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Haruta M, Arai Y, Okita H, Tanaka Y, Takimoto T, Kamijo T, Oue T, Souzaki R, Taguchi T, Kuwahara Y, Chin M, Nakadate H, Hiyama E, Ishida Y, Koshinaga T, Kaneko Y. Frequent breakpoints of focal deletion and uniparental disomy in 22q11.1 or 11.2 segmental duplication region reveal distinct tumorigenesis in rhabdoid tumor of the kidney. Genes Chromosomes Cancer 2021; 60:546-558. [PMID: 33896058 DOI: 10.1002/gcc.22952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
SMARCB1 is mutated in most rhabdoid tumors (RTs) developing in the kidney (RTK) and various other organs. Focal deletions found in patients with 22q11.2 deletion syndrome show breakpoints within clusters of segmental duplications (SDs), and those in some RTs show breakpoints in the 22q11-q12 region. SDs are known to cause focal deletion mediated by non-allelic homologous recombination. The present study identified SMARCB1 alterations in all 30 RTKs, using SNP array CGH, MLPA, and sequence analyses. Twenty-eight tumors had a total of 51 breakpoints forming focal 22q deletion and/or uniparental disomy (22qUPD), and the other two had compound mutation with no breakpoints in 22q. Twenty-four (47.1%) of the 51 breakpoints were within SDs, and occurred in 16 (53.3%) of the 30 tumors. The association of breakpoints with SDs was found not only in focal deletion, but also in 22qUPD, indicating that SDs mediate the first and second hits (focal deletion) and the second hit (22qUPD) of SMARCB1 alteration. Of the 51 breakpoints, 14 were recurrent, and 10 of the 14 were within SDs, suggesting the presence of hotspots in the 22q11.2 region. One recurrent breakpoint outside SDs resided in SMARCB1, suggesting inactivation of the gene by out-of-frame fusion. The association between SDs and focal deletion has been reported in two other types of cancer. RTKs may be the third example of SD-associated tumors. Thus, the present study indicated that RTKs exploit genomic instability in the 22q11.1-11.2 SDs region, and 22qUPD caused by mitotic recombination may also be mediated by SDs.
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Affiliation(s)
- Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Yasuhito Arai
- Cancer Genomics Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Kanagawa, Japan
| | - Tetsuya Takimoto
- Department of Childhood Cancer Data Management, Childhood Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Takaharu Oue
- Department of Pediatric Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Ryota Souzaki
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Motoaki Chin
- Department of Pediatrics, Nihon University School of Medicine, Tokyo, Japan
| | - Hisaya Nakadate
- Division of Hematology, National Center for Child Health and Development, Tokyo, Japan
| | - Eiso Hiyama
- Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Yasushi Ishida
- Pediatric Medical Center, Ehime Prefectural Central Hospital, Matsuyama, Ehime, Japan
| | - Tsugumichi Koshinaga
- Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Yasuhiko Kaneko
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
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Burnside RD. 22q11.21 Deletion Syndromes: A Review of Proximal, Central, and Distal Deletions and Their Associated Features. Cytogenet Genome Res 2015; 146:89-99. [PMID: 26278718 DOI: 10.1159/000438708] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 04/13/2024] Open
Abstract
Chromosome 22q11.21 contains a cluster of low-copy repeats (LCRs), referred to as LCR22A-H, that mediate meiotic non-allelic homologous recombination, resulting in either deletion or duplication of various intervals in the region. The deletion of the DiGeorge/velocardiofacial syndrome interval LCR22A-D is the most common recurrent microdeletion in humans, with an estimated incidence of ∼1:4,000 births. Deletion of other intervals in 22q11.21 have also been described, but the literature is often confusing, as the terms 'proximal', 'nested', 'distal', and 'atypical' have all been used to describe various of the other intervals. Individuals with deletions tend to have features with widely variable expressivity, even among families. This review concisely delineates each interval and classifies the reported literature accordingly.
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Affiliation(s)
- Rachel D Burnside
- Department of Cytogenetics, Laboratory Corporation of America Holdings, Center for Molecular Biology and Pathology, Research Triangle Park, N.C., USA
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Hwang VJ, Maar D, Regan J, Angkustsiri K, Simon TJ, Tassone F. Mapping the deletion endpoints in individuals with 22q11.2 deletion syndrome by droplet digital PCR. BMC MEDICAL GENETICS 2014; 15:106. [PMID: 25312060 PMCID: PMC4258952 DOI: 10.1186/s12881-014-0106-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/09/2014] [Indexed: 01/25/2023]
Abstract
Background Chromosome 22q11.2 deletion syndrome (22q11DS) is the most common human microdeletion syndrome and is associated with many cognitive, neurological and psychiatric disorders. The majority of individuals have a 3 Mb deletion while others have a nested 1.5 Mb deletion, but rare atypical deletions have also been described. To date, a study using droplet digital PCR (ddPCR) has not been conducted to systematically map the chromosomal breakpoints in individuals with 22q11DS, which would provide important genotypic insight into the various phenotypes observed in this syndrome. Methods This study uses ddPCR to assess copy number (CN) changes within the chromosome 22q11 deletion region and allows the mapping of the deletion endpoints. We used eight TaqMan assays interspersed throughout the deleted region of 22q11.2 to characterize the deleted region of chromosome 22 in 80 individuals known to have 22q11DS by FISH. Ten EvaGreen assays were used for finer mapping of the six identified individuals with 22q11DS atypical deletions and covering different regions of chromosome 22. Results ddPCR provided non-ambiguous CN measurements across the region, confirmed the presence of the deletion in the individuals screened, and led to the identification of five differently sized and located deletions. The majority of the participants (n = 74) had the large 3 Mb deletions, whereas three had the smaller 1.5 Mb deletions, and the remaining three had an interstitial deletion of different size. Conclusions The lower cost, rapid execution and high reliability and specificity provided by ddPCR for CN measurements in the 22q11 region constitutes a significant improvement over the variable CN values generated by other technologies. The ability of the ddPCR approach, to provide a high resolution mapping of deletion endpoints may result in the identification of genes that are haplo-insufficient and play a role in the pathogenesis of 22q11DS. Finally, this methodology can be applied to the characterization of other microdeletions throughout the genome.
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Affiliation(s)
| | | | | | | | | | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, UC Davis, 2700 Stockton Blvd, Suite 2102, Sacramento 95817, CA, USA.
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dos Santos PAC, de Oliveira SF, Freitas EL, Safatle HPN, Rosenberg C, Ferrari I, Mazzeu JF. Non-overlapping 22q11.2 microdeletions in patients with oculo-auriculo-vertebral spectrum. Am J Med Genet A 2013; 164A:551-3. [DOI: 10.1002/ajmg.a.36231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Pollyanna Almeida Costa dos Santos
- Programa de Pós-Graduação em Ciências da Saúde; Universidade de Brasília; DF Brazil
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de, Ciências Biológicas Universidade de Brasília; Brasília DF Brazil
| | - Silviene Fabiana de Oliveira
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de, Ciências Biológicas Universidade de Brasília; Brasília DF Brazil
| | - Erika L. Freitas
- Departamento de Genética e Biologia Evolutiva; Instituto de Biociências, Universidade de São Paulo; SP Brazil
| | | | - Carla Rosenberg
- Departamento de Genética e Biologia Evolutiva; Instituto de Biociências, Universidade de São Paulo; SP Brazil
| | - Iris Ferrari
- Laboratório de Genética, Departamento de Genética e Morfologia; Instituto de, Ciências Biológicas Universidade de Brasília; Brasília DF Brazil
| | - Juliana Forte Mazzeu
- Programa de Pós-Graduação em Ciências da Saúde; Universidade de Brasília; DF Brazil
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília DF Brazil
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Torti EE, Braddock SR, Bernreuter K, Batanian JR. Oculo-auriculo-vertebral spectrum, cat eye, and distal 22q11 microdeletion syndromes: a unique double rearrangement. Am J Med Genet A 2013; 161A:1992-8. [PMID: 23894059 DOI: 10.1002/ajmg.a.35918] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 02/03/2013] [Indexed: 01/30/2023]
Abstract
An array-CGH on 19-year-old male showed a proximal 1.11 Mb duplication and a distal 1.7 Mb deletion of 22q11.2 regions flanking the Velocardiofacial/DiGeorge syndrome region that remained intact. FISH analyses revealed both abnormalities to be on the same homolog 22. This double rearrangement lead to the co-existence of two syndromes: Cat eye and distal 22q11.2 microdeletion syndromes with a rare associated phenotype of oculo-auriculo-vertebral spectrum (OAVS). A review of the literature indicates that this is the second report of a proximal duplication and the fifth report of a distal deletion and OAVS suggestive of a possible OAVS candidate gene in this region.
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Affiliation(s)
- Erin E Torti
- Division of Medical Genetics, Department of Pediatrics, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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Atypical copy number abnormalities in 22q11.2 region: Report of three cases. Eur J Med Genet 2013; 56:515-20. [DOI: 10.1016/j.ejmg.2013.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022]
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7
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Heart defects and other features of the 22q11 distal deletion syndrome. Eur J Med Genet 2013; 56:98-107. [DOI: 10.1016/j.ejmg.2012.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/26/2012] [Indexed: 11/20/2022]
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Royer-Pokora B. Genetics of pediatric renal tumors. Pediatr Nephrol 2013; 28:13-23. [PMID: 22461142 DOI: 10.1007/s00467-012-2146-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 01/06/2023]
Abstract
Wilms tumor (WT) accounts for approximately 95 % of all pediatric renal tumors, with a peak incidence between 2 and 3 years of age. It occurs in sporadic and congenital forms, the latter often occurring before 1 year of age. Incidence declines with age, and WT rarely is observed in adults. WT is an embryonal tumor of the kidney caused by aberrant proliferation of early metanephric kidney cells. It can arise from more than one developmental error and therefore several subtypes can be defined. WT1, a zinc-finger transcription factor, was identified as the first WT gene. Other genes frequently altered somatically in subsets of WT are CTNNB1 and WTX; both genes influence the Wnt signalling pathway. Imprinting alterations of genes in 11p15 are also observed in a subset of WTs. Other pediatric renal tumors occur less often, e.g. malignant rhabdoid tumor of the kidney, clear-cell sarcoma, desmoplastic small-round-cell tumors, congenital mesoblastic nephroma, renal cell carcinoma of childhood, renal primitive neuroectodermal tumors, renal medullary carcinoma, and synovial sarcoma of the kidney. In most of these, characteristic genetic alterations have been identified that help in the unequivocal diagnosis of these childhood renal cancers that are often difficult to distinguish.
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Affiliation(s)
- Brigitte Royer-Pokora
- Institute for Human Genetics and Anthropology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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Congenital Extrarenal Malignant Rhabdoid Tumor in an Infant With Distal 22q11.2 Deletion Syndrome. Am J Dermatopathol 2012; 34:e77-80. [DOI: 10.1097/dad.0b013e31825793c3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Tan TY, Collins A, James PA, McGillivray G, Stark Z, Gordon CT, Leventer RJ, Pope K, Forbes R, Crolla JA, Ganesamoorthy D, Burgess T, Bruno DL, Slater HR, Farlie PG, Amor DJ. Phenotypic variability of distal 22q11.2 copy number abnormalities. Am J Med Genet A 2011; 155A:1623-33. [PMID: 21671380 DOI: 10.1002/ajmg.a.34051] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 03/17/2011] [Indexed: 01/09/2023]
Abstract
The availability of microarray technology has led to the recent recognition of copy number abnormalities of distal chromosome 22q11.2 that are distinct from the better-characterized deletions and duplications of the proximal region. This report describes five unrelated individuals with copy number abnormalities affecting distal chromosome 22q11.2. We report on novel phenotypic features including diaphragmatic hernia and uterine didelphys associated with the distal microdeletion syndrome; and frontomedial polymicrogyria and callosal agenesis associated with the distal microduplication syndrome. We describe the third distal chromosome 22q11.2 microdeletion patient with Goldenhar syndrome. Patients with distal chromosome 22q11.2 copy number abnormalities exhibit inter- and intra-familial phenotypic variability, and challenge our ability to draw meaningful genotype-phenotype correlations.
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Diagnosis of distal 22q11.2 deletion syndrome in a patient with a teratoid/rhabdoid tumour. Eur J Med Genet 2011; 54:295-8. [DOI: 10.1016/j.ejmg.2010.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 12/17/2010] [Indexed: 01/31/2023]
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12
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Finch PT, Pivnick EK, Furman W, Odom CC. Wilms tumor in a patient with 22q11.2 microdeletion. Am J Med Genet A 2011; 155A:1162-4. [DOI: 10.1002/ajmg.a.33957] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 12/30/2010] [Indexed: 11/06/2022]
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Toth G, Zraly CB, Thomson TL, Jones C, Lapetino S, Muraskas J, Zhang J, Dingwall AK. Congenital anomalies and rhabdoid tumor associated with 22q11 germline deletion and somatic inactivation of the SMARCB1 tumor suppressor. Genes Chromosomes Cancer 2011; 50:379-88. [PMID: 21412926 DOI: 10.1002/gcc.20862] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 01/26/2011] [Indexed: 12/31/2022] Open
Abstract
The most common microdeletion in humans involves the 22q11 region. Congenital anomalies associated with 22q11 loss include cardiac and facial defects. Less frequent is the co-presentation of malignant rhabdoid tumors that are highly aggressive childhood malignancies typically found in renal or extra-renal soft tissues and central nervous system. A newborn patient presented with multiple congenital anomalies consistent with 22q11 deletion syndrome including cleft lip and palate, ear tags and ventricular septal defects co-presenting with an axillary rhabdoid tumor. Comparative genomic hybridization revealed a 2.8 Mb germline deletion in the 22q11.2 region containing genes required for normal fetal development and the SMARCB1 tumor suppressor gene. Analysis of tumor DNA revealed a somatic deletion of exon 7 in the second allele of SMARCB1. Expression of SMARCB1 was absent, while tumor markers including MYC, GFAP, and CLAUDIN-6 were upregulated. The presence of tandem oriented BCRL modules located within interspersed low copy repeat elements throughout the 22q11 distal region may predispose this area for microdeletions through nonalleleic homologous recombination.
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Affiliation(s)
- George Toth
- Stritch School of Medicine, Loyola University of Chicago, Maywood, IL 60153, USA
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Bourdeaut F, Lequin D, Brugières L, Reynaud S, Dufour C, Doz F, André N, Stephan JL, Pérel Y, Oberlin O, Orbach D, Bergeron C, Rialland X, Fréneaux P, Ranchere D, Figarella-Branger D, Audry G, Puget S, Evans DG, Pinas JCF, Capra V, Mosseri V, Coupier I, Gauthier-Villars M, Pierron G, Delattre O. Frequent hSNF5/INI1 Germline Mutations in Patients with Rhabdoid Tumor. Clin Cancer Res 2011; 17:31-8. [DOI: 10.1158/1078-0432.ccr-10-1795] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Tan TY, Gordon CT, Amor DJ, Farlie PG. Developmental perspectives on copy number abnormalities of the 22q11.2 region. Clin Genet 2010; 78:201-18. [DOI: 10.1111/j.1399-0004.2010.01456.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Lafay-Cousin L, Payne E, Strother D, Chernos J, Chan M, Bernier FP. Goldenhar phenotype in a child with distal 22q11.2 deletion and intracranial atypical teratoid rhabdoid tumor. Am J Med Genet A 2010; 149A:2855-9. [PMID: 19938088 DOI: 10.1002/ajmg.a.33119] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosome-specific low copy repeats (LCRs) are implicated in several clinically significant microdeletion and microduplication syndromes. The well-recognized phenotype of DiGeorge/velocardiofacial syndrome (DG/VCF) results from deletions of the long arm of chromosome 22 (22q11.2) mediated by the proximal LCRs in this region. More recent evidence suggests that the distal LCRs within 22q11.2 are also implicated in microdeletions and microduplications with less characterized phenotypes. Here we report on an infant diagnosed with Goldenhar syndrome (GS) phenotype who developed an atypical teratoid rhabdoid tumor (AT/RT) of the brain due to a distal deletion of the chromosome 22q11.2 region encompassing the INI1/SMARCB1 tumor suppressor. We also discuss the phenotype of patients with germline deletions of this region and the possible implication of the 22q11.2 region in the GS.
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Affiliation(s)
- Lucie Lafay-Cousin
- Division of Pediatric Oncology and Bone Marrow Transplantation, Alberta Children's Hospital, 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8.
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A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review. BMC MEDICAL GENETICS 2009; 10:48. [PMID: 19490635 PMCID: PMC2700091 DOI: 10.1186/1471-2350-10-48] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 06/02/2009] [Indexed: 12/31/2022]
Abstract
Background Individuals affected with DiGeorge and Velocardiofacial syndromes present with both phenotypic diversity and variable expressivity. The most frequent clinical features include conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial dysmorphism. The etiology in most patients is a 3 Mb recurrent deletion in region 22q11.2. However, cases of infrequent deletions and duplications with different sizes and locations have also been reported, generally with a milder, slightly different phenotype for duplications but with no clear genotype-phenotype correlation to date. Methods We present a 7 month-old male patient with surgically corrected ASD and multiple VSDs, and dysmorphic facial features not clearly suggestive of 22q11.2 deletion syndrome, and a newborn male infant with cleft lip and palate and upslanting palpebral fissures. Karyotype, FISH, MLPA, microsatellite markers segregation studies and SNP genotyping by array-CGH were performed in both patients and parents. Results Karyotype and FISH with probe N25 were normal for both patients. MLPA analysis detected a partial de novo 1.1 Mb deletion in one patient and a novel partial familial 0.4 Mb duplication in the other. Both of these alterations were located at a distal position within the commonly deleted region in 22q11.2. These rearrangements were confirmed and accurately characterized by microsatellite marker segregation studies and SNP array genotyping. Conclusion The phenotypic diversity found for deletions and duplications supports a lack of genotype-phenotype correlation in the vicinity of the LCRC-LCRD interval of the 22q11.2 chromosomal region, whereas the high presence of duplications in normal individuals supports their role as polymorphisms. We suggest that any hypothetical correlation between the clinical phenotype and the size and location of these alterations may be masked by other genetic and/or epigenetic modifying factors.
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Neale G, Su X, Morton CL, Phelps D, Gorlick R, Lock RB, Reynolds CP, Maris JM, Friedman HS, Dome J, Khoury J, Triche TJ, Seeger RC, Gilbertson R, Khan J, Smith MA, Houghton PJ. Molecular characterization of the pediatric preclinical testing panel. Clin Cancer Res 2008; 14:4572-83. [PMID: 18628472 DOI: 10.1158/1078-0432.ccr-07-5090] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Identifying novel therapeutic agents for the treatment of childhood cancers requires preclinical models that recapitulate the molecular characteristics of their respective clinical histotypes. EXPERIMENTAL DESIGN AND RESULTS Here, we have applied Affymetrix HG-U133Plus2 profiling to an expanded panel of models in the Pediatric Preclinical Testing Program. Profiling led to exclusion of two tumor lines that were of mouse origin and five osteosarcoma lines that did not cluster with human or xenograft osteosarcoma samples. We compared expression profiles of the remaining 87 models with profiles from 112 clinical samples representing the same histologies and show that model tumors cluster with the appropriate clinical histotype, once "immunosurveillance" genes (contributed by infiltrating immune cells in clinical samples) are eliminated from the analysis. Analysis of copy number alterations using the Affymetrix 100K single nucleotide polymorphism GeneChip showed that the models have similar copy number alterations to their clinical counterparts. Several consistent copy number changes not reported previously were found (e.g., gain at 22q11.21 that was observed in 5 of 7 glioblastoma samples, loss at 16q22.3 that was observed in 5 of 9 Ewing's sarcoma and 4 of 12 rhabdomyosarcoma models, and amplification of 21q22.3 that was observed in 5 of 7 osteosarcoma models). We then asked whether changes in copy number were reflected by coordinate changes in gene expression. We identified 493 copy number-altered genes that are nonrandom and appear to identify histotype-specific programs of genetic alterations. CONCLUSIONS These data indicate that the preclinical models accurately recapitulate expression profiles and genetic alterations common to childhood cancer, supporting their value in drug development.
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Affiliation(s)
- Geoffrey Neale
- Hartwell Center of Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Huber J, Rainho CA, Gomes MV, Santos SA, Ramos ES. Velocardiofacial syndrome with a rare t(2;22). Clin Dysmorphol 2007; 16:181-183. [PMID: 17551333 DOI: 10.1097/mcd.0b013e3280fa81de] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rearrangements involving chromosomes 2 and 22 were described not only as acquired abnormalities in a variety of human neoplasias but also in the constitutional karyotype suggesting the existence of a greater fragility in some specific regions in these chromosomes. Patients with DiGeorge and Velocardiofacial syndromes have a deletion on 22q11 leading to haploinsufficiency for one or more gene(s). We report a patient with velocardiofacial syndrome in which cytogenetic and fluorescence in situ hybridization analysis showed a rare t(2;22) and deletion in the 22q11 region.
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Affiliation(s)
- Jair Huber
- Departments of Genetics Obstetrics and Gynecology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto Department of Genetics, Biosciences Institute, University of São Paulo State, Botucatu, São Paulo, Brazil
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Department für Medizinische Genetik an der Medizinischen Universität Wien. MED GENET-BERLIN 2007. [DOI: 10.1007/s11825-007-0017-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Sugahara T, Yamashita Y, Shinomi M, Yamanoha B, Iseki H, Takeda A, Okazaki Y, Hayashizaki Y, Kawai K, Suemizu H, Andoh T. Isolation of a novel mouse gene, mSVS-1/SUSD2, reversing tumorigenic phenotypes of cancer cells in vitro. Cancer Sci 2007; 98:900-8. [PMID: 17428258 PMCID: PMC11158758 DOI: 10.1111/j.1349-7006.2007.00466.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report isolation of a novel tumor-reversing gene, tentatively named SVS-1, encoding a protein of 820 amino acids with localization on the plasma membrane as a type I transmembrane protein. The gene was found among those downregulated in the activated oncogene-v-K-ras-transformed NIH3T3 cells, Ki3T3, with tumorigenic phenotype. SVS-1 protein harbors several functional domains inherent to adhesion molecules. Histochemical staining of mouse tissues using antibody raised against the protein showed the expression of the protein in restricted regions and cells, for example, strongly positive in apical membranes of epithelial cells in renal tubules and bronchial tubes. The protein inducibly expressed in human fibrosarcoma HT1080 cells and cervical carcinoma HeLa cells was found to be localized primarily on the plasma membrane, as stained with antibodies against FLAG tag in the N-terminus and against the C-terminal peptide of the protein. Expression of the protein in cells induced a variety of biological effects on cancer cells: detachment from the substratum and aggregation of cells and growth inhibition in HeLa cells, but no inhibition in non-tumorigenic mouse NIH3T3 cells. Inhibition of clonogenicity, anchorage-independent growth, migration and invasion through Matrigel was also observed. Taken together these results suggest that the SVS-1 gene is a possible tumor-reversing gene.
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Affiliation(s)
- Tetsuo Sugahara
- Department of Bioinformatics, Soka University, Hachioji, Tokyo, Japan
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Jackson EM, Shaikh TH, Gururangan S, Jones MC, Malkin D, Nikkel SM, Zuppan CW, Wainwright LM, Zhang F, Biegel JA. High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor. Hum Genet 2007; 122:117-27. [PMID: 17541642 DOI: 10.1007/s00439-007-0386-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 05/19/2007] [Indexed: 02/07/2023]
Abstract
Malignant rhabdoid tumors are highly aggressive neoplasms found primarily in infants and young children. The majority of rhabdoid tumors arise as a result of homozygous inactivating deletions or mutations of the INI1 gene located in chromosome band 22q11.2. Germline mutations of INI1 predispose to the development of rhabdoid tumors of the brain, kidney and extra-renal tissues, consistent with its function as a tumor suppressor gene. We now describe five patients with germline deletions in chromosome band 22q11.2 that included the INI1 gene locus, leading to the development of rhabdoid tumors. Two patients had phenotypic findings that were suggestive but not diagnostic for DiGeorge/Velocardiofacial syndrome (DGS/VCFS). The other three infants had highly aggressive disease with multiple tumors at the time of presentation. The extent of the deletions was determined by fluorescence in situ hybridization and high-density oligonucleotide based single nucleotide polymorphism arrays. The deletions in the two patients with features of DGS/VCFS were distal to the region typically deleted in patients with this genetic disorder. The three infants with multiple primary tumors had smaller but overlapping deletions, primarily involving INI1. The data suggest that the mechanisms underlying the deletions in these patients may be similar to those that lead to DGS/VCFS, as they also appear to be mediated by related, low copy repeats (LCRs) in 22q11.2. These are the first reported cases in which an association has been established between recurrent, interstitial deletions mediated by LCRs in 22q11.2 and a predisposition to cancer.
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Affiliation(s)
- Eric M Jackson
- Department of Neurosurgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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23
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Uddin RK, Zhang Y, Siu VM, Fan YS, O'Reilly RL, Rao J, Singh SM. Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions. BMC MEDICAL GENETICS 2006; 7:18. [PMID: 16512914 PMCID: PMC1413517 DOI: 10.1186/1471-2350-7-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Accepted: 03/02/2006] [Indexed: 11/10/2022]
Abstract
BACKGROUND Chromosome 22q11.2 region is highly susceptible to rearrangement, specifically deletions that give rise to a variety of genomic disorders including velocardiofacial or DiGeorge syndrome. Individuals with this 22q11 microdeletion syndrome are at a greatly increased risk to develop schizophrenia. METHODS Genotype analysis was carried out on the DNA from a patient with the 22q11 microdeletion using genetic markers and custom primer sets to define the deletion. Bioinformatic analysis was performed for molecular characterization of the deletion breakpoint sequences in this patient. RESULTS This 22q11 deletion patient was established to have a novel 2.3 Mb deletion with a proximal breakpoint located between genetic markers RH48663 and RH48348 and a distal breakpoint between markers D22S1138 and SHGC-145314. Molecular characterization of the sequences at the breakpoints revealed a 270 bp shared sequence of the breakpoint regions (SSBR) common to both ends that share >90% sequence similarity to each other and also to short interspersed nuclear elements/Alu elements. CONCLUSION This Alu sequence like SSBR is commonly in the proximity of all known deletion breakpoints of 22q11 region and also in the low copy repeat regions (LCRs). This sequence may represent a preferred sequence in the breakpoint regions or LCRs for intra-chromosomal homologous recombination mechanisms resulting in common 22q11 deletion.
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Affiliation(s)
- Raihan K Uddin
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Yang Zhang
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Victoria Mok Siu
- Division of Medical Genetics, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Yao-Shan Fan
- Division of Medical Genetics, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Richard L O'Reilly
- Department of Psychiatry, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Jay Rao
- Department of Psychiatry, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Shiva M Singh
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
- Division of Medical Genetics, University of Western Ontario, London, Ontario, N6A 5B7, Canada
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