Absence of heterozygosity due to template switching during replicative rearrangements

American Journal of Human Genetics

Volumn 96, Issue 4, 2015, Pages 555-564

  Carvalho, Claudia M B ^a,b   Pfundt, Rolph ^c   King, Daniel A ^d   Lindsay, Sarah J ^d   Zuccherato, Luciana W ^a   Macville, Merryn V E ^e   Liu, Pengfei ^a   Johnson, Diana ^f   Stankiewicz, Pawel ^a   Brown, Chester W ^a,g   Shaw, Chad A ^a   Hurles, Matthew E ^d   Ira, Grzegorz ^a   Hastings, P J ^a   Brunner, Han G ^c,e   Lupski, James R ^a,g  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b INSTITUTO OSWALDO CRUZ   (Brazil)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e MAASTRICHT UNIVERSITY MEDICAL CENTER   (Netherlands)

^f SHEFFIELD CHILDREN'S NHS FOUNDATION TRUST   (United Kingdom)

^g TEXAS CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHROMOSOME; CHROMOSOME ANALYSIS; CHROMOSOME INVERSION; COMPARATIVE GENOMIC HYBRIDIZATION; CONGENITAL DISORDER; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA REPLICATION; DNA TEMPLATE; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE REARRANGEMENT; HETEROZYGOSITY LOSS; HUMAN; MALE; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; SISTER CHROMATID; UNIPARENTAL DISOMY; BIOLOGICAL MODEL; DNA REPAIR; DNA SEQUENCE; GENETICS; NETHERLANDS; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; DNA COPY NUMBER VARIATIONS; DNA REPAIR; DNA REPLICATION; GENE REARRANGEMENT; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; LOSS OF HETEROZYGOSITY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NETHERLANDS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; UNIPARENTAL DISOMY;

EID: 84926246952     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.01.021     Document Type: Article

References (36)

1. E. Engel A new genetic concept: uniparental disomy and its potential effect, isodisomy Am. J. Med. Genet. 6 1980 137 143
2. J.E. Spence, R.G. Perciaccante, G.M. Greig, H.F. Willard, D.H. Ledbetter, J.F. Hejtmancik, M.S. Pollack, W.E. O'Brien, and A.L. Beaudet Uniparental disomy as a mechanism for human genetic disease Am. J. Hum. Genet. 42 1988 217 226
3. Y. Yang, D.M. Muzny, F. Xia, Z. Niu, R. Person, Y. Ding, P. Ward, A. Braxton, M. Wang, and C. Buhay Molecular findings among patients referred for clinical whole-exome sequencing JAMA 312 2014 1870 1879
4. C. Stern Somatic crossing over and segregation in Drosophila melanogaster Genetics 21 1936 625 730
5. C.E. Smith, B. Llorente, and L.S. Symington Template switching during break-induced replication Nature 447 2007 102 105
6. P.J. Hastings, G. Ira, and J.R. Lupski A microhomology-mediated break-induced replication model for the origin of human copy number variation PLoS Genet. 5 2009 e1000327
7. A. Fujita, H. Suzumura, M. Nakashima, Y. Tsurusaki, H. Saitsu, N. Harada, N. Matsumoto, and N. Miyake A unique case of de novo 5q33.3-q34 triplication with uniparental isodisomy of 5q34-qter Am. J. Med. Genet. A. 161A 2013 1904 1909
8. B. Rodríguez-Santiago, N. Malats, N. Rothman, L. Armengol, M. Garcia-Closas, M. Kogevinas, O. Villa, A. Hutchinson, J. Earl, and G. Marenne Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome Am. J. Hum. Genet. 87 2010 129 138
9. T. Sahoo, J.C. Wang, M.M. Elnaggar, P. Sanchez-Lara, L.P. Ross, L.W. Mahon, K. Hafezi, A. Deming, L. Hinman, and Y. Bruno Concurrent triplication and uniparental isodisomy: evidence for microhomology-mediated break-induced replication model for genomic rearrangements Eur. J. Hum. Genet. 23 2015 61 66
10. J. Wiszniewska, W. Bi, C. Shaw, P. Stankiewicz, S.H. Kang, A.N. Pursley, S. Lalani, P. Hixson, T. Gambin, and C.H. Tsai Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing Eur. J. Hum. Genet. 22 2014 79 87
11. P. Liu, C.M. Carvalho, P.J. Hastings, and J.R. Lupski Mechanisms for recurrent and complex human genomic rearrangements Curr. Opin. Genet. Dev. 22 2012 211 220
12. P. Liu, V. Gelowani, F. Zhang, V.E. Drory, S. Ben-Shachar, E. Roney, A.C. Medeiros, R.J. Moore, C. DiVincenzo, and W.B. Burnette Mechanism, prevalence, and more severe neuropathy phenotype of the Charcot-Marie-Tooth type 1A triplication Am. J. Hum. Genet. 94 2014 462 469
13. P. Liu, A. Erez, S.C. Nagamani, W. Bi, C.M. Carvalho, A.D. Simmons, J. Wiszniewska, P. Fang, P.A. Eng, and M.L. Cooper Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications Hum. Mol. Genet. 20 2011 1975 1988
14. C.M. Carvalho, M.B. Ramocki, D. Pehlivan, L.M. Franco, C. Gonzaga-Jauregui, P. Fang, A. McCall, E.K. Pivnick, S. Hines-Dowell, and L.H. Seaver Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome Nat. Genet. 43 2011 1074 1081
15. K. Shimojima, T. Mano, M. Kashiwagi, T. Tanabe, M. Sugawara, N. Okamoto, H. Arai, and T. Yamamoto Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region Eur. J. Med. Genet. 55 2012 400 403
16. S. Beri, M.C. Bonaglia, and R. Giorda Low-copy repeats at the human VIPR2 gene predispose to recurrent and nonrecurrent rearrangements Eur. J. Hum. Genet. 21 2013 757 761
17. C. Soler-Alfonso, C.M. Carvalho, J. Ge, E.K. Roney, P.I. Bader, K.E. Kolodziejska, R.M. Miller, J.R. Lupski, P. Stankiewicz, and S.W. Cheung CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a three-generation pedigree Eur. J. Hum. Genet. 22 2014 1071 1076
18. Y.Y. Teo, M. Inouye, K.S. Small, R. Gwilliam, P. Deloukas, D.P. Kwiatkowski, and T.G. Clark A genotype calling algorithm for the Illumina BeadArray platform Bioinformatics 23 2007 2741 2746
19. D.A. King, T.W. Fitzgerald, R. Miller, N. Canham, J. Clayton-Smith, D. Johnson, S. Mansour, F. Stewart, P. Vasudevan, M.E. Hurles DDD Study A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders Genome Res. 24 2014 673 687
20. J.M. Kidd, G.M. Cooper, W.F. Donahue, H.S. Hayden, N. Sampas, T. Graves, N. Hansen, B. Teague, C. Alkan, and F. Antonacci Mapping and sequencing of structural variation from eight human genomes Nature 453 2008 56 64
21. F. Zhang, M. Khajavi, A.M. Connolly, C.F. Towne, S.D. Batish, and J.R. Lupski The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans Nat. Genet. 41 2009 849 853
22. C.M. Carvalho, D. Pehlivan, M.B. Ramocki, P. Fang, B. Alleva, L.M. Franco, J.W. Belmont, P.J. Hastings, and J.R. Lupski Replicative mechanisms for CNV formation are error prone Nat. Genet. 45 2013 1319 1326
23. S.A. Hagstrom, and T.P. Dryja Mitotic recombination map of 13cen-13q14 derived from an investigation of loss of heterozygosity in retinoblastomas Proc. Natl. Acad. Sci. USA 96 1999 2952 2957
24. P.S. Lee, P.W. Greenwell, M. Dominska, M. Gawel, M. Hamilton, and T.D. Petes A fine-structure map of spontaneous mitotic crossovers in the yeast Saccharomyces cerevisiae PLoS Genet. 5 2009 e1000410
25. J.R. LaRocque, J.M. Stark, J. Oh, E. Bojilova, K. Yusa, K. Horie, J. Takeda, and M. Jasin Interhomolog recombination and loss of heterozygosity in wild-type and Bloom syndrome helicase (BLM)-deficient mammalian cells Proc. Natl. Acad. Sci. USA 108 2011 11971 11976
26. L. Costantino, S.K. Sotiriou, J.K. Rantala, S. Magin, E. Mladenov, T. Helleday, J.E. Haber, G. Iliakis, O.P. Kallioniemi, and T.D. Halazonetis Break-induced replication repair of damaged forks induces genomic duplications in human cells Science 343 2014 88 91
27. A.P. Davis, and L.S. Symington RAD51-dependent break-induced replication in yeast Mol. Cell. Biol. 24 2004 2344 2351
28. M.R. Lieber The mechanism of human nonhomologous DNA end joining J. Biol. Chem. 283 2008 1 5
29. A. Malkova, and G. Ira Break-induced replication: functions and molecular mechanism Curr. Opin. Genet. Dev. 23 2013 271 279
30. M.A. Wilson, Y. Kwon, Y. Xu, W.H. Chung, P. Chi, H. Niu, R. Mayle, X. Chen, A. Malkova, P. Sung, and G. Ira Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration Nature 502 2013 393 396
31. A. Deem, K. Barker, K. Vanhulle, B. Downing, A. Vayl, and A. Malkova Defective break-induced replication leads to half-crossovers in Saccharomyces cerevisiae Genetics 179 2008 1845 1860
32. P. Dittwald, T. Gambin, C. Gonzaga-Jauregui, C.M. Carvalho, J.R. Lupski, P. Stankiewicz, and A. Gambin Inverted low-copy repeats and genome instability - a genome-wide analysis Hum. Mutat. 34 2013 210 220
33. J.A. Lee, C.M. Carvalho, and J.R. Lupski A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders Cell 131 2007 1235 1247
34. A. Slack, P.C. Thornton, D.B. Magner, S.M. Rosenberg, and P.J. Hastings On the mechanism of gene amplification induced under stress in Escherichia coli PLoS Genet. 2 2006 e48
35. K. Mizuno, I. Miyabe, S.A. Schalbetter, A.M. Carr, and J.M. Murray Recombination-restarted replication makes inverted chromosome fusions at inverted repeats Nature 493 2013 246 249
36. A. Malkova, E.L. Ivanov, and J.E. Haber Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication Proc. Natl. Acad. Sci. USA 93 1996 7131 7136