Duplications and deletions are known to cause a number of genetic disorders, yet technical difficulties and financial considerations mean that screening for these mutations, especially duplications, is often not performed. We have adapted multiplex amplifiable probe hybridization (MAPH) for the screening of the DMD gene, mutations in which cause Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy. MAPH involves the quantitative recovery of specifically designed probes following hybridization to immobilized genomic DNA. We have engineered probes for each of the 79 exons of the DMD gene, and we analyzed them by using a 96-capillary sequencer. We screened 24 control individuals, 102 patients, and 23 potential carriers and detected a large number of novel rearrangements, especially small, one- and two-exon duplications. A duplication of exon 2 alone was the most frequently occurring mutation identified. Our analysis indicates that duplications occur in 6% of patients with DMD. The MAPH technique as modified here is simple, quick, and accurate; furthermore, it is based on existing technology (i.e., hybridization, PCR, and electrophoresis) and should not require new equipment. Together, these features should allow easy implementation in routine diagnostic laboratories. Furthermore, the methodology should be applicable to any genetic disease, it should be easily expandable to cover >200 probes, and its characteristics should facilitate high-throughput screening.

Email: Matthew S Hestand -M.S.Hestand@lumc.nl; Michiel van Galen -M.van_Galen@lumc.nl; Michel P Villerius -M.P.Villerius@lumc.nl; Gert-Jan B van Ommen -G.J.B.van_Ommen@lumc.nl; Johan T den Dunnen -DDunnen@humgen.nl; Peter AC 't Hoen* -P.A.C.Hoen@lumc.nl * Corresponding author Abstract Background: The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for overrepresentation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments.

The major public microarray repositories Gene Expression Omnibus and ArrayExpress are growing rapidly. This enables meta-analysis studies, in which expression data from multiple individual studies are combined. To facilitate these types of studies, we developed Microarray Retriever for searching and retrieval of data from GEO and ArrayExpress. The tool allows access to the two repositories simultaneously, to search in the repositories using complex queries, to retrieve microarray data for published articles and to download data in one structured archive. The tool is available on the web at: http://www.lgtc.nl/MaRe/