Intragenic deletions represent a significant disease causing mechanism: Evidence from a select group of rare genetic disorders. E.V. Haverfield, A.J. Platteter, M.A. Dempsey, W.B. Dobyns, S. Das Department of Human Genetics, University of Chicago, Chicago, IL.

   Genetic abnormalities associated with human diseases range from whole chromosome abnormalities to point mutations within genes. Chromosome gain or loss and structural rearrangements as well as most microdeletions or duplications are identified by chromosome analysis, FISH and array CGH. Point mutations and small insertions or deletions are detectable by DNA sequencing and mutation scanning methods. Intragenic deletions and duplications that affect single or multiple exons are an important disease-causing mechanism and are a category of mutations that remain undetected by these methods. We determined the frequency of intragenic deletions and duplications in a select group of rare genetic disorders: lissencephaly and subcortical band heterotopia (LIS1 and DCX genes), Sotos syndrome (NSD1 gene) and Cornelia de Lange syndrome (NIPBL gene). Analysis was performed with multiplex ligation probe amplification (MLPA) and real-time quantitative PCR. All patients were negative for mutations in their respective gene and large microdeletions were excluded in LIS1 and NSD1. In 43 phenotypically well-characterized patients with lissencephaly, deletions or duplications in the LIS1 gene were identified in 19 (44%). In 11 patients with subcortical band heterotopia, deletions in the DCX gene were identified in 3 (27%). NSD1 deletions were found in 1 of 6 patients (17%) with suspected Sotos syndrome and NIPBL deletions were observed in 1 of 52 patients (2%) with suspected Cornelia de Lange syndrome. Partial deletions of the PANK2 gene in patients with autosomal recessive pantothenate-kinase associated neurodegeneration were identified when apparent homozygosity for a rare mutation was due to compound heterozygosity for a mutation and an intragenic deletion. A systematic study of intragenic deletions in the PANK2 gene is in progress. Our studies illustrate the presence of intragenic deletions and duplications in rare genetic disorders and indicate that they may contribute significantly to disease etiology. Our results have important implications for the diagnostics of genetic disease.