Genetic dosage compensation in a family with velo-cardio-facial/DiGeorge/22q11.2 deletion syndrome

Abstract

Cytogenetic studies of a male child carrying the 22q11.2 deletion common in patients with velo-cardio-facial/DiGeorge syndrome showed an unexpected rearrangement of the 22q11.2 region in his normal appearing mother. The mother carried a 3 Mb deletion on one copy and a reciprocal, similar sized duplication on the other copy of chromosome 22q11.2 as shown by fluorescence in situ hybridization and array comparative genome hybridization analyses. The most parsimonious mechanism for the rearrangement is a mitotic non-allelic homologous recombination event in a cell in the early embryo soon after fertilization. The normal phenotype of the mother can be explained by the theory of genetic dosage compensation. This is the second documented case of such an event for this or any genomic disorder. This finding helps to reinforce this phenomenon in a human model, and has significant implications for recurrence risks for the dose-compensated mother.

Figure 1. Phenotype of the affected child and his normal mother

Figure 1A–1C shows the phenotype of the VCFS/DGS male child at age 2, 6, and 12 respectively. Note the periorbital fullness, narrow upslanting palpebral fissures, epicanthal folds, strabismus, thick lips with everted upper lip, and small everted ears. Figure 1D–1E shows the appearance of this child's mother at matching time intervals. The mother’s facial phenotype appears normal.

Figure 2. Results of fluorescence in situ hybridization analysis of cultured peripheral-blood lymphocytes from the VCFS/DGS son and his mother

A representative metaphasic spread of chromosomes are shown for the Son (2A) and Mother (2B). The green dots are chromosome 22 control probes (ARSA; 22q13) and the red dots are the 22q11.2 probes (TUPLE1). The son (2A) appears to have one signal for the 22q11.2 probe, showing a deletion of the 22q11.2 region. The mother’s chromosomes during metaphase (2B) have one signal for the 22q11.2 probe (red). However when the mother’s chromosomes were analyzed during interphase (2C), it is evident that two signals for the 22q11.2 probe are seen, likely resulting from a duplication of the 22q11.2 region. This was not seen in the interphase analysis of the son (Figure 2A).

Figure 3. Copy number variation analysis of the 22q11.2 region in the VCFS/DGS proband and his normal mother

(A) A cartoon of the 22q11.2 region is shown with the genes indicated as ovals. The segmental duplications spanning the interval are indicated as rectangles on the line representing the 22q11.2 region. Two genes, TBX1 and CRKL are shown to aid in orientation. The general position of the TUPLE1 probe used for FISH mapping in Figure 2, is indicated. (B) The DNA from the mother and son were analyzed by Affymetrix 6.0 arrays (the grandmother had normal dosage and is not shown). The samples were compared to Affymetrix 6.0 data from 100 normal controls run in the same core facility at Albert Einstein College of Medicine. The signal intensity at each CNV is averaged and found to lie near 0 as expected, however, the 22q11.2 region in the mother was slightly above the line, although not great enough to suggest the presence of three alleles. The mothers’ signal intensity of the SNP also revolves around 0, showing compensation for the lost region of one chromosome by the duplicated region in the homologous chromosome. The DNA from the VCFS/DGS son shows presence of one allele flanked by LCR22-2 and LCR22-4. This represents the typical ~3 Mb deleted region in patients with the disorder. (C) Affymetrix Cytogenetics Whole-Genome 2.7M Arrays were run from the mother and VCFS/DGS son were analyzed using Partek Genomics Suite. The upper track contains a heat map with one row for every sample. Regions appearing at increased in copy number are shown in red, and those at decreased copy number in blue. The lower track shows a detailed view of all the probes in this region.

Figure 3. Copy number variation analysis of the 22q11.2 region in the VCFS/DGS proband and his normal mother

(A) A cartoon of the 22q11.2 region is shown with the genes indicated as ovals. The segmental duplications spanning the interval are indicated as rectangles on the line representing the 22q11.2 region. Two genes, TBX1 and CRKL are shown to aid in orientation. The general position of the TUPLE1 probe used for FISH mapping in Figure 2, is indicated. (B) The DNA from the mother and son were analyzed by Affymetrix 6.0 arrays (the grandmother had normal dosage and is not shown). The samples were compared to Affymetrix 6.0 data from 100 normal controls run in the same core facility at Albert Einstein College of Medicine. The signal intensity at each CNV is averaged and found to lie near 0 as expected, however, the 22q11.2 region in the mother was slightly above the line, although not great enough to suggest the presence of three alleles. The mothers’ signal intensity of the SNP also revolves around 0, showing compensation for the lost region of one chromosome by the duplicated region in the homologous chromosome. The DNA from the VCFS/DGS son shows presence of one allele flanked by LCR22-2 and LCR22-4. This represents the typical ~3 Mb deleted region in patients with the disorder. (C) Affymetrix Cytogenetics Whole-Genome 2.7M Arrays were run from the mother and VCFS/DGS son were analyzed using Partek Genomics Suite. The upper track contains a heat map with one row for every sample. Regions appearing at increased in copy number are shown in red, and those at decreased copy number in blue. The lower track shows a detailed view of all the probes in this region.

Figure 4. Pedigree of the proband (son) with the 22q11.2 deletion syndrome and mother with the 22q11.2 deletion and duplication region

Circles represent female family members and squares represent males. The grandfather is deceased and therefore no genetic information is available. We were unable to obtain DNA samples from the father. It appears that the son received the 22q11.2 deletion region from the mother. However, based on our CNV analysis it appears that the mother did not receive the 22q11.2 duplication region from her mother.