We have identified a de novo
interstitial deletion of 21q21.1-q21.3 in a patient with an abnormal phenotype and an apparently balanced complex translocation. Initial comprehensive cytogenetic analysis revealed the complex translocation of chromosomes 6, 10, and 21 without any noticeable loss of genetic material. This is due to the fact that standard cytogenetic testing is limited in sensitivity to identifying chromosomal rearrangements smaller than 10-Mb. However, with the use of BAC-based array comparative genomic hybridization (CGH) and higher-density oligonucleotide microarrays, smaller deletions and duplications are being discovered and further characterized in patients with multiple congenital anomalies, developmental delays, mental retardation, and autism spectrum disorders [Shaw-Smith et al., 2004
; Rauch et al., 2004
; Ming et al., 2006
; Sebat et al., 2007
; Marshall et al., 2008
; Weiss et al., 2008
; Christian et al., 2008
We hypothesized that our patient's abnormal phenotype may have resulted from the disruption, loss or gain of an essential gene(s) near one or more of the rearrangement breakpoints, not detectable by the cytogenetic analysis. Therefore, a high-resolution oligonucleotide-based microarray was performed, revealing an 8.8-Mb deletion of 21q21.1-q21.3. The observation that the deletion in 21q21 is de novo, relatively large in size and contains 19 genes strongly supports a role for the deletion in the patient's phenotype. Although, it is equally possible that one or more of the complex rearrangement breakpoints may have directly disrupted a gene(s) relevant to the patient's phenotype, we were unable to address this possibility pending further analysis of the breakpoints.
Interestingly, this deletion is distal to the chromosome 21 translocation breakpoint at 21q11.2. FISH analysis in our patient using a BAC-clone approximately 1-Mb proximal to the deletion (RP11-49B5) showed the clone to be located on the derivative chromosome 6 (data not shown). Although the precise mechanisms are unclear, analyses in patients with apparently balanced translocations have previously identified similar findings, such as a deletion or duplication of different regions of the translocated chromosome or of a different chromosome not involved in the translocation [Ciccone et al., 2005
; De Gregori et al., 2007
; Sismani et al., 2008
]. In another study, approximately 1/3 of the patients with de novo
translocations had a copy number alteration unrelated to the translocation [Gribble et al., 2005
]. At this time, it is difficult to determine if the deletion preceded, succeeded, or occurred during the translocation. Parental chromosome and FISH analyses were normal and did not reveal an insertion or detectable inversion that may have predisposed to the deletion in the patient.
Chromosomal rearrangements may occur via several mechanisms, which typically reflect the underlying architecture of the genome in the regions surrounding the breakpoints [Gu et al., 2008
]. Non-allelic homologous recombination (NAHR) is the major mechanism underlying many of the recurrent genomic disorders (DiGeorge syndrome, Williams syndrome, etc) that are flanked by regions of segmental duplications or low-copy repeats (LCRs). These sequences with high sequence similarity may predispose to rearrangements by causing abnormal alignment of homologous chromosomes [Emanuel and Shaikh, 2001
]. Rearrangements produced by nonhomologous end-joining (NHEJ) occur when double-strand DNA breaks are incorrectly repaired, leading to deleted or duplicated genomic segments. Although NHEJ does not involve larger regions of sequence identity such as LCRs, microhomology of the DNA may be present at the breakpoints. More recently, FoSTeS (Fork Stalling and Template Switching) has been described as a mechanism associated with complex rearrangements caused by abnormal DNA replication. In this instance, DNA strands from one replication fork may switch and become integrated into a downstream replication fork [Gu et al., 2008
]. In the absence of precise mapping of the breakpoints, it is difficult to speculate which of these mechanisms may have played a role in the rearrangement observed in our patient. The lack of LCRs near the rearrangement breakpoints in our patient makes it highly unlikely that homology-based mechanisms like NAHR are involved.
To our knowledge, this particular 21q21.1-q21.3 deletion has not been described previously. However, there have been several reports of patients with overlapping deletions, most of whom have variable facial dysmorphia and clinical phenotypes, but commonly have mental retardation or developmental delays. A 12-year-old female with mild mental retardation and hypothyroidism was found to have a deletion of 21q11.1-q22.1 near marker D21S55 [Alhbom et al., 1996
]. Two patients with developmental delay due to deletions of 21q11.2-q21.1 and 21q21.1-q22.3 were previously described [Huret et al., 1995
]. Additionally, two patients with mild mental retardation and short stature were shown to have deletions of 21q11.2-q21.1 and 21q11.2-q21.3, respectively [Roland et al., 1990
]. Another child without mental retardation had small testes and was shown to have a deletion of 21q11.2-q21.3 [Korenberg et al., 1991
]. A familial deletion of 21q11.2-q21.3 was described where one of two children had normal intelligence while the other sibling developed mental retardation and sensorial neural hearing loss [Wakui et al., 2004
]. Another individual was reported with mental retardation, psychosis and dysmorphia and was shown to have a deletion at 21q21-q22.1 [Takhar et al., 2002
]. In addition, a search of the DECIPHER database (https://decipher.sanger.ac.uk/
) did not reveal any patients with significant overlapping regions and a similar clinical abnormality. It is worth noting that none of the other studies were performed using microarray analysis, and the breakpoint assignments are approximate, based upon cytogenetic analysis.
The region deleted in our patient leads to the loss or disruption of 19 genes, several of which may be involved in the phenotype based on the putative or known biological function (). The genes that are expressed in the brain are more likely to be responsible for some or all of the clinical abnormalities, such as the speech delay and autistic features. The proximal and distal end-points of the deletion fall within two genes, NCAM2
, respectively. Both of these genes are the good candidates in the etiology of the phenotype as they are expressed throughout the developing and adult brain, and appear to be important for proper brain maturation and function. NCAM2
is part of the neural cell adhesion molecule family, which participates in many cellular processes, including neuronal migration, cell survival, outgrowth of neurites, and formation and plasticity of synapses [Kulahin and Walmod, 2008
has also been implicated as a candidate gene following analyses of autistic patients by linkage studies [Molloy et al., 2005
) encodes a protein belonging to the kainate family of glutamate receptors that function as ligand-activated ion channels. Collectively, the glutamate receptors have been associated with various neurobehavioral phenotypes, including anxiety disorders, addictions, schizophrenia, epilepsy, learning, and cognition [Lipsky and Goldman, 2003
; Pinheiro and Mulle, 2008
polymorphisms were shown to be associated with schizophrenia, bipolar disorder, and epilepsy in humans [Sander et al.,1997
; Shibata et al., 2001
; Lucarini et al., 2007
; Woo et al., 2007
; Dracheva et al., 2008
], as well as anxiety-like behaviors in GRIK1
knockout mice due to its regulation of inhibitory circuits in the amygdala [Wu et al., 2007
]. The phenotype observed in our patient suggests that NCAM2
may have a role in autism, mental retardation, and other neurobehavioral disorders.
In summary, we report here on a case of an almost 8-year-old male with PDD-NOS who was found to have an apparently balanced complex chromosomal rearrangement by classic cytogenetic techniques. However, further analysis by high-density oligonucleotide microarray showed loss of 21q21.1-q21.3, resulting in partial monosomy for this region. This report provides additional support for the use of high-density microarray analysis in the detection of various cryptic rearrangements in patients with apparently balanced chromosomal translocations and abnormal phenotypes. Furthermore, characterization of the deleted genes in this region may provide additional insight into their association with autism spectrum disorders.