- Case report
- Open Access
Identification of a rare de novo three-way complex t(5;20;8)(q31;p11.2;p21) with microdeletions on 5q31.2, 5q31.3, and 8p23.2 in a patient with hearing loss and global developmental delay: case report
© Haj et al; licensee BioMed Central Ltd. 2009
- Received: 06 November 2008
- Accepted: 07 January 2009
- Published: 07 January 2009
Complex chromosome rearrangements (CCRs), which involve more than two breakpoints on two or more chromosomes, are uncommon occurrences. Although most CCRs appear balanced at the level of the light microscope, many demonstrate cryptic, submicroscopic imbalances at the translocation breakpoints.
We report a female with hearing loss and global developmental delay with a complex three-way unbalanced translocation (5;20;8)(q31;p11.2;p21) resulting in microdeletions on 5q31.2, 5q31.3, and 8p23.2 identified by karyotyping, microarray analysis and fluorescence in situ hybridization.
The microdeletion of bands 8p23.2 may be associated with the hearing impairment. Furthermore, the characterization of this patient's chromosomal abnormalities demonstrates the importance of integrated technologies within contemporary cytogenetics laboratories.
- Hearing Loss
- Bacterial Artificial Chromosome
- Bacterial Artificial Chromosome Clone
- Sensorineural Hearing Loss
- Global Developmental Delay
Reciprocal de novo translocations occur in about 1 in 2,000 newborns . Although balanced translocations are not often associated with abnormal phenotypes, unbalanced translocations resulting in deleted or altered gene sequences usually cause appreciable clinical features [2, 3]. Even more unusual than unbalanced translocations are complex chromosome rearrangements (CCRs). CCRs are structural abnormalities that involve more than two breakpoints and exchange of genetic material between two or more chromosomes [4, 5]. The most common CCRs involve three chromosomes with breakpoints on each chromosome. The occurrence of three-way multiple translocations is rare and often difficult to distinguish from balanced translocations without the aid of additional diagnostic tools such as fluorescence in situ hybridization (FISH)  or microarray-based comparative genomic hybridization (array CGH) [7, 8].
We report on an 8-month-old female with hearing loss, global developmental delay and myopathic face in whom we found a de novo complex translocation (5;20;8)(q31;p11.2;p21) and three microdeletions del(5)(q31.2q31.2), del(5)(q31.3q32) and del(8)(p23.2) identified by traditional and molecular cytogenetic methods.
The proband is an 8-month-old female who was referred for global developmental delay and hearing loss. She was born at term by cesarean section to a 31-year-old mother. The proband's birth weight was 4 kg (90th centile) and her length was 48 cm (25th centile). The mother reports that she did not drink alcohol, smoke cigarettes, or use any unusual medications during the pregnancy. The father of the proband was 32 years old with no prior family history of congenital abnormalities.
FISH was performed to confirm the results of the microarray analysis. A BAC clone from the deleted 5q31.2 region (RP11-264B21) showed a diminished signal on the short arm of the abnormal derivative chromosome 20 and no signal on the derivative 5, suggesting the BAC contains the breakpoint of the 5q31.2 deletion. The probe from the non-deleted region between the two 5q31 deletions (RP11-166J22) also hybridized to the der 20, as did a probe to the 8p22 region (RP11-447G11).
FISH using BAC clones from the deleted 5q31.3 region (RP11-1104L21) and the deleted 8p32.2 region (RP11-1148N20) confirmed the deletions at 5q31.3 and 8p23.2, respectively. The 5q telomeric probe (RP11-69N15) was used as a control, and it showed hybridization to the der 20. The 20p telomeric probe (RP11-530N10) was used as a second control, and it showed hybridization on the short arm of the abnormal derivative 8. The 8p telomeric probe (RP11-412M23) was used as a third control and hybridized to the long arm of the derivative 5.
Thus, this individual has a three-way complex translocation between the long arm of chromosome 5, the short arm of chromosome 20 and the short arm of chromosome 8 resulting in three interstitial deletions at bands 5q31.2, 5q31.3, and 8p23.2 with respective deletion sizes of approximately 240 kb, 4.1 Mb, and 1.5 Mb as estimated by array CGH.
We report the molecular and cytogenetic finding of a patient with a complex chromosome rearrangement involving 5q31, 20p11.2 and 8p21 resulting in microdeletions of bands 5q31.2, 5q31.3, and 8p23.2. The proband's phenotype is nondescript; global developmental delay and sensorineural hearing loss are associated with many microdeletions including 1p36, 7q21.13-q22.1, 11q25, and Xq21 [9–13]. Many genomic regions are associated with hearing loss because of the complexity of and number of genes involved in hearing development.
5q31.2, 5q31.3, and 8p23.2 may be potential regions of the genome critical to hearing development. However, abnormalities involving 5q are rarely associated with hearing loss, with the exception of Treacher Collins syndrome, an autosomally dominant trait associated with severe craniofacial malformation that maps to 5q32-5q33.1 . Because the patient has no familial history of Treacher Collins or the characteristic facial features, this syndrome has been excluded as a possible diagnosis in this patient. The short arm of chromosome 8 may contain one or more genes directly or indirectly involved in the formation of functional hearing pathways. Masuda et al.  and Devriendt et al.  report sensorineural hearing loss in patients with 8p abnormalities proximal to the telomere resulting in partial 8p monosomy similar in size and location to the deletion in our patient. In contrast, Fryns et al. , Hutchinson et al. , and Devriendt et al.  report patients with deletions of 8p23.1pter without noting sensioneural hearing loss. CMSD1 is the only known gene in the 1.5 Mb region on 8p23.2 deleted in this individual. The deletion of CMSD1 has not been directly implicated in sensorineural hearing loss or a similar phenotype, but CMSD1 is known to play a role in neuronal migration and development of the central nervous system . The deletion may be causing a position effect on the chromosome and may play a role in the proband's phenotype, either because the chromosomal rearrangement separated a promoter from its transcriptional regulatory element, resulting in gene silencing; the rearrangement juxtaposed a gene with an enhancer from another gene, leading to inappropriate gene expression; or the rearrangement moved a gene and its regulatory elements to a region of the genome that is transcriptionally silent, such as heterochromatin. Alternatively, the translocation breakpoints may have interrupted a gene or genes. The ascertainment of additional individuals with similar rearrangement breakpoints on 8p23.2 is necessary for further genotype-phenotype correlation.
Because of the complexity of the CCR, none of the technologies could accurately confirm the de novo complex CCR independently. Two of the microdeletions initially went undetected by traditional cytogenetic analysis, which is consistent with previous research on CCRs [7, 8, 21]. Only after identification of the approximate breakpoints by microarray analysis was it possible to determine the location and order of the de novo CCR within the patients' genome using the appropriate FISH probes to locate the translocated sections of chromosomes 8p and 5q. Our results suggest the successful integration of multiple cytogenetic techniques–karyotyping, aCGH, and FISH – is necessary in the diagnostic laboratory for the characterization of complex chromosomal rearrangements.
Cytogenetic analysis was performed on peripheral blood lymphocytes by G-banding according to standard procedures.
BAC array CGH
Array CGH was performed with a bacterial artificial chromosome (BAC) microarray (the SignatureChip®; Signature Genomic Laboratories, Spokane, WA) that was developed for the detection of microdeletions, microduplications, aneuploidy, unbalanced translocations, and subtelomeric and pericentromeric copy-number alterations . The current version of the SignatureChip, the SignatureChip Whole Genome™ (SignatureChipWG), contains 4670 BACs representing 1543 loci with each locus being represented by a minimum of three overlapping clones. The subtelomeric and pericentromeric regions are represented with a higher density of overlapping BAC clones, targeted to the unique sequences adjacent to these repetitive regions and consist of contigs of clones located approximately every 0.5 Mb spanning more than 5 Mb. Genes in important developmental pathways are also covered by contigs of BACs to fill in the chromosome arms and provide higher resolution with an average gap size between contigs of ~1.6 Mb .
Microarray analysis was performed as described , with the following modifications: Briefly, genomic DNA was extracted from peripheral blood using a Qiagen M48 Biorobot automated DNA extraction system. Purified genomic DNA was then sonicated and labeled with Alexaflour dyes 555 or 647 using a BioPrime Total DNA labeling kit (Invitrogen Corp). Microarrays were hybridized as previously described (8) and washed using a Little Dipper automated microarray washing station (SciGene). Microarrays were scanned on an Axon 4000B scanner (Molecular Devices) and signal intensity ratios were analyzed as described (8) using a custom analysis and display interface (Genoglyphix™).
All abnormalities detected by array CGH were confirmed and visualized by metaphase or interphase fluorescence in situ hybridization (FISH) using one or more BAC clones determined to be abnormal by array CGH .
This case report is presented with the consent of the patient's family.
We thank Aaron Theisen (Signature Genomic Laboratories, Spokane, WA) for editing our manuscript.
- Warburton D: De novo balanced chromosome rearrangements and extra marker chromosomes identified at prenatal diagnosis: clinical significance and distribution of breakpoints. Am J Hum Genet 1991, 49: 995–1013.PubMed CentralPubMedGoogle Scholar
- Kim HG, Herrick SR, Lemyre E, Kishikawa S, Salisz JA, Seminara S, MacDonald ME, Bruns GA, Morton CC, Quade BJ, Gusella JF: Hypogonadotropic hypogonadism and cleft lip and palate caused by a balanced translocation producing haploinsufficiency for FGFR1. J Med Genet 2005, 42: 666–672. 10.1136/jmg.2004.026989PubMed CentralPubMedView ArticleGoogle Scholar
- Ligon AH, Moore SD, Parisi MA, Mealiffe ME, Harris DJ, Ferguson HL, Quade BJ, Morton CC: Constitutional rearrangement of the architectural factor HMGA2: a novel human phenotype including overgrowth and lipomas. Am J Hum Genet 2005, 76: 340–348. 10.1086/427565PubMed CentralPubMedView ArticleGoogle Scholar
- Kleczkowska A, Fryns JP, Berghe H: Complex chromosomal rearrangements (CCR) and their genetic consequences. J Genet Hum 1982, 30: 199–214.PubMedGoogle Scholar
- Berend SA, Bodamer OA, Shapira SK, Shaffer LG, Bacino CA: Familial complex chromosomal rearrangement resulting in a recombinant chromosome. Am J Med Genet 2002, 109: 311–317. 10.1002/ajmg.10334PubMedView ArticleGoogle Scholar
- Spikes AS, Hegmann K, Smith JL, Shaffer LG: Use of fluorescence in situ hybridization to clarify a complex chromosomal rearrangement in a child with multiple congenital anomalies. Am J Med Genet 1995, 57: 31–34. 10.1002/ajmg.1320570109PubMedView ArticleGoogle Scholar
- De Gregori M, Ciccone R, Magini P, Pramparo T, Gimelli S, Messa J, Novara F, Vetro A, Rossi E, Maraschio P, et al.: Cryptic deletions are a common finding in "balanced" reciprocal and complex chromosome rearrangements: a study of 59 patients. J Med Genet 2007, 44: 750–762. 10.1136/jmg.2007.052787PubMed CentralPubMedView ArticleGoogle Scholar
- Gribble SM, Prigmore E, Burford DC, Porter KM, Ng BL, Douglas EJ, Fiegler H, Carr P, Kalaitzopoulos D, Clegg S, et al.: The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J Med Genet 2005, 42: 8–16. 10.1136/jmg.2004.024141PubMed CentralPubMedView ArticleGoogle Scholar
- Bernardini L, Palka C, Ceccarini C, Capalbo A, Bottillo I, Mingarelli R, Novelli A, Dallapiccola B: Complex rearrangement of chromosomes 7q21.13-q22.1 confirms the ectrodactyly-deafness locus and suggests new candidate genes. Am J Med Genet A 2008, 146A: 238–244. 10.1002/ajmg.a.32093PubMedView ArticleGoogle Scholar
- Battaglia A, Hoyme HE, Dallapiccola B, Zackai E, Hudgins L, McDonald-McGinn D, Bahi-Buisson N, Romano C, Williams CA, Brailey LL, et al.: Further delineation of deletion 1p36 syndrome in 60 patients: a recognizable phenotype and common cause of developmental delay and mental retardation. Pediatrics 2008, 121: 404–410. 10.1542/peds.2007-0929PubMedView ArticleGoogle Scholar
- Gripp KW, Nicholson L, Scott CI Jr: Apparently new syndrome of congenital cataracts, sensorineural deafness, Down syndrome-like facial appearance, short stature, and mental retardation. Am J Med Genet 1996, 61: 382–386. Publisher Full Text 10.1002/(SICI)1096-8628(19960202)61:4<382::AID-AJMG14>3.0.CO;2-OPubMedView ArticleGoogle Scholar
- Keppler-Noreuil K, Welch J, Baker-Lange K: Syndrome of congenital cataracts, sensorineural deafness, Down syndrome-like facial appearance, short stature, and mental retardation: two additional cases. Am J Med Genet A 2007, 143A: 2581–2587. 10.1002/ajmg.a.31990PubMedView ArticleGoogle Scholar
- Piussan C, Hanauer A, Dahl N, Mathieu M, Kolski C, Biancalana V, Heyberger S, Strunski V: X-linked progressive mixed deafness: a new microdeletion that involves a more proximal region in Xq21. Am J Hum Genet 1995, 56: 224–230.PubMed CentralPubMedView ArticleGoogle Scholar
- Dixon MJ, Dixon J, Houseal T, Bhatt M, Ward DC, Klinger K, Landes GM: Narrowing the position of the Treacher Collins syndrome locus to a small interval between three new microsatellite markers at 5q32–33.1. Am J Hum Genet 1993, 52: 907–914.PubMed CentralPubMedGoogle Scholar
- Masuda K, Nomura Y, Yoshinaga M, Nakamura M, Matsuda Y, Oku S, Miyata K: Inverted duplication/deletion of the short arm of chromosome 8 in two patients with tetralogy of Fallot. Pediatr Int 2002, 44: 534–536. 10.1046/j.1442-200X.2002.01593.xPubMedView ArticleGoogle Scholar
- Devriendt K, Matthijs G, Van Dael R, Gewillig M, Eyskens B, Hjalgrim H, Dolmer B, McGaughran J, Brondum-Nielsen K, Marynen P, et al.: Delineation of the critical deletion region for congenital heart defects, on chromosome 8p23.1. Am J Hum Genet 1999, 64: 1119–1126. 10.1086/302330PubMed CentralPubMedView ArticleGoogle Scholar
- Fryns JP, Kleczkowska A, Vogels A, Berghe H: Normal phenotype and slight mental retardation in de novo distal 8p deletion (8pter----8p23.1:). Ann Genet 1989, 32: 171–173.PubMedGoogle Scholar
- Hutchinson R, Wilson M, Voullaire L: Distal 8p deletion (8p23.1----8pter): a common deletion? J Med Genet 1992, 29: 407–411. 10.1136/jmg.29.6.407PubMed CentralPubMedView ArticleGoogle Scholar
- Devriendt K, De Mars K, De Cock P, Gewillig M, Fryns JP: Terminal deletion in chromosome region 8p23.1–8pter in a child with features of velo-cardio-facial syndrome. Ann Genet 1995, 38: 228–230.PubMedGoogle Scholar
- Kraus DM, Elliott GS, Chute H, Horan T, Pfenninger KH, Sanford SD, Foster S, Scully S, Welcher AA, Holers VM: CSMD1 is a novel multiple domain complement-regulatory protein highly expressed in the central nervous system and epithelial tissues. J Immunol 2006, 176: 4419–4430.PubMedView ArticleGoogle Scholar
- Borg K, Nowakowska B, Obersztyn E, Cheung SW, Brycz-Witkowska J, Korniszewski L, Mazurczak T, Stankiewicz P, Bocian E: Complex balanced translocation t(1;5;7)(p32.1;q14.3;p21.3) and two microdeletions del(1)(p31.1p31.1) and del(7)(p14.1p14.1) in a patient with features of Greig cephalopolysyndactyly and mental retardation. Am J Med Genet A 2007, 143A: 2738–2743. 10.1002/ajmg.a.32017PubMedView ArticleGoogle Scholar
- Bejjani BA, Saleki R, Ballif BC, Rorem EA, Sundin K, Theisen A, Kashork CD, Shaffer LG: Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am J Med Genet A 2005, 134: 259–267.PubMedView ArticleGoogle Scholar
- Shaffer LG, McCaskill C, Han JY, Choo KH, Cutillo DM, Donnenfeld AE, Weiss L, Van Dyke DL: Molecular characterization of de novo secondary trisomy 13. Am J Hum Genet 1994, 55: 968–974.PubMed CentralPubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.