Walking through the human genome bit by bit in search of copy number variation

P Kersbergen^1,2, E. Bakker², JT den Dunnen², SM van der Maarel², P de Knijff<sup>2

1</sup>Netherlands Forensic Institute, Ypenburg, The Hague; ²Department of Human and Clinical Genetics, LUMC, Leiden

DNA copy number changes occur - randomly? - throughout the human genome and are thought to be the basis of an unknown number of disorders. Detecting DNA copy number variation at a genome wide scale with a high resolution (< 1 MB) was hitherto not possible. Recently, because of the release of Affymetrix Human Mapping 10K arrays and their successors, it became possible to perform a fast search for such polymorphisms across the human genome with minimal amounts of DNA. The Mapping 10-500K arrays genotype between 10,000 – 500,000 Single Nucleotide Polymorphisms in a single effort with only 250 nanograms of starting material. DNA copy number changes can be detected with an average inter-SNP distance of 210 – 5.8 kb. Several tools have been developed in order to identify and visualize the copy numbers based on SNP array data. Currently, three software tools facilitate genome wide copy number changes. The use of SNP-arrays to detect DNA copy number variation and the various features of the three software tools will be discussed.