Molecular Cytogenetic Analysis of Telomere Rearrangements

Christa Lese Martin1, David H. Ledbetter1

1 Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 8.11
DOI:  10.1002/0471142905.hg0811s84
Online Posting Date:  January, 2015
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Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several methodologies that can be employed to study these unique regions of human chromosomes. It is a revision of the original version of the unit published in 2000, now including an introductory section describing advances in the discipline that have taken place since the original publication. © 2015 by John Wiley & Sons, Inc.

Keywords: telomere; copy number variants; chromosomal microarray

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Table of Contents

  • Introduction: Advances in the Field of Molecular Cytogenetic Analysis of Telomere Rearrangements Since 2000
  • Acknowledgements for the Revised Unit
  • Molecular Cytogenetic Analysis of Telomere Rearrangements (Original Version)
  • Telomere Structure and Function
  • Development of Unique Human Telomere Probes
  • Methods for Identifying Telomere Rearrangements
  • Clinical Applications/Future Research
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
  Aradhya, S., Manning, M.A., Splendore, A., and Cherry, A.M. 2007. Whole‐genome array‐CGH identifies novel contiguous gene deletions and duplications associated with developmental delay, mental retardation, and dysmorphic features. Am. J. Med. Genet. 143:1431‐1441.
  Altherr, M.R., Bengtsson, U., Elder, F.F.B., Ledbetter, D.H., Wasmuth, J.J., McDonald, M.E., Gusella, J.F., and Greenberg, F. 1991. Molecular confirmation of Wolf‐Hirschhorn syndrome with a subtle translocation of chromosome 4. Am. J. Hum. Genet. 49:1235‐1242.
  Baldwin, E.L., Lee, J.Y., Blake, D.M., Bunke, B.P., Alexander, C.R., Kogan, A.L., Ledbetter, D.H., and Martin, C.L. 2008. Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet. Med. 10:415‐429.
  Ballif, B.C., Sulpizio, S.G., Lloyd, R.M., Minier, S.L., Theisen, A., Bejjani, B.A., and Shaffer, L.G. 2007. The clinical utility of enhanced subtelomeric coverage in array CGH. Am. J. Med. Genet. 143:1850‐1857.
  Bass, H.W., Marshall, W.F., Sedat, J.W., Agard, D.A., and Cande, W.Z. 1997. Telomeres cluster de novo before the initiation of synapsis: A three‐dimensional spatial analysis of telomere positions before and during meiotic prophase. Cell Biol. 137:5‐18.
  Biesecker, L.G. 2002. The end of the beginning of chromosome ends. Am. J. Med. Genet. 107:263‐266.
  Blackburn, E.H. 1990. Telomeres: Structure and synthesis. J. Biol. Chem. 265:5919‐5921.
  Blouin, J.‐L., Christie, D.H., Gos, A., Lynn, A., Morris, M.A., Ledbetter, D.H., Chakravarti, A., and Antonarakis, S.E. 1995. A new dinucleotide repeat polymorphism at the telomere of chromosome 21q reveals a significant difference between male and female rates of recombination. Am. J. Hum. Genet. 57:388‐394.
  Brackley, K.J., Kilby, M.D., Morton, J., Whittle, M.J., Knight, S.J., and Flint, J. 1999. A case of recurrent congenital fetal anomalies associated with a familial subtelomeric translocation. Prenat. Diagn. 19:570‐574.
  Brkanac, Z., Cody, J.D., Leach, R.J., and DuPont, B.R. 1998. Identification of cryptic rearrangements in patients with 18q‐ deletion syndrome. Am. J. Hum. Genet. 62:1500‐1506.
  Brown, W.R., Dobson, M.J., and MacKinnon, P. 1990a. Telomere cloning and mammalian chromosome analysis. J. Cell Sci. 95:521‐526.
  Brown, W.R., MacKinnon, P.J., Villasante, A., Spurr, N., Buckle, V.J., and Dobson, M.J. 1990b. Structure and polymorphism of human telomere‐associated DNA. Cell 63:119‐132.
  Cross, S.H., Allshire, R.C., McKay, S.J., McGill, N.I., and Cooke, H.J. 1989. Cloning of human telomeres by complementation in yeast. Nature. 338:771‐774.
  Corpas, M., Bragin, E., Clayton, S., Bevan, P. and Firth, H. V. 2012. Interpretation of genomic copy number variants using DECIPHER. Curr. Protoc. Hum. Genet. 72:8.14.1‐8.14.17.
  Cross, S., Lindsey, J., Fantes, J., McKay, S., McGill, N., and Cooke, J. 1990. The structure of a subterminal repeated sequence present on many human chromosomes. Nucl. Acids Res. 18:6649‐6657.
  Delaney, A.D., Qian, H., Friedman, J.M. and Marra, M.A. 2008. Use of Affymetrix mapping arrays in the diagnosis of gene copy number variation. Curr. Protoc. Hum. Genet. 59:8.13.1‐8.13.16.
  DeVries, S., Gray, J.W., Pinkel, D., Waldman, F.M. and Sudar, D. 1995. Comparative genomic hybridization. Curr. Protoc. Hum. Genet. 6:4.6:4.6.1‐4.6.18.
  Donis‐Keller, H., Green, P., Helms, C., Cartinhour, S., Weiffenbach, B., et al. 1987. A genetic linkage map of the human genome. Cell 51:319‐337.
  du Manoir, S., Speicher, M.R., Joos, S., Schröck, E., Popp, S., et al. 1993. Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum. Genet. 90:590‐610.
  Eils, R., Uhrig, S., Saracoglu, K., Sätzler, K., Bolzer, A., Petersen, I., Charssery, J.‐M., Ganser, M., and Speicher, M.R. 1998. An optimized, fully automated system for fast and accurate identification of chromosomal rearrangements by multiplex‐FISH (M‐FISH). Cytogenet. Cell Genet. 82:160‐171.
  Flint, J., Wilkie, A.O., Buckle, V.J., Winter, R.M., Holland, A.J., and McDermid, H.E. 1995. The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation. Nature Genet. 9:132‐140.
  Flint, J., Rochette, J., Craddock, C.F., Dodem, C., Vignes, B., Horsley, S.W., Kearney, L., Buckle, V.J., Ayyub, H., and Higgs, D.R. 1996. Chromosomal stabilisation by a subtelomeric rearrangement involving two closely related Alu elements. Hum. Mol. Genet. 5:1163‐1169.
  Flint, J., Bates, G.P., Clark, K., Dorman, A., Willingham, D., Roe, B.A., Micklem, G., Higgs, D.R., and Louis, E.J. 1997a. Sequence comparison of human and yeast telomeres identifies structurally distinct subtelomeric domains. Hum. Mol. Genet. 6:1305‐1313.
  Flint, J., Thomas, K., Micklem, G., Raynham, H., Clark, K., Doggett, N.A., King, A., and Higgs, D.R. 1997b. The relationship between chromosome structure and function at a human telomeric region. Nature Genet. 15:252‐257.
  Heilstedt, H.A., Ballif, B.C., Howard, L.A., Lewis, R.A., Stal, S., Kashork, C.D., Bacino, C.A., Shapira, S.K., and Shaffer, L.G. 2003. Physical map of 1p36, placement of breakpoints in monosomy 1p36, and clinical characterization of the syndrome. Am. J. Hum. Genet. 72:1200‐1212.
  Horsley, S.W., Knight, S.J., Nixon, J., Huson, S., Fitchett, M., Boone, R.A., Hilton‐Jones, D., Flint, J., and Kearney, L. 1998. Del(18p) shown to be a cryptic translocation using a multiprobe FISH assay for subtelomeric chromosome rearrangements. J. Med. Genet. 35:722‐726.
  Jarcho, J. 2000. Restriction fragment length polymorphism analysis. Curr. Protoc. Hum. Genet. 1:2.7.1‐2.7.15.
  Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutovitz, D., Gray, J.W., Waldman, F., and Pinkel, D. 1992. Comparative genomic hybridization: A powerful new method for cytogenetic analysis of solid tumors. Science 258:818‐821.
  Kashork, C.D., Theisen, A. and Shaffer, L.G. 2010. Diagnosis of cryptic chromosomal syndromes by fluorescence in situ hybridization (FISH). Curr. Protoc. Hum. Genet. 67:8.10.1‐8.10.20.
  Knight, S.J., Horsley, S.W., Regan, R., Lawrie, N.M., Maher, E.J. Cardy, D.L., Flint, J., and Kearney, L. 1997. Development and clinical application of an innovative fluorescence in situ hybridization technique which detects submicroscopic rearrangements involving telomeres. Eur. J. Hum. Genet. 5:1‐8.
  Knight, S.J., Regan, R., Nicod, A., Horsley, S.W., Kearney, L., Homfray, T., Winter, R.M., Bolton, P., and Flint, J. 1999. Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet 354:1676‐1681.
  Knight, S.J., Lese, C.M., Precht, K.S., Kuc, J., Ning, Y., Lucas, S., Regan, R., Brenan, M., Nicod, A., Lawrie, N.M., Cardy, D.L., Nguyen, H., Hudson, T.J., Riethman, H.C., Ledbetter, D.H., and Flint, J. 2000. An optimized set of human telomere clones for studying telomere integrity and architecture. Am. J. Hum. Genet. 67:320‐332.
  Knoll, J. H. M. and Lichter, P. 2005. In situ hybridization to metaphase chromosomes and interphase nuclei. Curr. Protoc. Hum. Genet. 45:4.3.1‐4.3.31.
  Kuwano, A., Ledbetter, S.A., Dobyns, W.B., Emanuel, B.S., and Ledbetter, D.H. 1991. Detection of deletions and cryptic translocations in Miller‐Dieker syndrome by in situ hybridization. Am. J. Hum. Genet. 49:707‐714.
  Lahn, B.T., Ma, N., Breg, W.R., Stratton, R., Surti, U., and Page, D.C. 1994. Xq‐Yq interchange resulting in supernormal X‐linked gene expression in severely retarded males with 46, XYq‐karyotype. Nature Genet. 8:243‐250.
  Lamb, J., Harris, P.C., Lindenbaum, R.H., Reeders, S.T., Wilkie, A.O.M., Buckle, V.J., and Barton, N.J. 1989. Detection of breakpoints in submicroscopic chromosomal translocation, illustrating an important mechanism for genetic disease. Lancet 2:819‐824.
  Ledbetter, D.H. 1992. Cryptic translocations and telomere integrity. Am. J. Hum. Genet. 51:451‐456.
  Ledbetter, D.H. and Martin, C.L. 2007. Cryptic telomere imbalance: a 15‐year update. Am. J. Med. Genet. 145:327‐334.
  Lee, C., Rens, W., and Yang, F. 2000. Multicolor fluorescence in situ hybridization (FISH) approaches for simultaneous analysis of the entire human genome. Curr. Protoc. Hum. Genet. 24:4.9.1‐4.9.11.
  Lese, C.M., Fantes, J.A., Riethman, H.C., and Ledbetter, D.H. 1999. Characterization of physical gap sizes at human telomeres. Genome Res. 9:888‐894.
  Macina, R.A., Negorev, D.G., Spais, C., Ruthig, L.A., Hu, X.L., and Riethman, H.C. 1994. Sequence organization of the human chromosome 2q telomere. Hum. Mol. Genet. 3:1847‐1853.
  Manning, M., Hudgins, L., and Professional Practice and Guidelines Committee. 2010. Array‐based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet. Med. 12:742‐745.
  Martin, C.L., Nawaz, Z., Baldwin, E.L., Wallace, E.J., Justice, A.N., and Ledbetter, D.H. 2007. The evolution of molecular ruler analysis for characterizing telomere imbalances: from fluorescence in situ hybridization to array comparative genomic hybridization. Genet. Med. 9:566‐573.
  Meyne, J., Ratliff, R.L., and Moyzis, R.K. 1989. Conservation of the human telomere sequence (TTAGGG)n among vertebrates. Proc. Natl. Acad. Sci. U.S.A. 86:7049‐7053.
  Miller, D.T., Adam, M., Aradhya, S., Biesecker, L., Brothman, A., Carter, N.P., Church, D.M., Crolla, J.A., Eichler, E.E., Epstein, C.J., Faucett, W.A., Feuk, L., Friedman, J.M., Hamosh, A., Jackson, L., Kaminsky, E.B., Kok, K., Krantz, I.D., Kuhn, R.M., Lee, C., Ostell, J.M., Rosenberg, C., Scherer, S.W., Spinner, N.B., Stavropoulos, D.J., Tepperberg, J.H., Thorland, E.C., Vermeesch, J.R., Waggoner, D.J., Watson, M.S., Martin, C.L., and Ledbetter, D.H. 2010. Consensus statement: Chromosomal microarray is a first‐tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Genet. 586:749‐764.
  Miller, D. T., Shen, Y. and Wu, B.‐L. 2012. Oligonucleotide microarrays for clinical diagnosis of copy number variation and zygosity status. Curr. Protoc. Hum. Genet. 74:8.12:8.12.1‐8.12.17.
  Moyzis, R.K., Buckingham, J.M., Cram, L.S., Dani, M., Deaven, L.L., Jones, M.D., Meyne, J., Ratliff, R.L., and Wu, J.R. 1988. A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc. Natl. Acad. Sci. U.S.A. 85:6622‐6626.
  National Institutes of Health and Institute of Molecular Medicine Collaboration. 1996. A complete set of human telomeric probes and their clinical application. Nature Genet. 14:86‐89.
  Ning, Y., Rosenberg, M., Biesecker, L.G., and Ledbetter, D.H. 1996. Isolation of the human chromosome 22q telomere and its application to detection of cryptic chromosomal abnormalities. Hum. Genet. 97:765‐769.
  Overhauser, J., Bengtsson, U., McMahon, J., Ulm, J., Butler, M.G., Santiago, L., and Wasmuth, J.J. 1989. Prenatal diagnosis and carrier detection of a cryptic translocation by using DNA markers from the short arm of chromosome 5. Am. J. Hum. Genet. 45:296‐303.
  Penny, L.A., Dell'Aquila, M., Jones, M.C., Bergoffen, J., Cunniff, C., Fryns, J.‐P., Grace, E., Graham, J.M., Kousseff, B., Mattina, T., et al. 1995. Clinical and molecular characterization of patients with distal 11q deletions. Am. J. Hum. Genet. 56:676‐683.
  Phelan, M.C., Thomas, G.R., Saul, R.A., Rogers, R.C., Taylor, H.A., Wenger, D.A., and McDermid, H.E. 1992. Cytogenetic, biochemical, and molecular analyses of a 22q13 deletion. Am. J. Med. Genet. 43:872‐876.
  Phelan, M.C., Rogers, R.C., Clarkson, K.B., Bowyer, F.P., Levine, M.A., Estabrooks, L.L., Severson, M.C., and Dobyns, W.B. 1995. Albright Hereditary Osteodystrophy and del(2)(q37.3) in four unrelated individuals. Am. J. Med. Genet. 58:1‐7.
  Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.‐L., Chen, C., Zhai, et al. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet. 20:207‐211.
  Pollack, J.R., Perou, C.M., Alizadeh, A.A., Eisen, M.B., Pergamenschikov, A., Wiliams, C.F., Jeffrey, S.S., Botstein, D., and Brown, P.O. 1999. Genome‐wide analysis of DNA copy‐number changes using cDNA microarrays. Nature Genet. 23:41‐46.
  Precht, K.S., Lese, C.M., Spiro, R.P., Huttenlocher, P.R., Johnston, K.M., Baker, J.C., Christian, S.L., Kittikamron, K., and Ledbetter, D.H. 1998. Two 22q telomere deletions serendipitously detected by FISH. J. Med. Genet. 35:939‐942.
  Ravnan, J.B., Tepperberg, J.H., Papenhausen, P., Lamb, A.N., Hedrick, J., Eash, D., Ledbetter, D.H., and Martin, C.L. 2006. Subtelomere FISH analysis of 11,688 cases: An evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. J. Med. Genet. 43:478‐489.
  Riegel, M., Castellan, C., Balmer, D., Brecevic, L., and Schinzel, A. 1999. Terminal deletion, del(1)(p36.3), detected through screening for terminal deletions in patients with unclassified malformation syndromes. Am. J. Med. Genet. 82:249‐253.
  Riethman, H. 1997. Closing in on telomeric closure. Genome Res. 7:853‐855.
  Riethman, H.C., Moyzis, R.K., Meyne, J., Burke, D.T., and Olson, M.V. 1989. Cloning human telomeric DNA fragments into Saccharomyces cerevesiae using a yeast artificial chromosome vector. Proc. Natl. Acad. Sci. U.S.A. 86:6240‐6244.
  Rouyer, F., Simmler, M.‐C., Page, D.C., and Weissenbach, J. 1987. A sex chromosome rearrangement in a human XX male caused by Alu‐Alu recombination. Cell 51:417‐425.
  Rouyer, F., de la Chapelle, A., Andersson, M., and Weissenbach, J. 1990. An interspersed repeated sequence specific for human subtelomeric regions. EMBO J. 9:505‐514.
  Saccone, S., De Sario, A., Valle, Della G., and Bernardi, G. 1992. The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc. Natl. Acad. Sci., U.S.A. 89:4913‐4917.
  Scherthan, H., Weich, S., Schwegler, H., Heyting, C., and Harle, M. 1996. Centromere and telomere movements during early meiotic prophase of mouse and man are associated with the onset of chromosome pairing. Cell Biol. 134:1109‐1125.
  Shao, L., Shaw, C.A., Lu, X.Y., Sahoo, T., Bacino, C.A., Lalani, S.R., Stankiewicz, P., Yatsenko, S.A., Li, Y., Neill, S., Pursley, A.N., Chinault, A.C., Patel, A., Beaudet, A.L., Lupski, J.R., and Cheung, S.W. 2008. Identification of chromosome abnormalities in subtelomeric regions by microarray analysis: A study of 5,380 cases. Am. J. Med. Genet. 146:2242‐2251.
  Schreck, R.R. and Distèche, C.M. 1994. Chromosome banding techniques. Curr. Protoc. Hum. Genet. 00:4.2:4.2.1‐4.2.36.
  Schröck, E., du Manoir, S., Veldman, T., Schoell, B., Wienberg, J., Ferguson‐Smith, M.A., Ning, Y., Ledbetter, D.H., Bar‐Am, I., Soenksen, D., Garini, Y., and Ried, T. 1996. Multicolor spectral karyotyping of human chromosomes. Science 273:494‐497.
  Shapira, S.K., McCaskill, C., Northrup, H., Spikes, A.S., Elder, F.F., et al. 1997. Chromosome 1p36 deletions: The clinical phenotype and molecular characterization of a common newly delineated syndrome. Am. J. Hum. Genet. 61:642‐650.
  Solinas‐Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, J., Benner, A., Döhner, H., Cremer, T., and Lichter, P. 1997. Matrix‐based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chrom. Cancer 20:399‐407.
  South, S.T., Lee, C., Lamb, A.N., Higgins, A.W., and Kearney, H.M. 2013. ACMG standards and guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: Revision 2013. Genet. Med. 15:901‐909.
  Speed, R.M. 1988. The possible role of meiotic pairing anomalies in the atresia of human fetal oocytes. Hum. Genet. 78:260‐266.
  Speicher, M.R., Gwyn, Ballard S., and Ward, D.C. 1996. Karyotyping human chromosomes by combinatorial multi‐fluor FISH. Nature Genet. 12:368‐375.
  Weil, D., Wang, I., Dietrich, A., Poustka, A., Weissenbach, J., and Petit, C. 1994. Highly homologous loci on the X and Y chromosomes are hot‐spots for ectopic recombinations leading to XX maleness. Nature Genet. 7:414‐419.
  Wilkie, A.O., Higgs, D.R., Rack, K.A., Buckle, V.J., Spurr, N.K., Fischel‐Ghodsian, N., Ceccherini, I., Brown, W.R., and Harris, P.C. 1991. Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16. Cell 64:595‐606.
  Wilson, L.C., Leverton, K., Oude, Luttikhuis M.E., Oley, C.A., Flint, J., Wolstenholme, J., Duckett, D.P., Barrow, M.A., Leonard, J.V., Read, A.P., et al. 1995. Brachydactyly and mental retardation: An Albright hereditary osteodystrophy‐like syndrome localized to 2q37. Am. J. Hum. Genet. 56:400‐407.
  Wintle, R.F., Nygaard, T.G., Herbrick, J.A., Kvaloy, K., and Cox, D.W. 1997. Genetic polymorphism and recombination in the subtelomeric region of chromosome 14q. Genomics 40:409‐414.
  Wong, A.C., Ning, Y., Flint, J., Clark, K., Dumanski, J.P., Ledbetter, D.H., and McDermid, H.E. 1997. Molecular characterization of a 130‐kb terminal microdeletion at 22q in a child with mild mental retardation. Am. J. Hum. Genet. 60:113‐120.
  Wu, Y.‐Q., Heilstedt, H.S., Bedell, J.A., May, K.M., Starkey, D.E., McPherson, J.D., Shapira, S.K., and Shaffer, L.G. 1999. Molecular refinement of the 1p36 deletion syndrome reveals size diversity and a preponderance of maternally derived deletions. Hum. Mol. Genet. 8:313‐321.
  Youngman, S., Bates, G.P., Williams, S., McClatchey, A.I., Baxendale, S., et al. 1992. The telomeric 60 kb of chromosome 4p is homologous to telomeric regions on 13p, 15p, 21p, and 22p. Genomics 14:350‐356.
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