1. ¹Institute of Human Genetics, University of Ulm, Ulm, Germany
2. ²Department of Maxillofacial Surgery, University Hospital Eppendorf, Hamburg, Germany
3. ³Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
4. ⁴Department of Human Genetics, Catholic University Leuven, Leuven, Belgium

Correspondence: Dr H Kehrer-Sawatzki, Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm 89081, Germany. Tel: +0049 731 500 65421; Fax: +0049 731 500 65402; E-mail: hildegard.kehrer-sawatzki@uni-ulm.de

Received 18 September 2007; Revised 12 November 2007; Accepted 11 December 2007; Published online 23 January 2008.

Abstract

Gross deletions of the NF1 gene at 17q11.2 belong to the group of 'genomic disorders' characterized by local sequence architecture that predisposes to genomic rearrangements. Segmental duplications within regions associated with genomic disorders are prone to non-allelic homologous recombination (NAHR), which mediates gross rearrangements. Copy number variants (CNVs) without obvious phenotypic consequences also occur frequently in regions of genomic disorders. In the NF1 gene region, putative CNVs have been reportedly detected by array comparative genomic hybridization (array CGH). These variants include duplications and deletions within the NF1 gene itself (CNV1) and a duplication that encompasses the SUZ12 gene, the distal NF1-REPc repeat and the RHOT1 gene (CNV2). To explore the possibility that these CNVs could have played a role in promoting deletion mutagenesis in type-1 deletions (the most common type of gross NF1 deletion), non-affected transmitting parents of patients with type-1 NF1 deletions were investigated by multiplex ligation-dependent probe amplification (MLPA). However, neither CNV1 nor CNV2 were detected. This would appear to exclude these variants as frequent mediators of NAHR giving rise to type-1 deletions. Using MLPA, we were also unable to confirm CNV1 in healthy controls as previously reported. We conclude that locus-specific techniques should be used to independently confirm putative CNVs, originally detected by array CGH, to avoid false-positive results. In one patient with an atypical deletion, a duplication in the region of CNV2 was noted. This duplication could have occurred concomitantly with the deletion as part of a complex rearrangement or may alternatively have preceded the deletion.