A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review

Abstract

Background: Individuals affected with DiGeorge and Velocardiofacial syndromes present with both phenotypic diversity and variable expressivity. The most frequent clinical features include conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial dysmorphism. The etiology in most patients is a 3 Mb recurrent deletion in region 22q11.2. However, cases of infrequent deletions and duplications with different sizes and locations have also been reported, generally with a milder, slightly different phenotype for duplications but with no clear genotype-phenotype correlation to date.

Methods: We present a 7 month-old male patient with surgically corrected ASD and multiple VSDs, and dysmorphic facial features not clearly suggestive of 22q11.2 deletion syndrome, and a newborn male infant with cleft lip and palate and upslanting palpebral fissures. Karyotype, FISH, MLPA, microsatellite markers segregation studies and SNP genotyping by array-CGH were performed in both patients and parents.

Results: Karyotype and FISH with probe N25 were normal for both patients. MLPA analysis detected a partial de novo 1.1 Mb deletion in one patient and a novel partial familial 0.4 Mb duplication in the other. Both of these alterations were located at a distal position within the commonly deleted region in 22q11.2. These rearrangements were confirmed and accurately characterized by microsatellite marker segregation studies and SNP array genotyping.

Conclusion: The phenotypic diversity found for deletions and duplications supports a lack of genotype-phenotype correlation in the vicinity of the LCRC-LCRD interval of the 22q11.2 chromosomal region, whereas the high presence of duplications in normal individuals supports their role as polymorphisms. We suggest that any hypothetical correlation between the clinical phenotype and the size and location of these alterations may be masked by other genetic and/or epigenetic modifying factors.

Figure 1

Facial appearance of Patients 1 and 2. Patient 1 (a, b); Patient 2 (c).

Figure 2

MLPA results of Patients 1 and 2. Gene dosage of Patient 1 and Patient 2 observed by MLPA. Kit P250 (a) showed deletion of probes SNAP29, LZTR1 and HIC2 in Patient 1 and duplication of probes SNAP29 and LZTR1 in Patient 2, whereas kit P324-A1 (b) showed deletion of both LCRD probes in Patient 1 and duplication of only the proximal one in Patient 2. Data from both kits were analysed with Coffalyser v8 and v9, respectively.

Figure 3

Array-CGH SNP genotyping of Patients 1 and 2. Chromosome 22 plot of Patients 1 (a) and 2 (b). The upper panels show the genic dosage (Log R ratio) and the homozygous/heterozygous distribution (B allele frequency) for all the SNPs genotyped. Both parameters are used together for interpretation of deletions and duplications. The region showing copy number alterations is zoomed in below, indicating the flanking SNPs and the genes in the region. A copy number decrease and loss of heterozygosity was found in Patient 1 (pink shading, a), whereas a copy number increase with four different allele populations was found in Patient 2 (blue shading, b).

Figure 4

Detailed map of the distal TDR in 22q11.2. The relative location of the informative MLPA probes (blue font), STRs (black font) and SNPs (gray, small-sized font) sizing the shortest deletion and duplication size are shown above the line. Green boxes indicate LCRs, purple boxes indicate the discussed genes and the pink bar and the blue bar below the line indicate the deleted and the duplicated segment, respectively. Cen: centromere; tel: telomere.