Structural variation in subtelomeres

Methods in Molecular Biology

Volumn 838, Issue , 2012, Pages 137-149

  Rudd, M Katharine ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Array CGH; Chromosome; CNV; FISH; Polymorphism; Structural variation; Subtelomere

Indexed keywords

ARTICLE; CHEMISTRY; COPY NUMBER VARIATION; EVOLUTION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DUPLICATION; GENE REARRANGEMENT; GENE TRANSLOCATION; GENETICS; HUMAN; HUMAN GENOME; INTELLECTUAL IMPAIRMENT; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; TELOMERE;

BASE SEQUENCE; BIOLOGICAL EVOLUTION; DNA COPY NUMBER VARIATIONS; GENE DUPLICATION; GENE REARRANGEMENT; GENOME, HUMAN; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INTELLECTUAL DISABILITY; MOLECULAR SEQUENCE DATA; TELOMERE; TRANSLOCATION, GENETIC;

EID: 84856255614     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-507-7_6     Document Type: Article

References (42)

1. Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W., and Eichler, E. E. (2002) Recent segmental duplications in the human genome. Science 297, 1003-7. (Pubitemid 34856032)
2. Linardopoulou, E. V., Williams, E. M., Fan, Y., Friedman, C., Young, J. M., and Trask, B. J. (2005) Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437, 94-100. (Pubitemid 41613430)
3. Trask, B. J., Friedman, C., Martin-Gallardo, A., Rowen, L., Akinbami, C., Blankenship, J., Collins, C., Giorgi, D., Iadonato, S., Johnson, F., Kuo, W. L., Massa, H., Morrish, T., Naylor, S., Nguyen, O. T., Rouquier, S., Smith, T., Wong, D. J., Youngblom, J., and van den Engh, G. (1998) Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum Mol Genet 7, 13-26. (Pubitemid 28040733)
4. Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Cho, E. K., Dallaire, S., Freeman, J. L., Gonzalez, J. R., Gratacos, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J. R., Marshall, C. R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, L., Conrad, D. F., Estivill, X., Tyler-Smith, C., Carter, N. P., Aburatani, H., Lee, C., Jones, K. W., Scherer, S. W., and Hurles, M. E. (2006) Global variation in copy number in the human genome. Nature 444, 444-54. (Pubitemid 44809057)
5. 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 A 143, 1850-7. (Pubitemid 47206059)
6. 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, 566-73. (Pubitemid 47415265)
7. Ballif, B. C., Kashork, C. D., and Shaffer, L. G. (2000) The promise and pitfalls of telomere region-specific probes. Am J Hum Genet 67, 1356-9.
8. 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, 320-32. (Pubitemid 30618039)
9. Adeyinka, A., Adams, S. A., Lorentz, C. P., Van Dyke, D. L., and Jalal, S. M. (2005) Subtelomere deletions and translocations are frequently familial. Am J Med Genet A 135, 28-35. (Pubitemid 40627660)
10. Barber, J. C. (2005) Directly transmitted unbalanced chromosome abnormalities and euchromatic variants. J Med Genet 42, 609-29. (Pubitemid 41129033)
11. 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, 478-89. (Pubitemid 43927321)
12. Biesecker, L. G. (2002) The end of the beginning of chromosome ends. Am J Med Genet 107, 263-6. (Pubitemid 34062078)
13. 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) Identifi cation of chromosome abnormalities in subtelomeric regions by microarray analysis: a study of 5,380 cases. Am J Med Genet A 146A, 2242-51.
14. Willatt, L., Cox, J., Barber, J., Cabanas, E. D., Collins, A., Donnai, D., FitzPatrick, D. R., Maher, E., Martin, H., Parnau, J., Pindar, L., Ramsay, J., Shaw-Smith, C., Sistermans, E. A., Tettenborn, M., Trump, D., de Vries, B. B., Walker, K., and Raymond, F. L. (2005) 3q29 microdeletion syndrome: clinical and molecular characterization of a new syndrome. Am J Hum Genet 77, 154-60. (Pubitemid 40848047)
15. Lisi, E. C., Hamosh, A., Doheny, K. F., Squibb, E., Jackson, B., Galczynski, R., Thomas, G. H., and Batista, D. A. (2008) 3q29 interstitial microduplication: a new syndrome in a threegeneration family. Am J Med Genet A 146A, 601-9.
16. Harada, N., Visser, R., Dawson, A., Fukamachi, M., Iwakoshi, M., Okamoto, N., Kishino, T., Niikawa, N., and Matsumoto, N. (2004) A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome. J Hum Genet 49, 440-4. (Pubitemid 39243751)
17. Stewart, D. R., Huang, A., Faravelli, F., Anderlid, B. M., Medne, L., Ciprero, K., Kaur, M., Rossi, E., Tenconi, R., Nordenskjold, M., Gripp, K. W., Nicholson, L., Meschino, W. S., Capua, E., Quarrell, O. W., Flint, J., Irons, M., Giampietro, P. F., Schowalter, D. B., Zaleski, C. A., Malacarne, M., Zackai, E. H., Spinner, N. B., and Krantz, I. D. (2004) Subtelomeric deletions of chromosome 9q: a novel microdeletion syndrome. Am J Med Genet A 128A, 340-51. (Pubitemid 38988635)
18. Kleefstra, T., Brunner, H. G., Amiel, J., Oudakker, A. R., Nillesen, W. M., Magee, A., Genevieve, D., Cormier-Daire, V., van Esch, H., Fryns, J. P., Hamel, B. C., Sistermans, E. A., de Vries, B. B., and van Bokhoven, H. (2006) Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Am J Hum Genet 79, 370-7. (Pubitemid 44141836)
19. Phelan, M. C., Rogers, R. C., Saul, R. A., Stapleton, G. A., Sweet, K., McDermid, H., Shaw, S. R., Claytor, J., Willis, J., and Kelly, D. P. (2001) 22q13 deletion syndrome. Am J Med Genet 101, 91-9.
20. Wilson, H. L., Wong, A. C., Shaw, S. R., Tse, W. Y., Stapleton, G. A., Phelan, M. C., Hu, S., Marshall, J., and McDermid, H. E. (2003) Molecular characterisation of the 22q13 deletion syndrome supports the role of haploinsuffi ciency of SHANK3/PROSAP2 in the major neurological symptoms. J Med Genet 40, 575-84. (Pubitemid 37046910)
21. Durand, C. M., Betancur, C., Boeckers, T. M., Bockmann, J., Chaste, P., Fauchereau, F., Nygren, G., Rastam, M., Gillberg, I. C., Anckarsater, H., Sponheim, E., Goubran-Botros, H., Delorme, R., Chabane, N., Mouren-Simeoni, M. C., de Mas, P., Bieth, E., Roge, B., Heron, D., Burglen, L., Gillberg, C., Leboyer, M., and Bourgeron, T. (2007) Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are associated with autism spectrum disorders. Nat Genet 39, 25-7. (Pubitemid 46026497)
22. National Institutes of Health and Institute of Molecular Medicine Collaboration (1996) A complete set of human telomeric probes and their clinical application. Nat Genet 14, 86-9.
23. 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. (Pubitemid 27197238)
24. 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, 1676-81. (Pubitemid 29533057)
25. 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, 415-29.
26. Gajecka, M., Pavlicek, A., Glotzbach, C. D., Ballif, B. C., Jarmuz, M., Jurka, J., and Shaffer, L. G. (2006) Identifi cation of sequence motifs at the breakpoint junctions in three t(1;9) (p36.3;q34) and delineation of mechanisms involved in generating balanced translocations. Hum Genet 120, 519-26. (Pubitemid 44669785)
27. Gajecka, M., Gentles, A. J., Tsai, A., Chitayat, D., Mackay, K. L., Glotzbach, C. D., Lieber, M. R., and Shaffer, L. G. (2008) Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13). Genome Res 18, 1733-42.
28. Yatsenko, S. A., Brundage, E. K., Roney, E. K., Cheung, S. W., Chinault, A. C., and Lupski, J. R. (2009) Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum Mol Genet 18, 1924-36.
29. Monfouilloux, S., Avet-Loiseau, H., Amarger, V., Balazs, I., Pourcel, C., and Vergnaud, G. (1998) Recent human-specific spreading of a subtelomeric domain. Genomics 51, 165-76. (Pubitemid 28395021)
30. Martin, C. L., Wong, A., Gross, A., Chung, J., Fantes, J. A., and Ledbetter, D. H. (2002) The evolutionary origin of human subtelomeric homologies -or where the ends begin. Am J Hum Genet 70, 972-84. (Pubitemid 34259313)
31. Rudd, M. K., Friedman, C., Parghi, S. S., Linardopoulou, E. V., Hsu, L., and Trask, B. J. (2007) Elevated rates of sister chromatid exchange at chromosome ends. PLoS Genet 3, e32.
32. Rudd, M. K., Endicott, R. M., Friedman, C., Walker, M., Young, J. M., Osoegawa, K., de Jong, P. J., Green, E. D., and Trask, B. J. (2009) Comparative sequence analysis of primate subtelomeres originating from a chromosome fi ssion event. Genome Res 19, 33-41.
33. Itsara, A., Cooper, G. M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R. M., Myers, R. M., Ridker, P. M., Chasman, D. I., Mefford, H., Ying, P., Nickerson, D. A., and Eichler, E. E. (2009) Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 84, 148-61.
34. Wang, K., Chen, Z., Tadesse, M. G., Glessner, J., Grant, S. F., Hakonarson, H., Bucan, M., and Li, M. (2008) Modeling genetic inheritance of copy number variations. Nucleic Acids Res 36, e138.
35. Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S. F., Hakonarson, H., and Bucan, M. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17, 1665-74. (Pubitemid 350074862)
36. Baptista, J., Mercer, C., Prigmore, E., Gribble, S. M., Carter, N. P., Maloney, V., Thomas, N. S., Jacobs, P. A., and Crolla, J. A. (2008) Breakpoint mapping and array CGH in translocations: comparison of a phenotypically normal and an abnormal cohort. Am J Hum Genet 82, 927-36.
37. McClintock, B. (1941) The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics 26, 234-82.
38. Ballif, B. C., Yu, W., Shaw, C. A., Kashork, C. D., and Shaffer, L. G. (2003) Monosomy 1p36 breakpoint junctions suggest pre-meiotic breakage-fusion-bridge cycles are involved in generating terminal deletions. Hum Mol Genet 12, 2153-65. (Pubitemid 37098986)
39. Stetten, G., Charity, L. L., Kasch, L. M., Scott, A. F., Berman, C. L., Pressman, E., and Blakemore, K. J. (1997) A paternally derived inverted duplication of 7q with evidence of a telomeric deletion. Am J Med Genet 68, 76-81. (Pubitemid 27023846)
40. Jenderny, J., Poetsch, M., Hoeltzenbein, M., Friedrich, U., and Jauch, A. (1998) Detection of a concomitant distal deletion in an inverted duplication of chromosome 3. Is there an overall mechanism for the origin of such duplications/defi ciencies? Eur J Hum Genet 6, 439-44. (Pubitemid 28486338)
41. Bonaglia, M. C., Giorda, R., Poggi, G., Raggi, M. E., Rossi, E., Baroncini, A., Giglio, S., Borgatti, R., and Zuffardi, O. (2000) Inverted duplications are recurrent rearrangements always associated with a distal deletion: description of a new case involving 2q. Eur J Hum Genet 8, 597-603. (Pubitemid 30639366)
42. Cotter, P. D., Kaffe, S., Li, L., Gershin, I. F., and Hirschhorn, K. (2001) Loss of subtelomeric sequence associated with a terminal inversion duplication of the short arm of chromosome Am J Med Genet 102, 76-80. (Pubitemid 32623270)