samples. Specifically, we designed an array for parallel analysis of 1,500 genomic loci, which allows detection of all known trisomies, sub-telomeric rearrangements and micro-deletion syndromes as well as providing a low-resolution whole genome CNV scan. We first assayed genomic DNA isolated from patient blood samples. Analysis of X- and Y-chromosome probes showed excellent quantitative discrimination between males and females. We applied the assay to a variety of known variations, from whole-chromosome trisomies to subtle DMD-gene rearrangements (deletions, duplications, triplications), and were able to detect all known rearrangements reliably. Analysis of samples from 170 patients with mental retardation of unknown etiology revealed, based on the criteria selected, 20-30 new CNV's, which are currently being analyzed in more detail. We also analyzed 43 pairs of gDNA extracted from formalin-fixed cancerous and adjacent normal tissues of esophageal cancer patients. Highly reproducible genomic deletions and amplifications were detected in these archived tissue samples. Our data indicate that screening a selected set of 1500 loci using a bead-based assay is a rapid, sensitive and cost-effective method for detecting copy number changes in up to 96 samples simultaneously.