Complex gene rearrangements caused by serial replication slippage

Human Mutation

Volumn 26, Issue 2, 2005, Pages 125-134

  Chen, Jian Min ^a,c   Chuzhanova, Nadia ^b   Stenson, Peter D ^b   Férec, Claude ^a   Cooper, David N ^b  

^a UNIVERSITÉ DE BRETAGNE OCCIDENTALE   (France)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c ETABLISSEMENT FRANÇAIS DU SANG   (France)

Author keywords

Complex gene rearrangements; Complexity; Deletion junctions; Double mutations; Indel; Mutational mechanism; Serial replication slippage

Indexed keywords

ARTICLE; CHROMOSOME REPLICATION; DNA SEQUENCE; F9 GENE; GENE; GENE CONVERSION; GENE DELETION; GENE DUPLICATION; GENE INSERTION; GENE MUTATION; GENE REARRANGEMENT; GENE REPLICATION; HUMAN; MECP2 GENE; MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REPLICATION SLIPPAGE;

EID: 22844446638     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20202     Document Type: Article

References (51)

1. Ahmed ZM, Smith TN, Riazuddin S, Makishima T, Ghosh M, Bokhari S, Menon PS, Deshmukh D, Griffith AJ, Riazuddin S, Friedman TB, Wilcox ER. 2002. Nonsyndromic recessive deafness DFNB18 and Usher syndrome type IC are allelic mutations of USHIC. Hum Genet 110:527-531.
2. Audrezet MP, Chen JM, Raguenes O, Chuzhanova N, Giteau K, Le Marechal C, Quere I, Cooper DN, Férec C. 2004. Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms. Hum Mutat 23:343-357.
3. Bacolla A, Jaworski A, Larson JE, Jakupciak JP, Chuzhanova N, Abeysinghe SS, O'Connell CD, Cooper DN, Wells RD. 2004. Breakpoints of gross deletions coincide with non-B DNA conformations. Proc Natl Acad Sci USA 101:14162-14167.
4. Bassi MT, Schiaffino MV, Renieri A, De Nigris F, Galli L, Bruttini M, Gebbia M, Bergen AA, Lewis RA, Ballabio A. 1995. Cloning of the gene for ocular albinism type 1 from the distal short arm of the X chromosome. Nat Genet 10:13-19.
5. Baysal BE, Willett-Brozick JE, Filho PA, Lawrence EC, Myers EN, Ferrell RE. 2004. An Alu-mediated partial SDHC deletion causes familial and sporadic paraganglioma. J Med Genet 41:703-709.
6. Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM. 2003. Mutations in SBDS are associated with Shwachman-Diamond syndrome. Nat Genet 33:97-101.
7. Buyse IM, Fang P, Hoon KT, Amir RE, Zoghbi HY, Roa BB. 2000. Diagnostic testing for Rett syndrome by DHPLC and direct sequencing analysis of the MECP2 gene: identification of several novel mutations and polymorphisms. Am J Hum Genet 67:1428-1436.
8. Chen JM, Férec C. 2003. Trypsinogen genes: evolution. In: Cooper DN, editor. Nature encyclopedia of the human genome. Vol. 5. London: Nature Publishing Group. p 645-650.
9. Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN. 2005a. Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum Mutat 25:207-221.
10. Chen JM, Stenson PD, Cooper DN, Férec C. 2005b. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet in press.
11. Chillon M, Casals T, Nunes V, Gimenez J, Estivill X. 1993. Identification of a 31-bp insertion (3860ins31) in exon 20 of the cystic fibrosis (CFTR) gene. Hum Mol Genet 2:1317-1318.
12. Chuzhanova NA, Anassis EJ, Ball EV, Krawczak M, Cooper DN. 2003. Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 21:28-44.
13. Cserhalmi-Friedman PB, Baden H, Burgeson RE, Christiano AM. 1998. Molecular basis of non-lethal junctional epidermolysis bullosa: identification of a 38 base pair insertion and a splice site mutation in exon 14 of the LAMB3 gene. Exp Dermatol 7: 105-111.
14. Cymerman U, Vera S, Pece-Barbara N, Bourdeau A, White RI Jr, Dunn J, Letarte M. 2000. Identification of hereditary hemorrhagic telangiectasia type 1 in newborns by protein expression and mutation analysis of endoglin. Pediatr Res 47:24-35.
15. De Bona C, Zappella M, Hayek G, Meloni I, Vitelli F, Bruttini M, Cusano R, Loffredo P, Longo I, Renieri A. 2000. Preserved speech variant is allelic of classic Rett syndrome. Eur J Hum Genet 8:325-330.
16. den Dunnen JT, Paalman MH. 2003. Standardizing mutation nomenclature: why bother? Hum Mutat 22:181-182.
17. Friedl W, Caspari R, Sengteller M, Uhlhaas S, Lamberti C, Jungck M, Kadmon M, Wolf M, Fahnenstich J, Gebert J, Moslein G, Mangold E, Propping P. 2001. Can APC mutation analysis contribute to therapeutic decisions in familial adenomatous polyposis? Experience from 680 FAP families. Gut 48:515-521.
18. Fukui T, Yamamoto S, Nakano K, Tsujikawa M, Morimura H, Nishida K, Ohguro N, Fujikado T, Irifune M, Kuniyoshi K, Okada AA, Hirakata A, Miyake Y, Tano Y. 2002. ABCA4 gene mutations in Japanese patients with Stargardt disease and retinitis pigmentosa. Invest Ophthalmol Vis Sci 43:2819-2824.
19. Gallou C, Chauveau D, Richard S, Joly D, Giraud S, Olschwang S, Martin N, Saquet C, Chretien Y, Mejean A, Correas JM, Benoit G, Colombeau P, Grunfeld JP, Junien C, Beroud C. 2004. Genotype-phenotype correlation in von Hippel-Lindau families with renal lesions. Hum Mutat 24:215-224.
20. Gismondi V, Bafico A, Biticchi R, Pedemonte S, Di Pietri S, Ponz de Leon M, Groden J, Varesco L. 1998. 310 basepair APC deletion with duplication of breakpoint (439ins15del310) in an Italian polyposis patient. Hum Mutat Suppl 1:S220-S222.
21. Gitomer WL, Reed BY, Ruml LA, Sakhaee K, Pak CY. 1998. Mutations in the genomic deoxyribonucleic acid for SLC3A1 in patients with cystinuria. J Clin Endocrinol Metab 83: 3688-3694.
22. Gusev VD, Nemytikova LA, Chuzhanova NA. 1999. On the complexity measures of genetic sequences. Bioinformatics 15: 994-999.
23. Hilal L, Rochat A, Duquesnoy P, Blanchet-Bardon C, Wechsler J, Martin N, Christiano AM, Barrandon Y, Uitto J, Goossens M, Hovnanian A. 1993. A homozygous insertion-deletion in the type VII collagen gene (COL7A1) in Hallopeau-Siemens dystrophic epidermolysis bullosa. Nat Genet 5:287-293.
24. Hori T, Tomatsu S, Nakashima Y, Uchiyama A, Fukuda S, Sukegawa K, Shimozawa N, Suzuki Y, Kondo N, Horiuchi T, Ogura S, Orii T. 1995. Mucopolysaccharidosis type IVA: common double deletion in the N-acetylgalactosamine-6-sulfatase gene (GALNS). Genomics 26:535-542.
25. Huopaniemi L, Tyynismaa H, Rantala A, Rosenberg T, Alitalo T. 2000. Characterization of two unusual RS1 gene deletions segregating in Danish retinoschisis families. Hum Mutat 16: 307-314.
26. Karsten SL, Lagerstedt K, Carlberg BM, Kleijer WJ, Zaremba J, Van Diggelen OP, Czartoryska B, Pettersson U, Bondeson ML. 1997. Two distinct deletions in the IDS gene and the gene W: a novel type of mutation associated with the Hunter syndrome. Genomics 43:123-129.
27. Ketterling RP, Vielhaber EL, Lind TJ, Thorland EC, Sommer SS. 1994. The rates and patterns of deletions in the human factor IX gene. Am J Hum Genet 54:201-213.
28. Kunkel TA. 1990. Misalignment-mediated DNA synthesis errors. Biochemistry 29:8003-8011.
29. Lee MH, Lu K, Hazard S, Yu H, Shulenin S, Hidaka H, Kojima H, Allikmets R, Sakuma N, Pegoraro R, Srivastava AK, Salen G, Dean M, Patel SB. 2001. Identification of a gene, ABCG5, important in the regulation of dietary cholesterol absorption. Nat Genet 27:79-83.
30. Lieber MR, Ma Y, Pannicke U, Schwarz K. 2003. Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol 4:712-720.
31. Lovett ST. 2004. Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Mol Microbiol 52:1243-1253.
32. Marlin S, Blanchard S, Slim R, Lacombe D, Denoyelle F, Alessandri JL, Calzolari E, Drouin-Garraud V, Ferraz FG, Fourmaintraux A, Philip N, Toublanc JE, Petit C. 1999. Townes-Brocks syndrome: detection of a SALL1 mutation hot spot and evidence for a position effect in one patient. Hum Mutat 14:377-386.
33. Morisawa T, Yagi M, Surono A, Yokoyama N, Ohmori M, Terashi H, Matsuo M. 2004. Novel double-deletion mutations of the OFD1 gene creating multiple novel transcripts. Hum Genet 115:97-103.
34. Niel F, Martin J, Dastot-Le Moal F, Costes B, Boissier B, Delattre V, Goossens M, Girodon E. 2004. Rapid detection of CFTR gene rearrangements impacts on genetic counselling in cystic fibrosis. J Med Genet 41:e118.
35. Regis S, Corsolini F, Stroppiano M, Cusano R, Filocamo M. 2002. Contribution of arylsulfatase A mutations located on the same allele to enzyme activity reduction and metachromatic leukodystrophy severity. Hum Genet 110:351-355.
36. Robertson SP, Twigg SR, Sutherland-Smith AJ, Biancalana V, Gorlin RJ, Horn D, Kenwrick SJ, Kim CA, Morava E, Newbury-Ecob R, Orstavik KH, Quarrell OW, Schwartz CE, Shears DJ, Suri M, Kendrick-Jones J, Wilkie AO, OPD-Spectrum Disorders Clinical Collaborative Group. 2003. Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans. Nat Genet 33:487-491.
37. Rohlfs EM, Chung CH, Yang Q, Skrzynia C, Grody WW, Graham ML, Silverman LM. 2000. In-frame deletions of BRCA1 may define critical functional domains. Hum Genet 107:385-390.
38. Roth DB, Chang XB, Wilson JH. 1989. Comparison of filler DNA at immune, nonimmune, and oncogenic rearrangements suggests multiple mechanisms of formation. Mol Cell Biol 9: 3049-3057.
39. Sillen A, Anton-Lamprecht I, Braun-Quentin C, Kraus CS, Sayli BS, Ayuso C, Jagell S, Kuster W, Wadelius C. 1998. Spectrum of mutations and sequence variants in the FALDH gene in patients with Sjögren-Larsson syndrome. Hum Mutat 12:377-384.
40. 0-thalassemia gene. Nuc Acids Res 10:8025-8029.
41. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN. 2003. Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21:577-581.
42. Strachan T, Read AP. 2004. Human molecular genetics 3. New York: John Wiley and Sons, Inc. p 333.
43. Strand M, Prolla TA, Liskay RM, Petes TD. 1993. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365: 274-276.
44. Streisinger G, Okada Y, Emrich J, Newton J, Tsugita A, Terzaghi E, Inouye M. 1966. Frameshift mutations and the genetic code. Cold Spring Harb Symp Quant Biol 31:77-84.
45. Su LK, Steinbach G, Sawyer JC, Hindi M, Ward PA, Lynch PM. 2000. Genomic rearrangements of the APC tumor-suppressor gene in familial adenomatous polyposis. Hum Genet 106: 101-107.
46. Tancredi M, Sensi E, Cipollini G, Aretini P, Lombardi G, Di Cristofano C, Presciuttini S, Bevilacqua G, Caligo MA. 2004. Haplotype analysis of BRCA1 gene reveals a new gene rearrangement: characterization of a 19.9 KBP deletion. Eur J Hum Genet 12:775-777.
47. Tavassoli K, Eigel A, Horst J. 1999. A deletion/insertion leading to the generation of a direct repeat as a result of slipped mispairing and intragenic recombination in the factor VIII gene. Hum Genet 104:435-437.
48. Tvrdik T, Marcus S, Hou SM, Falt S, Noori P, Podlutskaja N, Hanefeld F, Stromme P, Lambert B. 1998. Molecular characterization of two deletion events involving Alu-sequences, one novel base substitution and two tentative hotspot mutations in the hypoxanthine phosphoribosyltransferase (HPRT) gene in five patients with Lesch-Nyhan syndrome. Hum Genet 103: 311-318.
49. van Gent DC, Hoeijmakers JH, Kanaar R. 2001. Chromosomal stability and the DNA double-stranded break connection. Nat Rev Genet 2:196-206.
50. Weterings E, van Gent DC. 2004. The mechanism of non-homologous end-joining: a synopsis of synapsis. DNA Repair (Amst) 3:1425-1435.
51. Wojciechowska M, Bacolla A, Larson JE, Wells RD. 2005. The myotonic dystrophy type 1 triplet repeat sequence induces gross deletions and inversions. J Biol Chem 280:941-952.