High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH

Abstract

Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder whose hallmark is bilateral vestibular schwannoma. It displays a pronounced clinical heterogeneity with mild to severe forms. The NF2 tumor suppressor (merlin/schwannomin) has been cloned and extensively analyzed for mutations in patients with different clinical variants of the disease. Correlation between the type of the NF2 gene mutation and the patient phenotype has been suggested to exist. However, several independent studies have shown that a fraction of NF2 patients with various phenotypes have constitutional deletions that partly or entirely remove one copy of the NF2 gene. The purpose of this study was to examine a 7 Mb interval in the vicinity of the NF2 gene in a large series of NF2 patients in order to determine the frequency and extent of deletions. A total of 116 NF2 patients were analyzed using high-resolution array-comparative genomic hybridization (CGH) on an array covering at least 90% of this region of 22q around the NF2 locus. Deletions, which remove one copy of the entire gene or are predicted to truncate the schwannomin protein, were detected in 8 severe, 10 moderate and 6 mild patients. This result does not support the correlation between the type of mutation affecting the NF2 gene and the disease phenotype. This work also demonstrates the general usefulness of the array-CGH methodology for rapid and comprehensive detection of small (down to 40 kb) heterozygous and/or homozygous deletions occurring in constitutional or tumor-derived DNA.

Chromosome 22q12.1 microdeletions: confirmation of the MN1 gene as a candidate gene for cleft palate

“…We propose that the patients with a microdeletion comprising NF2 should be followed by a multidisciplinary NF2 team in addition to the follow-up for cleft palate and intellectual disability. Combining our results with those provided in the literature, 9,[11][12][13][14] eight patients are recorded with palatal defects in association with a 22q12 deletion, involving the MN1 gene. These observations, together with an increased MN1 SNP frequency in patients with submucous cleft palate, 20 with the mouse expression data and the finding of craniofacial malformations including cleft palate in a Mn1-knockout mouse model further suggest that this gene contributes to the cleft palate observed in the reported patients.…”

“…Clinical and molecular details are provided in Table 2 and Figure 2. Review of the literature for 22q12.2 deletions reveals a further three patients with vestibular schwannoma but without palatal defects, 13,14 and one additional Decipher patient (Decipher 999) 9 with poor clinical data (Supplementary Table 1). Combining our data with those provided in literature, we discern 22q12.2 deletions in six patients with an overt cleft secondary palate (Figure 2), and in three with minor palatal defects, including velopharyngeal insufficiency, high arched palate and cleft uvula.…”

A tiling resolution DNA microarray with complete coverage of the human genome

“…These arrays are sensitive enough to detect singlecopy changes, but the technique is limited by the small number of BAC markers representing the genome on the slide, rather than the methodology. Even at this resolution, array CGH is useful for detecting chromosomal aberrations associated with congenital abnormalities and somatic malignancies [9][10][11][12] .Recent studies focused on higher-density regional arrays for fine mapping and identifying new genes in specific chromosomal regions [13][14][15][16][17][18] . For example, a candidate oncogene for association with…”

“…Recent studies focused on higher-density regional arrays for fine mapping and identifying new genes in specific chromosomal regions [13][14][15][16][17][18] . For example, a candidate oncogene for association with breast cancer (CYP24A1) was identified on 20q13.2 using an array of 29 overlapping clones spanning this region 18 .…”

Identification and characterisation of constitutional chromosome abnormalities using arrays of bacterial artificial chromosomes

“…Thus, Veltman et al (2002) used CGHa arrays which comprised o100 BACs from the subtelomeric regions of the human chromosomes to identify subterminal deletions. Similarly, Veltman et al (2003b) used approximately 100 BACs from chromosome 18 to specifically investigate the deletions associated with congenital aural atresia, and approximately 100 BACs from chromosome 22 were used to identify deletions of the NF2 gene in NF2 patients (Bruder et al, 2001). In these cases, it was necessary to know where in the genome to look and, if there has been any other genetic change in the genome, these would be missed.…”