Although we have not applied the multi-sample analysis mode of QuantiSNP to any real datasets, we believe that there is a great scope for use and development of such a technique in population and case-control studies involving large numbers of individuals. Shared copy number variant regions have already been identified in a recent study using the HapMap population (8) and a joint analysis could reveal even more common copy number polymorphisms. As the high-throughput genotyping platform market matures it is now possible to profile larger sized cohorts at ever increasing resolutions. In this environment, analytical tools for the detection of genetic variation need to accommodate increasing volumes of data while moving towards precision that is appropriate for diagnostic and clinical applications. We are also currently working on extending QuantiSNP to integrate information from multiple array platforms (Affymetrix Genechip®, BeadArray™ and oligonucleotides/BAC array CGH) to improve resolution and precision.
