Design and validation of a pericentromeric BAC clone set aimed at improving diagnosis and phenotype prediction of supernumerary marker chromosomes

Molecular Cytogenetics

Palma Finelli⁵  Lidia Larizza²  Maria Teresa Bonati³  Daniela Giardino⁴  Pietro Cavalli⁷  Enrico Grosso⁶  Donatella Milani⁹  Lucia Ballarati⁴  Daniela Rusconi⁴  Silvana Guerneri¹  Maria Cristina Amione⁶  Lorenza Romitti⁸  Sara Tedoldi⁷  Milena Crippa⁴  Emanuele Valtorta⁴  Chiara Castronovo⁴ 

[1] Laboratorio di Genetica Medica, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122, Milano, Italy;Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, via Antonio di Rudinì 8, 20142, Milano, Italy;Ambulatorio di Genetica Medica, Ospedale San Luca, IRCCS Istituto Auxologico Italiano, piazzale Brescia 20, 20149, Milano, Italy;Laboratorio di Citogenetica Medica e Genetica Molecolare, IRCCS Istituto Auxologico Italiano, via Ariosto 13, 20145, Milano, Italy;Dipartmento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Viotti 3/5, 20133, Milano, Italy;S.C.D.U. Genetica Medica, A.O.S. Giovanni Battista, corso Bramante 88, 10126, Torino, Italy;Servizio di Genetica, A.O. Istituti Ospitalieri, viale Concordia 1, 26100, Cremona, Italy;S.C. Anatomia, Istologia Patologica e Citogenetica, Ospedale Niguarda Ca’ Granda, piazza dell’Ospedale Maggiore 3, 20162, Milano, Italy;Clinica Pediatrica 1, Dipartmento di Patofisiologia e Trapianti, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122, Milano, Italy

关键词: Phenotype prediction;    Array CGH analysis;    FISH analysis;    Heterochromatin/euchromatin boundary;    Pericentromeric clone set;    Small supernumerary marker chromosomes;   

Others  :  1150768
DOI  :  10.1186/1755-8166-6-45

 received in 2013-08-08, accepted in 2013-10-08,  发布年份 2013

【 摘 要 】

Background

Small supernumerary marker chromosomes (sSMCs) are additional, structurally abnormal chromosomes, generally smaller than chromosome 20 of the same metaphase spread. Due to their small size, they are difficult to characterize by conventional cytogenetics alone. In regard to their clinical effects, sSMCs are a heterogeneous group: in particular, sSMCs containing pericentromeric euchromatin are likely to be associated with abnormal outcomes, although exceptions have been reported. To improve characterization of the genetic content of sSMCs, several approaches might be applied based on different molecular and molecular-cytogenetic assays, e.g., fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (array CGH), and multiplex ligation-dependent probe amplification (MLPA).

To provide a complementary tool for the characterization of sSMCs, we constructed and validated a new, FISH-based, pericentromeric Bacterial Artificial Chromosome (BAC) clone set that with a high resolution spans the most proximal euchromatic sequences of all human chromosome arms, excluding the acrocentric short arms.

Results

By FISH analysis, we assayed 561 pericentromeric BAC probes and excluded 75 that showed a wrong chromosomal localization. The remaining 486 probes were used to establish 43 BAC-based pericentromeric panels. Each panel consists of a core, which with a high resolution covers the most proximal euchromatic ~0.7 Mb (on average) of each chromosome arm and generally bridges the heterochromatin/euchromatin junction, as well as clones located proximally and distally to the core. The pericentromeric clone set was subsequently validated by the characterization of 19 sSMCs. Using the core probes, we could rapidly distinguish between heterochromatic (1/19) and euchromatic (11/19) sSMCs, and estimate the euchromatic DNA content, which ranged from approximately 0.13 to more than 10 Mb. The characterization was not completed for seven sSMCs due to a lack of information about the covered region in the reference sequence (1/19) or sample insufficiency (6/19).

Conclusions

Our results demonstrate that this pericentromeric clone set is useful as an alternative tool for sSMC characterization, primarily in cases of very small SMCs that contain either heterochromatin exclusively or a tiny amount of euchromatic sequence, and also in cases of low-level or cryptic mosaicism. The resulting data will foster knowledge of human proximal euchromatic regions involved in chromosomal imbalances, thereby improving genotype–phenotype correlations.

【 授权许可】

   
2013 Castronovo et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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【 参考文献 】

• [1]Liehr T, Claussen U, Starke H: Small supernumerary marker chromosomes (sSMC) in humans. Cytogenet Genome Res 2004, 107:55-67.
• [2]Battaglia A: The inv dup (15) or idic (15) syndrome (tetrasomy 15q). Orphanet J Rare Dis 2008, 3:30. BioMed Central Full Text
• [3]Liehr T, Mrasek K, Weise A, Dufke A, Rodríguez L, Martínez Guardia N, Sanchís A, Vermeesch JR, Ramel C, Polityko A, Haas OA, Anderson J, Claussen U, von Eggeling F, Starke H: Small supernumerary marker chromosomes-progress towards a genotype-phenotype correlation. Cytogenet Genome Res 2006, 112:23-34.
• [4]Liehr T: Small supernumerary marker chromosomes (sSMC). Institute of Human Genetics and Anthropology, University of Jena; http://www.med.uni-jena.de/fish/sSMC/00START.htm webcite. Accessed 08/08/2013
• [5]Liehr T: Basics and literature on multicolor fluorescence in situ hybridization application. http://www.fish.uniklinikum-jena.de/mFISH.html webcite
• [6]Speicher MR, Gwyn Ballard S, Ward DC: Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 1996, 12:368-375.
• [7]Schröck E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, Garini Y, Ried T: Multicolor spectral karyotyping of human chromosomes. Science 1996, 273:494-497.
• [8]Nietzel A, Rocchi M, Starke H, Heller A, Fiedler W, Wlodarska I, Loncarevic IF, Beensen V, Claussen U, Liehr T: A new multicolor-FISH approach for the characterization of marker chromosomes: centromere-specific multicolor-FISH (cenM-FISH). Hum Genet 2001, 108:199-204.
• [9]Starke H, Nietzel A, Weise A, Heller A, Mrasek K, Belitz B, Kelbova C, Volleth M, Albrecht B, Mitulla B, Trappe R, Bartels I, Adolph S, Dufke A, Singer S, Stumm M, Wegner RD, Seidel J, Schmidt A, Kuechler A, Schreyer I, Claussen U, von Eggeling F, Liehr T: Small supernumerary marker chromosomes (SMCs): genotype-phenotype correlation and classification. Hum Genet 2003, 114:51-67.
• [10]Liehr T, Starke H, Heller A, Kosyakova N, Mrasek K, Gross M, Karst C, Steinhaeuser U, Hunstig F, Fickelscher I, Kuechler A, Trifonov V, Romanenko SA, Weise A: Multicolor fluorescence in situ hybridization (FISH) applied to FISH-banding. Cytogenet Genome Res 2006, 114:240-244.
• [11]Engelen JJ, Albrechts JC, Hamers GJ, Geraedts JP: A simple and efficient method for microdissection and microFISH. J Med Genet 1998, 35:265-268.
• [12]Liehr T, Heller A, Starke H, Rubtsov N, Trifonov V, Mrasek K, Weise A, Kuechler A, Claussen U: Microdissection based high resolution multicolour banding for all 24 human chromosomes. Int J Mol Med 2002, 9:335-339.
• [13]Hamid AB, Kreskowski K, Weise A, Kosayakova N, Mrasek K, Voigt M, Santos Guilherme R, Wagner R, Hardekopf D, Pekova S, Karamysheva T, Liehr T, Klein E: How to narrow down chromosomal breakpoints in small and large derivative chromosomes – a new probe set. J Appl Genetics 2012, 53:259-269.
• [14]Baldwin EL, May LF, Justice AN, Martin CL, Ledbetter DH: Mechanisms and consequences of small supernumerary marker chromosomes: from barbara McClintock to modern genetic-counselling issues. Am J Hum Genet 2008, 82:398-410.
• [15]Ballif BC, Rorem EA, Sundin K, Lincicum M, Gaskin S, Coppinger J, Kashork CD, Shaffer LG, Bejjani BA: Detection of low-level mosaicism by array CGH in routine diagnostic specimens. Am J Med Genet A 2006, 140:2757-2767.
• [16]Ballif BC, Hornor SA, Sulpizio SG, Lloyd RM, Minier SL, Rorem EA, Theisen A, Bejjani BA, Shaffer LG: Development of a high-density pericentromeric region BAC clone set for the detection and characterization of small supernumerary marker chromosomes by array CGH. Genet Med 2007, 9:150-162.
• [17]Sheth F, Andrieux J, Ewers E, Kosyakova N, Weise A, Sheth H, Romana SP, LeLorc’h M, Delobel B, Theisen O, Liehr T, Nampoothiri S, Sheth J: Characterization of sSMC by FISH and molecular techniques. Eur J Med Genet 2011, 54:247-255.
• [18]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, 55:185-190.
• [19]Reddy KS, Aradhya S, Meck J, Tiller G, Abboy S, Bass H: A systematic analysis of small supernumerary marker chromosomes using array CGH exposes unexpected complexity. Genet Med 2013, 15:3-13.
• [20]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 A, Quilichini B, Simon-Bouy B, Bazin A, Becker M, Stora H, Amblard S, Doco-Fenzy M, Molina Gomes D, Girard-Lemaire F, Cordier M, Satre V, Schneider A, Lemeur N, Chambon P, Jacquemont S, Fellmann F, Vigouroux-Castera A, Molignier R, et al.: Molecular characterization of 39 de novo sSMC: contribution to prognosis and genetic counseling, a prospective study. Clin Genet 2013. 10.1111/cge.12138. [Epub ahead of print]
• [21]Bui TH, Vetro A, Zuffardi O, Shaffer LG: Current controversies in prenatal diagnosis 3: is conventional chromosome analysis necessary in the post-array CGH era? Prenat Diagn 2011, 31:235-243.
• [22]Manolakos E, Kefalas K, Neroutsou R, Lagou M, Kosyakova N, Ewers E, Ziegler M, Weise A, Tsoplou P, Rapti SM, Papoulidis I, Anastasakis E, Garas A, Sotiriou S, Eleftheriades M, Peitsidis P, Malathrakis D, Thomaidis L, Kitsos G, Orru S, Liehr T, Petersen MB, Kitsiou-Tzeli S: Characterization of 23 small supernumerary marker chromosomes detected at pre-natal diagnosis: the value of fluorescence in situ hybridization. Mol Med Rep 2010, 3:1015-1022.
• [23]Van Opstal D, Boter M, Noomen P, Srebniak M, Hamers G, Galjaard RJ: Multiplex ligation dependent probe amplification (MLPA) for rapid distinction between unique sequence positive and negative marker chromosomes in prenatal diagnosis. Mol Cytogenet 2011, 4:2. BioMed Central Full Text
• [24]She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE: The structure and evolution of centromeric transition regions within the human genome. Nature 2004, 430:857-864.
• [25]Lengauer C, Green ED, Cremer T: Fluorescence in situ hybridization of YAC clones after Alu-PCR amplification. Genomics 1992, 13:826-828.
• [26]Liehr T, Heller A, Starke H, Claussen U: FISH banding methods: applications in research and diagnostics. Exp Rev Mol Diagn 2002, 2:217-225.
• [27]Weise A, Starke H, Heller A, Tönnies H, Volleth M, Stumm M, Senger G, Nietzel A, Claussen U, Liehr T: Chromosome 2 aberrations in clinical cases characterised by high resolution multicolour banding and region specific FISH probes. J Med Genet 2002, 39:434-439.
• [28]Manvelyan M, Schreyer I, Höls-Herpertz I, Köhler S, Niemann R, Hehr U, Belitz B, Bartels I, Götz J, Huhle D, Kossakiewicz M, Tittelbach H, Neubauer S, Polityko A, Mazauric ML, Wegner R, Stumm M, Küpferling P, Süss F, Kunze H, Weise A, Liehr T, Mrasek K: Forty-eight new cases with infertility due to balanced chromosomal rearrangements: detailed molecular cytogenetic analysis of the 90 involved breakpoints. Int J Mol Med 2007, 19:855-864.
• [29]Liehr T, Karamysheva T, Merkas M, Brecevic L, Hamid AB, Ewers E, Mrasek K, Kosyakova N, Weise A: Somatic mosaicism in cases with small supernumerary marker chromosomes. Curr Genomics 2010, 11:432-439.
• [30]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, 56:487-493.
• [31]Christian SL, Fantes JA, Mewborn SK, Huang B, Ledbetter DH: Large genomic duplicons map to sites of instability in the prader-willi/angelman syndrome chromosome region (15q11-q13). Hum Mol Genet 1999, 8:1025-1037.
• [32]Torres-Juan L, Rosell J, Sanchez-de-la-Torre M, Fibla J, Heine-Suñer D: Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications. BMC Med Genet 2007, 8:14.
• [33]Li P, Pomianowski P, DiMaio MS, Florio JR, Rossi MR, Xiang B, Xu F, Yang H, Geng Q, Xie J, Mahoney MJ: Genomic characterization of prenatally detected chromosomal structural abnormalities using oligonucleotide array comparative genomic hybridization. Am J Med Genet A 2011, 155:1605-1615.
• [34]Slavin TP, Kuruvilla K, Curtis CA, Christ LA, Mitchell AL: Isolated skeletal malformations in a child with a small mosaic ring microduplication of 18 p11.21q11.2: Genotype-phenotype correlations. Am J Med Genet A 2011, 155:618-621.
• [35]Giardino D, Bettio D, Gottardi G, Rizzi N, Pierluigi M, Perfumo C, Calì A, Dagna Bricarelli F, Larizza L: FISH characterization of two supernumerary r(1) associated with distinct clinical phenotypes. Am J Med Genet 1999, 84:3770-3780.
• [36]Kosztolányi G, Brecevic L, Bajnòczky K, Schinzel A, Riegel M: Mosaic supernumerary ring chromosome 1 in a three-generational family: 10-year follow-up report. Eur J Med Genet 2011, 54:152-156.
• [37]Liehr T, Nietzel A, Starke H, Heller A, Weise A, Kuechler A, Senger G, Ebner S, Martin T, Stumm M, Wegner R, Tönnies H, Hoppe C, Claussen U, Von Eggeling F: Characterization of small marker chromosomes (SMC) by recently developed molecular cytogenetic approaches. J Ass Genet Techn 2003, 29:5-10.
• [38]Tönnies H, Hennies HC, Spohr HL, Neitzel H: Characterization of the first supernumerary tricentric ring chromosome 1 mosaicism by conventional and molecular cytogenetic techniques. Cytogenet Genome Res 2003, 103:28-33.
• [39]Rodriguez L, Starke H, Guardia NM, Tönnies H, Neitzel H, Kozlowski P, Mazauric ML, Heller A, Grondona FL, Mansilla E, Santos Muñoz MJ, Liehr T, Martínez-Frías ML: Three new cases with a supernumerary ring chromosome 1. Clin Dysmorphol 2005, 14:169-175.
• [40]Liehr T, Stumm M, Wegner RD, Bhatt S, Hickmann P, Patsalis PC, Meins M, Morlot S, Klaschka V, Ewers E, Hinreiner S, Mrasek K, Kosyakova N, Cai WW, Cheung SW, Weise A: 10p11.2 to 10q11.2 is a yet unreported region leading to unbalanced chromosomal abnormalities without phenotypic consequences. Cytogenet Genome Res 2009, 124:102-105.
• [41]Lichter P, Tang Ghang CJ, Call K, Hermanson G, Evans GA, Housman D, Ward DC: High resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 1990, 247:64-69.
• [42]Lichter P, Cremer T: Chromosome analysis by non-isotopic in situ hybridization. In Human cytogenetics. A practical approach. Edited by Rooney DE, Czepulkowski BH. Oxford: IRL Press at Oxford University Press; 1992:157-192.