Familial deletion 11q14.3–q22.1 without apparent phenotypic consequences: A haplosufficient 8.5 Mb region^†

INTRODUCTION

Cytogenetically detectable deletions of euchromatic segments are generally expected to result in an abnormal phenotype. There is, however, a small group of several chromosomal regions that upon deletion do not seem to cause an abnormal phenotype [Barber, 2005; Kowalczyk et al., 2007]. Identification of such deletions is essential for prenatal diagnosis and genetic counseling. Here we report on the second-trimester prenatal diagnosis of an interstitial 11q14.3–q22.1 deletion with direct transmission in three generations without apparent phenotypic effect. The complete characterization of the abnormality by CGH and FISH as well as the control analysis of parental chromosomes were performed. Finally, we consider the possible contributory factors which might explain the lack of clinical significance of this large deletion.

CLINICAL REPORT AND CYTOGENETIC STUDY

The patient was a G2P1 25-year-old woman, who had amniocentesis because of a positive Down syndrome maternal serum-screening result at 15 weeks' gestation. Ultrasound scans at 11 and 15 weeks gestation were normal. The family history was unremarkable.

Chromosome analysis was performed on amniocyte cultures with GTG-banding according to standard methods and revealed a deletion of the long arm of chromosome 11 (Fig. 1a).

Molecular Cytogenetic Analysis

Comparative genomic hybridization (CGH) was performed on chromosome spreads using DNA extracted from cultured amniocytes, as previously described [du Manoir et al., 1995; Goumy et al., 2005], with a resolution of 3–5 Mb determined in our laboratory. The CGH confirmed the 11q deletion and mapped the breakpoints at 11q14.3 and 11q22.1 (Fig. 1b). FISH (fluorescence in situ hybridization) experiments were performed on metaphase spreads with a commercial probe (LSI API2, Vysis) according to the manufacturer's instructions, and with bacterial artificial chromosome (BAC) selected from the human library RPCI-11 according to the UCSC Human Genome Assembly (March 2006). BAC DNA extraction was done using the NucleoSpin® Plasmid kit (Macherey-Nagel GmbH, Hoerdt, France). BAC DNAs were then labeled with Fluorescein-12-dUTP (Roche Diagnostics GmbH, Meylan, France) by nick translation (Abbott Molecular, Rungis, France).

FISH results with a BAC clone localized at 11q14.2 (RP11-12D16) showed two signals, confirming a breakpoint location between 11q14.2 and 11q14.3, whereas the commercial probe LSI API2 at 11q21 also showed two signals which was not concordant with the 11q22.1 breakpoint shown by CGH (Fig. 1c). FISH with BAC clones localized at 11q14.3 (RP11-372E19), 11q21 (RP11-16K5), 11q22.1 (RP11-775E2) showed one signal on one of the chromosome 11 homologues (Fig. 1d) and made it possible to confirm that the deletion extended to the 11q22.1 band. Using the University of California Santa Cruz (UCSC) genome browser (http://genome.ucsc.edu) with the last genome assembly (NCBI Build 36.1, March 2006), we were able to replace the position of the commercial probe LSI API2 from 11q21, as given by the manufacturer, to 11q22.2. This new localization explained the presence of two FISH signals with this probe and confirmed the breakpoint in 11q22.1.

By combining karyotype, CGH and FISH results, the karyotype was described as follows: 46,XX.ish del(11)(q14.3q22.1)(RP11-372E19-,RP11-16K5-,RP11-775E2-). The minimal deletion size estimated as the distance between the proximal edge of BAC RP11-372E19 and the distal edge of BAC RP11-775E2 was 8.5 Mb and the maximal deleted size evaluated between the distal edge of RP11-12D16 and the proximal edge of the LSI API2 probe was 16 Mb (Fig. 2).

DISCUSSION

This case provides further evidence that rare unbalanced deletions of specific chromosomal regions may result in the absence of phenotypic effect and underlines the importance of obtaining parental karyotypes before making a clinical decision. The interstitial deletion 11q14.3–q22.1 described here was identified in three individuals from three generations without apparent phenotypic consequences. The camptodactyly of the toes and ophthalmological features observed in the mother were not present in the grandfather. These features are common in the general population and are unlikely to be related to the deletion.

In 2007, Kowalczyk et al. reviewed cases of euchromatic chromosome imbalances, mainly inherited, without phenotypic abnormalities. They found 15 chromosomal regions on chromosomes 2, 3, 5, 7, 8, 9, 10, 11, 13, 16, and 18 for which deletions are observed in phenotypically normal individuals. Some of these, namely deletions 5p14 [Overhauser et al., 1986; Johnson et al., 2000], 10q11 [Bisgaard et al., 2007], 16q21 [Hand et al., 2000], and 2p12 [Barber, 2005] have each been found in more than one independent family and transmitted without consistent phenotypic consequences. In the review by Barber 2005, the average size of such deletions was 8.2 Mb (range 4.2–16 Mb) and these deletions generally involved G dark bands to which few genes map.

To our knowledge, only one asymptomatic deletion of the long arm of chromosome 11 has been described [Li et al., 2002]. This report identified a 3.6 Mb deletion at 11q14.3–q21 in five individuals representing three generations of kindred. Only one carrier showed mild clinical features, which were probably unrelated to the deletion.

In our case, the deletion was visible on standard karyotype with a resolution of about 10 Mb. FISH with commercial and BAC probes mapped the breakpoints at 11q14.3 and 11q22.1 and made it possible to estimate the size of the deletion between 8.5 and 16 Mb. Thus, our report enables the haplosufficient region initially described by Li et al. to be extended from 3.6 Mb to at least 8.5 Mb. This 8.5 Mb region contains only 22 protein coding genes (Table I; http://www.ncbi.nlm.nih.gov/mapview).

Stratton et al. 1994 described a chromosome11q14.1–q21 deletion in a 4-year-old girl with moderate developmental delay, horseshoe kidney, bilateral duplication of the ureters with right upper pole obstruction, hydronephrosis and Wilms tumor. In this case, the 11q14.3–q21 region of deletion overlaps with the haplosufficient region described here, suggesting that the genes responsible for the abnormal phenotype may be localized between 11q14.1 and 11q14.3.

Horelli-Kuitunen et al. 1999 described a de novo deletion of 11q21–q22.3 in a 3-year-old girl with disproportionate short stature, hypotonia with “myopatic changes” at the muscle biopsy, developmental delay, hypertelorism, low-set ears, pes equinovarus of the right foot, mild hydronephrosis, enlarged cerebral lateral ventricles and thin corpus callosum. Meyer et al. 2000 reported a 11q21–q23.1 deletion in a 21-year-old woman associated with motor and speech developmental delay in infancy, congenital heart defect, craniofacial anomalies, menstrual irregularity, hirsutism, elevated serum androgen levels and polycystic ovary syndrome. Likewise, Li et al. 2006 reported an 11q14.1–q23.2 deletion and predicted that the distal segment 11q21–q23.3 may be responsible for the varying degrees of growth retardation, mental retardation, cleft palate and minor digital anomalies of the patient. Assuming that the 11q14.3–q22.1 region might be haplosufficient, the regions responsible for the abnormal phenotype in these three cases could be reduced to 11q22.1–q22.3, 11q22.1–q23.1, and 11q22.1–q23.2, respectively.

The hypotheses proposed to explain the lack of clinical consequences in case of such large deletions were the low density of genes in the deleted region, the haplosufficiency of the majority of these genes or the presence of genes with similar function located elsewhere in the genome and a possible genomic imprinting effect leading to the loss of inactive material [Li et al., 2002; Barber, 2005].

Our observation does not support the genomic imprinting hypothesis [Bortotto et al., 1990; Li et al., 2002] because the transmission of the deletion in three generations of apparently normal individuals was of both paternal and maternal origin, even if the psychomotor development of the newborn is difficult to assess.

The majority of the deleted genes have related loci on other chromosomes, suggesting that functional complementation can arise from isoform expression or that alternative metabolic pathways can substitute those affected (Table I). The other genes are probably not dosage sensitive.

Recently, identification of inherited and de novo imbalances of uncertain clinical significance has progressively escalated with the increasing use of array technology in diagnostic laboratories. Knowledge of such harmless imbalances is particularly helpful for prenatal diagnosis and genetic counseling.