Characterization of a complex chromosomal rearrangement using chromosome, FISH, and microarray assays in a girl with multiple congenital abnormalities and developmental delay
© Hemmat et al.; licensee BioMed Central Ltd. 2014
Received: 13 March 2014
Accepted: 27 May 2014
Published: 29 August 2014
Complex chromosomal rearrangements (CCRs) are balanced or unbalanced structural rearrangements involving three or more cytogenetic breakpoints on two or more chromosomal pairs. The phenotypic anomalies in such cases are attributed to gene disruption, superimposed cryptic imbalances in the genome, and/or position effects. We report a 14-year-old girl who presented with multiple congenital anomalies and developmental delay. Chromosome and FISH analysis indicated a highly complex chromosomal rearrangement involving three chromosomes (3, 7 and 12), seven breakpoints as a result of one inversion, two insertions, and two translocations forming three derivative chromosomes. Additionally, chromosomal microarray study (CMA) revealed two submicroscopic deletions at 3p12.3 (467 kb) and 12q13.12 (442 kb). We postulate that microdeletion within the ROBO1 gene at 3p12.3 may have played a role in the patient’s developmental delay, since it has potential activity-dependent role in neurons. Additionally, factors other than genomic deletions such as loss of function or position effects may also contribute to the abnormal phenotype in our patient.
KeywordsComplex chromosomal rearrangement (CCR) microarray CMA Whole chromosome painting (WCP) FISH
Complex chromosomal rearrangements (CCRs) are balanced or unbalanced structural rearrangements involving three or more cytogenetic breakpoints on two or more chromosomes [1–5]. The apparently balanced CCRs range from simple three-way exchanges between three chromosomes to highly complex translocations involving many chromosomes and multiple breaks .
Chromosomal rearrangements may occur via several mechanisms , including non-allelic homologous recombination (NAHR) [8, 9] and nonhomologous end-joining (NHEJ), which both lead to deleted or duplicated genomic segments. However, a number of disease-associated rearrangements are not explained readily by either the NAHR or simple NHEJ recombination mechanisms. Fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR) have been described as a mechanism associated with complex rearrangements caused by abnormal DNA replication [7, 10, 11]. More recently, Liber et al. and Tsai et al. proposed a mechanism in which simultaneous double-strand DNA breaks were induced by an unknown stimulus, such as free radicals or ionizing radiation. This is followed by joining of the break fragments in the wrong place due to the microhomology shared by these regions [12, 13].
Balanced and unbalanced CCRs are associated with a significant risk of mental retardation and phenotypic anomalies attributable to gene disruption, cryptic imbalances and/or from position effects [14–18]. Fluorescence in situ hybridization (FISH) and/or high resolution chromosomal microarray studies have identified cryptic CCRs as a cause of abnormal phenotype in a significant number of patients with apparently balanced chromosomal rearrangements [19–23].
We report a patient with multiple congenital anomalies and developmental delay who presented with a CCR involving three chromosomes 3, 7 and 12. G-banding, chromosomal microarray (CMA), and FISH were performed to clarify the nature of this complex abnormality.
The patient was a 14-year-old female who presented clinically with developmental delay and multiple congenital anomalies including abnormal teeth and abnormal faces. No further clinical information was available regarding this patient.
Methods and results
The combination of cytogenetic, FISH, and array analysis revealed a complex rearrangement with nine breakpoints:
46,××, der (3) (3pter → 3p12::7q11.2 → 7q22::3q27 → 3p12::12q13 → 12q24.3::7p22 → 7pter), der (7) (12qter → 2q24.3::7p22 → 7q11.2::7q22 → 7qter), der (12) (12pter → 12q13::3q27 → 3qter).arr [hg19] 3p12.3(78,952,028-79,418,897) ×1, 12q13.12 (49,988,357-50,429,906)×1.
The disease-associated CCRs are frequently used to establish the genotype-phenotype relationship [28, 29]. A combination of several different approaches, including karyotype, FISH, and CMA studies, has been useful in identifying several disease-associated genes and regions [28–35]. The phenotype of our patient with multiple congenital abnormalities and developmental delay with the apparently balanced CCR led us to perform CMA testing to rule out cryptic copy number variations (CNVs). According to the NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/mapview/), the 3p12.3 deletion was within the ROBO1 gene, while the deletion at 12q13.12 involved thirteen genes (FAM186B, PRPF40B, FMNL3, TMBIM6, NCKAP5L, BCDIN3D-AS1, BCDIN3D, FAIM2, LOC283332, AQP2, AQP5, AQP6, RACGAP1). It is not clear if these copy number losses are de novo or paternally inherited, since the patient’s father was not available for follow up studies. The ROBO1 gene encodes a receptor that is a member of the neural cell adhesion molecule (NCAM; 116930) family of receptors, acting as an axon guidance receptor. ROBO1 may play a role in neuronal development, and its disruption may predispose humans to developmental dyslexia [36, 37]. Among the genes deleted at 12q13 three are OMIM genes including NCKAP5L (OMIM 615104), AQP2 (OMIM 107777) and AQP5 (OMIM 600442). NCKAP5L gene encodes a protein involved in proteolysis, GTPase-mediated signaling, cytoskeletal organization, and other pathways. Furthermore, neuronal depolarization regulates the transcription of these genes, suggesting potential activity-dependent roles in neurons . Mutation in AQP2 is associated with diabetes insipidus and in AQP5 with palmoplantar keratoderma, Bothnian type. However, copy number losses or gains at these loci have not yet been associated with a clinical phenotype. We propose that microdeletion within ROBO1 may play a role in our patient’s developmental delay.
Since the exact genomic location of at least five out of seven breakpoints in our patient is unknown, we can only speculate as to the disruption of genes resulting in loss of function [21, 39] or position effects  in these chromosomal breakpoints. For example, inversion of 3p12q27 may interrupt the DYX5 gene (OMIM 606896) at 3p12, which is associated with neurofunctional disorder, developmental dyslexia , or speech sound disorder . Furthermore, interruption in MASP1 (OMIM 257920) located at the distal end (3q27) of the inversion 3 may have resulted in 3MC syndrome, which encompasses four rare autosomal recessive disorders previously designated as the Carnevale, Mingarelli, Malpuech, and Michels syndromes, respectively. The main features of these syndromes are facial dysmorphism, cleft lip and palate, postnatal growth deficiency, cognitive impairment, and craniosynostosis . The other gene interruption may have occurred in the complex der (3) ins (3;7), where one of the breakpoints maps to 7q11.21. This was previously suggested as a candidate region for ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome (designated EEC1) . Alternatively, fusion of these genes at the breakpoints where insertion has occurred may generate a gain-of-function mutation . Additional molecular studies are needed in order to determine whether any interruption or disruption of the genes caused by the chromosomal rearrangements.
Two sub-microscopic deletions resulted from this apparently balanced CCR. Microdeletion within the ROBO1 gene with potential activity-dependent roles in neurons may have played a role in our patient’s developmental delay. Furthermore, gene disruptions or position effects altering gene regulation by chromosomal rearrangements due to interference with some gene regulatory elements, may have also contributed to our patient’s abnormal phenotype.
These studies were performed on anonymized samples received in the clinical laboratory and thus were exempted from the requirement for consent by an opinion for the Western Institutional review Board.
Complex chromosomal rearrangement
Single nucleotide polymorphism.
The authors would like to express their thanks to Jeff Radcliff (Quest Diagnostics) for critical review of the manuscript.
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