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Sun M, Zhang H, Li G, Guy CJ, Wang X, Lu X, Gong F, Lee J, Hassed S, Li S. Molecular characterization of 20 small supernumerary marker chromosome cases using array comparative genomic hybridization and fluorescence in situ hybridization. Sci Rep 2017; 7:10395. [PMID: 28871159 PMCID: PMC5583289 DOI: 10.1038/s41598-017-10466-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 08/10/2017] [Indexed: 12/25/2022] Open
Abstract
The variability of a small supernumerary marker chromosome (sSMC)-related phenotype is determined by the molecular component, the size, and shape of the marker chromosome. As fluorescence in situ hybridization has limitations regarding the resolution, efficiency, and accuracy. Recently, array comparative genomic hybridization (aCGH) was used for sSMC characterization. In this study, twenty cases with sSMCs were characterized by aCGH and FISH. Chromosomal origin of the marker chromosomes were successfully identified in seventeen of them. For the three cases with negative aCGH results, two of them were more likely due to that the sSMCs only contained centromere heterochromatin, whereas the reason for the remaining case with negative aCGH finding was uncertain. In order to establish a stronger genotype-phenotype correlation for clinical service in the future and avoid miss characterization, more sSMC cases were needed to be detailed characterized. This will help to clarify the variable clinical characteristics of sSMCs and provide additional information to aid clinical service and future research.
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Affiliation(s)
- Mingran Sun
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Department of Hematology and Oncology, Anshan Hospital, the First Hospital of China Medical University, Anshan City, Liaoning, 114000, China.,Key Laboratory for Molecular Enzymology and Engineering, College of Life Sciences, Jilin University, Changchun City, Jilin, 130012, China
| | - Han Zhang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Center for Reproductive Medicine, Center for Prenatal Diagnosis, the First Hospital of Jilin University, Changchun City, Jilin, 130021, China
| | - Guiying Li
- Key Laboratory for Molecular Enzymology and Engineering, College of Life Sciences, Jilin University, Changchun City, Jilin, 130012, China
| | - Carrie J Guy
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Xianfu Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Xianglan Lu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Fangchao Gong
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Department of Urology, the First Hospital of Jilin University, Changchun City, Jilin, 130000, China
| | - Jiyun Lee
- Department of Pathology, College of Medicine, Korea University, Seoul, 02841, Korea
| | - Susan Hassed
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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Ma R, Peng Y, Zhang Y, Xia Y, Tang G, Chang J, Guo R, Gui B, Huang Y, Chen C, Liang D, Wu L. Partial trisomy 2q33.3-q37.3 in a patient with an inverted duplicated neocentric marker chromosome. Mol Cytogenet 2015; 8:10. [PMID: 25774219 PMCID: PMC4359772 DOI: 10.1186/s13039-015-0111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/15/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Increasing number of cases with small supernumerary marker chromosomes (sSMCs) without centromeric DNA and dozens of cases with trisomy 2q3 have been reported in recent years. However, cases of simultaneous sSMC and partial trisomy of chromosome 2q have been rarely described. RESULTS We report the case of a young girl patient with growth retardation and mild facial features due to a partial trisomy 2q33.3-37.3. The 34.3 Mb-duplication of the 2q33.3 to q37.3 region found in the patient constituted a supernumerary inverted duplicated neocentric marker chromosome. CONCLUSIONS This is the first case of a patient with partial trisomy 2q33.3-37.3 presenting an inverted duplicated neocentric marker chromosome. Based on the case, this study will help further understanding the genotype/phenotype correlations of partial 2q3 duplication and exploring the relationship between neocentric sSMC and human diseases.
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Affiliation(s)
- Ruiyu Ma
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Ying Peng
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Yanghui Zhang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Yan Xia
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Guizhi Tang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Jiazhen Chang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Ruolan Guo
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Baoheng Gui
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Yanru Huang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Chen Chen
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
- />Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan P.R China
| | - Desheng Liang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Lingqian Wu
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
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Marle N, Martinet D, Aboura A, Joly-Helas G, Andrieux J, Flori E, Puechberty J, Vialard F, Sanlaville D, Fert Ferrer S, Bourrouillou G, Tabet AC, Quilichini B, Simon-Bouy B, Bazin A, Becker M, Stora H, Amblard S, Doco-Fenzy M, Molina Gomes D, Girard-Lemaire F, Cordier MP, Satre V, Schneider A, Lemeur N, Chambon P, Jacquemont S, Fellmann F, Vigouroux-Castera A, Molignier R, Delaye A, Pipiras E, Liquier A, Rousseau T, Mosca AL, Kremer V, Payet M, Rangon C, Mugneret F, Aho S, Faivre L, Callier P. Molecular characterization of 39 de novo sSMC: contribution to prognosis and genetic counselling, a prospective study. Clin Genet 2013; 85:233-44. [PMID: 23489061 DOI: 10.1111/cge.12138] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/05/2012] [Accepted: 03/05/2012] [Indexed: 11/27/2022]
Abstract
Small supernumerary marker chromosomes (sSMCs) are structurally abnormal chromosomes that cannot be characterized by karyotype. In many prenatal cases of de novo sSMC, the outcome of pregnancy is difficult to predict because the euchromatin content is unclear. This study aimed to determine the presence or absence of euchromatin material of 39 de novo prenatally ascertained sSMC by array-comparative genomic hybridization (array-CGH) or single nucleotide polymorphism (SNP) array. Cases were prospectively ascertained from the study of 65,000 prenatal samples [0.060%; 95% confidence interval (CI), 0.042-0.082]. Array-CGH showed that 22 markers were derived from non-acrocentric markers (56.4%) and 7 from acrocentic markers (18%). The 10 additional cases remained unidentified (25.6%), but 7 of 10 could be further identified using fluorescence in situ hybridization; 69% of de novo sSMC contained euchromatin material, 95.4% of which for non-acrocentric markers. Some sSMC containing euchromatin had a normal phenotype (31% for non-acrocentric and 75% for acrocentric markers). Statistical differences between normal and abnormal phenotypes were shown for the size of the euchromatin material (more or less than 1 Mb, p = 0.0006) and number of genes (more or less than 10, p = 0.0009). This study is the largest to date and shows the utility of array-CGH or SNP array in the detection and characterization of de novo sSMC in a prenatal context.
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Affiliation(s)
- N Marle
- Département de Génétique, Hôpital Le Bocage, Université de Bourgogne, Dijon, France
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4
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Rao KP, Belogolovkin V. Marker chromosomes. Fetal Pediatr Pathol 2013; 32:97-112. [PMID: 22587446 DOI: 10.3109/15513815.2012.681425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Kiran Prabhaker Rao
- Department of Obstetrics and Gynecology, University of South Florida College of Medicine, Tampa, FL 33606, USA
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Vetro A, Manolakos E, Petersen MB, Thomaidis L, Liehr T, Croci G, Franchi F, Marinelli M, Meneghelli E, Dal Bello B, Cesari S, Iasci A, Arrigo G, Zuffardi O. Unexpected results in the constitution of small supernumerary marker chromosomes. Eur J Med Genet 2012; 55:185-90. [PMID: 22342433 DOI: 10.1016/j.ejmg.2012.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/16/2012] [Indexed: 11/30/2022]
Abstract
Traditional approaches for the classification of Small Supernumerary Marker Chromosomes (sSMC), mostly based on FISH techniques, are time-consuming and not always sufficient to fully understand the true complexity of this class of rearrangements. We describe four supernumerary marker chromosomes that, after array-CGH, were interpreted rather differently in respect to the early classification made by conventional cytogenetics and FISH investigations, reporting two types of complex markers which DNA content was overlooked by conventional approaches: 1. the sSMC contains non-contiguous regions of the same chromosome and, 2. the sSMC, initially interpreted as a supernumerary del(15), turns out to be a derivative 15 to which the portion of another chromosome was attached. All are likely derived from partial trisomy rescue events, bringing further demonstration that germline chromosomal imbalances are submitted to intense reshuffling during the embryogenesis, leading to unexpected complexity and changing the present ideas on the composition of supernumerary marker chromosomes.
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6
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Yu S, Fiedler S, Brawner S, Joyce J, Zhou X, Liu H. Characterizing Small Supernumerary Marker Chromosomes with Combination of Multiple Techniques. Cytogenet Genome Res 2011; 136:6-14. [DOI: 10.1159/000334271] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2011] [Indexed: 01/24/2023] Open
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Chromosome 5 derived small supernumerary marker: towards a genotype/phenotype correlation of proximal chromosome 5 imbalances. J Appl Genet 2011; 52:193-200. [PMID: 21437654 DOI: 10.1007/s13353-011-0035-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 02/11/2011] [Accepted: 02/15/2011] [Indexed: 12/12/2022]
Abstract
Small supernumerary marker chromosomes (sSMC) are a morphological heterogeneous group of additional abnormal chromosomes that cannot be characterized alone by conventional banding cytogenetics. Molecular cytogenetic techniques are valuable tools for the accurate identification of sSMC and a prerequisite for sound genetic counseling based on refined genotype/phenotype correlation. We describe a new case of a retarded patient with an sSMC derived from chromosome 5. The characterization of the sSMC was done by subcentromere-specific multicolor (subcenM) fluorescence in-situ hybridization (FISH) and by full tilling resolution array analysis, after microdissection and amplification of the marker DNA. Uniparental disomy for normal sister chromosomes of the sSMC(5) was excluded. The karyotype was mos47,XX,+r(5)(::p11.1 → q12.1::)[70%]/46,XX[30%], being the trisomic region between 46.15 ∼ 49.56 Mb and 61.25 ∼ 61.335 Mb, a region known to harbor ∼45 annotated genes. Together with a review of the previously described cases of sSMC(5) and duplications involving the 5q proximal region, we can conclude that trisomy of the 5q11 region is associated with learning difficulties and speech delay.
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Liehr T, Wegner RD, Stumm M, Martin T, Gillessen-Kaesbach G, Kosyakova N, Ewers E, Hamid AB, von Eggeling F, Hentschel J, Ziegler M, Weise A. Small supernumerary marker chromosomes 1 with a normal phenotype. J Chin Med Assoc 2010; 73:205-7. [PMID: 20457442 DOI: 10.1016/s1726-4901(10)70042-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 02/09/2010] [Indexed: 10/19/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) are a major problem in prenatal cytogenetic diagnostics. Over two-thirds of cases carrying an sSMC derived from chromosome 1 are associated with clinical abnormalities. We report 3 further cases of such sSMCs that did not show any clinical abnormalities. All 3 sSMCs studied were detected prenatally and characterized comprehensively for their genetic content by molecular cytogenetics using subcentromere-specific multicolor fluorescence in situ hybridization, and for a possibly associated uniparental disomy. After exclusion of additional euchromatin due to the presence of sSMCs and a uniparental disomy, parents opted for continuation of the pregnancies and healthy children were born in all 3 cases. It is important to quickly and clearly characterize prenatal sSMCs. Also, all available sSMC cases need to be collected on a homepage such as the Jena Institute of Human Genetics and Anthropology sSMC homepage (http://www.med.uni-jena.de/fish/sSMC/00START.htm).
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Institute of Human Genetics and Anthropology, Germany.
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9
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Balkan M, Duran H, Budak T. Tetrasomy 18p in a male dysmorphic child in southeast Turkey. J Genet 2009; 88:337-40. [DOI: 10.1007/s12041-009-0049-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Liehr T, Ewers E, Kosyakova N, Klaschka V, Rietz F, Wagner R, Weise A. Handling small supernumerary marker chromosomes in prenatal diagnostics. Expert Rev Mol Diagn 2009; 9:317-24. [PMID: 19435454 DOI: 10.1586/erm.09.17] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Small supernumerary marker chromosomes (sSMCs) are structurally abnormal chromosomes that cannot be thoroughly characterized by conventional banding cytogenetics and are equal in size or smaller than chromosome 20. They are present in 0.075% of prenatal cases and, overall, approximately 3 million people worldwide are carriers of a sSMC. In prenatal cases with ultrasound abnormalities, sSMCs are found in up to approximately 0.2% of the cases. First described in 1961, it is now known that sSMCs have no phenotypic effects in approximately 70% of de novo cases. Nonetheless, in at least 30-50% of prenatally detected sSMC cases, the pregnancy is terminated; that is, for a certain percentage of potentially healthy children with a sSMC, an abortion is induced. This situation can only be improved by providing increased amounts of and more reliable information on sSMCs. This article provides an overview on current state-of-the-art technologies and how sSMC analysis can be optimized in prenatal diagnostics.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
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11
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Chan LW, Choy KW, Leung TY, Lau TK. Prenatal diagnosis by array-comparative genomic hybridization. ACTA ACUST UNITED AC 2009; 3:649-57. [DOI: 10.1517/17530050903222247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Tsuchiya KD, Opheim KE, Hannibal MC, Hing AV, Glass IA, Raff ML, Norwood T, Torchia BA. Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization. Mol Cytogenet 2008; 1:7. [PMID: 18471320 PMCID: PMC2375883 DOI: 10.1186/1755-8166-1-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 04/21/2008] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Supernumerary marker chromosomes (SMCs) are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s) involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients) that were characterized by microarray comparative genomic hybridization (array CGH). RESULTS In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. CONCLUSION The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation.
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Affiliation(s)
- Karen D Tsuchiya
- Department of Laboratories, Children's Hospital & Regional Medical Center, Seattle, WA, USA.
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Weise A, Mrasek K, Fickelscher I, Claussen U, Cheung SW, Cai WW, Liehr T, Kosyakova N. Molecular definition of high-resolution multicolor banding probes: first within the human DNA sequence anchored FISH banding probe set. J Histochem Cytochem 2008; 56:487-93. [PMID: 18256020 DOI: 10.1369/jhc.2008.950550] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) banding approaches are standard for the exact characterization of simple, complex, and even cryptic chromosomal aberrations within the human genome. The most frequently applied FISH banding technique is the multicolor banding approach, also abbreviated as m-band, MCB, or in its whole genomic variant multitude MCB (mMCB). MCB allows the differentiation of chromosome region-specific areas at the GTG band and sub-band level and is based on region-specific microdissection libraries, producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first bacterial artificial chromosome (BAC) array comparative genomic hybridization (aCGH) mapped, comprehensive, genome-wide human MCB probe set. All 169 region-specific microdissection libraries were characterized in detail for their size and the regions of overlap. In summary, the unique possibilities of the MCB technique to characterize chromosomal breakpoints in one FISH experiment are now complemented by the feature of being anchored within the human DNA sequence at the BAC level.
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Affiliation(s)
- Anja Weise
- Institute of Human Genetics and Anthropology, D-07740 Jena, Germany.
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Marshall OJ, Chueh AC, Wong LH, Choo KA. Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. Am J Hum Genet 2008; 82:261-82. [PMID: 18252209 PMCID: PMC2427194 DOI: 10.1016/j.ajhg.2007.11.009] [Citation(s) in RCA: 291] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 10/26/2007] [Accepted: 11/05/2007] [Indexed: 11/30/2022] Open
Abstract
Since the discovery of the first human neocentromere in 1993, these spontaneous, ectopic centromeres have been shown to be an astonishing example of epigenetic change within the genome. Recent research has focused on the role of neocentromeres in evolution and speciation, as well as in disease development and the understanding of the organization and epigenetic maintenance of the centromere. Here, we review recent progress in these areas of research and the significant insights gained.
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Affiliation(s)
- Owen J. Marshall
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Anderly C. Chueh
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Lee H. Wong
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - K.H. Andy Choo
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
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15
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Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues. Am J Hum Genet 2008; 82:398-410. [PMID: 18252220 DOI: 10.1016/j.ajhg.2007.10.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 10/05/2007] [Accepted: 10/18/2007] [Indexed: 11/22/2022] Open
Abstract
Supernumerary marker chromosomes (SMCs) are common, but their molecular content and mechanism of origin are often not precisely characterized. We analyzed all centromere regions to identify the junction between the unique chromosome arm and the pericentromeric repeats. A molecular-ruler clone panel for each chromosome arm was developed and used for the design of a custom oligonucleotide array. Of 27 nonsatellited SMCs analyzed by array comparative genomic hybridization (aCGH) and/or fluorescence in situ hybridization (FISH), seven (approximately 26%) were shown to be unique sequence negative. Of the 20 unique-sequence-positive SMCs, the average unique DNA content was approximately 6.5 Mb (range 0.3-22.2 Mb) and 33 known genes (range 0-149). Of the 14 informative nonacrocentric SMCs, five (approximately 36%) contained unique DNA from both the p and q arms, whereas nine (approximately 64%) contained unique DNA from only one arm. The latter cases are consistent with ring-chromosome formation by centromere misdivision, as first described by McClintock in maize. In one case, a r(4) containing approximately 4.4 Mb of unique DNA from 4p was also present in the proband's mother. However, FISH revealed a cryptic deletion in one chromosome 4 and reduced alpha satellite in the del(4) and r(4), indicating that the mother was a balanced ring and deletion carrier. Our data, and recent reports in the literature, suggest that this "McClintock mechanism" of small-ring formation might be the predominant mechanism of origin. Comprehensive analysis of SMCs by aCGH and FISH can distinguish unique-negative from unique-positive cases, determine the precise gene content, and provide information on mechanism of origin, inheritance, and recurrence risk.
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