Characterization of a 7.6-Mb germline deletion encompassing the NF1 locus and about a hundred genes in an NF1 contiguous gene syndrome patient

Abstract

We describe a large germline deletion removing the NF1 locus, identified by heterozygosity mapping based on microsatellite markers, in an 8-year-old French girl with a particularly severe NF1 contiguous gene syndrome. We used gene-dose mapping with sequence-tagged site real-time PCR to locate the deletion end points, which were precisely characterized by means of long-range PCR and nucleotide sequencing. The deletion is located on chromosome arm 17q and is exactly 7 586 986 bp long. It encompasses the entire NF1 locus and about 100 other genes, including numerous chemokine genes, an attractive in silico-selected cerebrally expressed candidate gene (designated NUFIP2, for nuclear fragile X mental retardation protein interacting protein 2; NM_020772) and four microRNA genes. Interestingly, the centromeric breakpoint is located in intron 4 of the PIPOX gene (pipecolic acid oxidase; NM_016518) and the telomeric breakpoint in intron 5 of the GGNBP2 gene (gametogenetin binding protein 2; NM_024835) coding a transcription factor. As PIPOX and GGNBP2 have the same transcriptional orientation, we postulated, and then confirmed, the existence of a chimeric transcript. This transcript, and/or haploinsufficiency of one or several deleted genes, could explain the clinical severity of the syndrome in this patient.

NF1 microdeletions in neurofibromatosis type 1: from genotype to phenotype

“…The typical type-2 microdeletion is smaller (1.2 Mb) and has breakpoints located in the SUZ12 gene (suppressor of zeste 12 homolog; NM_015355) and its pseudogene SUZ12P (Petek et al, 2003;KehrerSawatzki et al, 2004;Steinmann et al, 2007;Roehl et al, 2010). Even less frequent, atypical NF1 microdeletions with non-recurring breakpoints have also been reported (Riva et al, 2000;Kehrer-Sawatzki et al, 2003Venturin et al, 2004a;Mantripragada et al, 2006;Pasmant et al, 2008).…”

“…The array comprised a total of 14,207 oligonucleotide probes spanning the whole of chromosome 17, including 12 314 probes spanning a ~8 Mb interval surrounding the NF1 locus (~300 kb). This 8-Mb interval spanned the NF1 gene region and included the largest NF1 atypical microdeletions described in the literature (Riva P et al, 2000;Kehrer-Sawatzki et al, 2003;Venturin et al, 2004a;Pasmant et al, 2008). Details of the microarray design, including the 14,207 oligonucleotide probe chromosome locations, has been deposited in NCBI's GEO (Edgar et al, 2002) and are accessible through the GEO accession number GSE19730.…”

“…P. Wolkenstein, Henri Mondor Hospital, Créteil, France) to constitute the so-called 'NF-France database', as previously described (Sabbagh et al 2008). The mutation screening of the NF1 gene was performed using a variety of NF1 gene screening methodologies that included, DNA and RNA sequencing, for small lesions, polymorphic microsatellite marker analysis and multiplex ligation-dependent probe amplification (MLPA) or real-time PCRbased gene-dosage analysis to permit microdeletion assessment, as previously described (Pasmant et al, 2008;Upadhyaya et al, 2008). Among the 561 NF1 index cases, 512 individuals presented a NF1 alteration, 2 showed a SPRED1 (sprouty-related, EVH1 domain containing 1; NM_152594) mutation, and no NF1 and SPRED1 mutation was identified in the 47 remaining patients, as previously described (Pasmant et al, 2009b).…”

First description of ABCB4 gene deletions in familial low phospholipid-associated cholelithiasis and oral contraceptives-induced cholestasis

“…We also quantified the ALB gene (encoding albumin) as an endogenous DNA control, and each sample was normalized on the basis of its ALB content, as previously described. 38 ALB was selected as an endogenous control, because it maps to chromosome 4q11-q13, while ABCB4 is at chromosome 7q21.1. The relative copy number of the ABCB4 exon targets was also normalized to a calibrator, consisting of genomic DNA from a normal subject.…”

Sella turcica measurements on lateral cephalograms of patients with neurofibromatosis type 1

“…For example, neurofibromin is expressed in neural cells during brain development. Furthermore, the effect of modifying genes on the NF1 phenotype is further discussed in the literature [6], [7], [8]. …”