Copy number variations in the NF1 gene region are infrequent and do not predispose to recurrent type-1 deletions

European Journal of Human Genetics

Volumn 16, Issue 5, 2008, Pages 572-580

  Steinmann, Katharina ^a   Kluwe, Lan ^b   Cooper, David N ^c   Brems, Hilde ^d   De Raedt, Thomas ^d   Legius, Eric ^d   Mautner, Viktor Felix ^b   Kehrer Sawatzki, Hildegard ^a  

^a UNIVERSITY OF ULM   (Germany)

^b UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^c CARDIFF UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

NEUROFIBROMIN;

ADULT; ARTICLE; CARCINOGENESIS; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; FEMALE; GENE AMPLIFICATION; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENE REARRANGEMENT; GENETIC PREDISPOSITION; GENETIC VARIABILITY; HUMAN; MALE; MUTAGENESIS; NEUROFIBROMATOSIS; PRIORITY JOURNAL; VERTICAL TRANSMISSION;

ADULT; CHROMOSOMES, HUMAN; FEMALE; GENE DELETION; GENE DOSAGE; GENE DUPLICATION; GENES, NEUROFIBROMATOSIS 1; HUMANS; INHERITANCE PATTERNS; MALE; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PARENTS; VARIATION (GENETICS);

EID: 42649085379     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5202002     Document Type: Article

References (57)

1. Eichler EE: Widening the spectrum of human genetic variation. Nat Genet 2006; 38: 9-11.
2. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet 2006; 7: 85-97.
3. Freeman JL, PerryNGH, Feuk L et al: Copy number variation: new insights in genome diversity. Genome Res 2006; 16: 949-961.
4. Shianna KVI Willard HF: Human genomics: in search of normality. Nature 2006; 444: 428-429.
5. Beckmann JS, Estivill X, Antonarakis SE: Copy number variants and genetic traits: Closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 2007; 8: 639-646.
6. Kehrer-Sawatzki H: What a difference copy number variation makes. BioEssays 2007; 29: 311-313.
7. Shelling AN, Ferguson LR: Genetic variation in human disease and a new role for copy number variants. Mutat Res 2007; 622: 33-41
8. Iafrate AJ, Feuk L, Rivera MN et al: Detection of large-scale variation in the human genome. Nat Genet 2004; 36: 949-951.
9. Sebat J, Lakshmi B, Troge J et al: Large-scale copy number polymorphism in the human genome. Science 2004; 305: 525-528.
10. Sharp AJ, Locke DP, McGrath SD et al: Segmental duplications and copy number variation in the human genome. Am J Hum Genet 2005; 77: 78-88.
11. Goidts V, Cooper DN, Armengol L et al: Complex Patterns of copy number variation at sites of segmental duplications: An important category of structural variation in the human genome. Hum Gene 2006; 120: 270-284.
12. Fiegler H, Redon R, Andrews D: Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res 2006; 16: 1566-1574.
13. Khaja R, Zhang J, Macdonald JR et al: Genome assembly comparison identifies structural variants in the human genome. Nat Genet 2006; 38: 1413-1418.
14. Redon R, Ishikawa S, Fitch KR et al: Global variation in copy number in the human genome. Nature 2006; 444: 444-454.
15. Wong KK, Deleeuw Rj, Dosanjh NS et al: A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 2007; 80: 91-104.
16. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK: A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 2006; 38: 75-81.
17. Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA: Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 2006; 38: 82-85.
18. McCarroll SA, Hadnott TN, Perry GH, et al, The International HapMap Consortium: Common deletion polymorphisms in the human genome. Nat Genet 2006; 38: 86-92.
19. Smith AJ, Tsalenko A, Sampas N et al: Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: Implications for association studies of complex diseases. Hum Mol Genet 2007; 16: 2783-2794.
20. Zogopoulos G, Ha KC, Naqib F et al: Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet 2007; 122: 345-353.
21. Tuzun E, Sharp AJ, Bailey JA et al: Fine-scale structural variation of the human genome. Nat Genet 2005; 37: 727-732.
22. Cnossen MH, van der Est MN, Breuning MH et al: Deletions spanning the neurofibromatosis type 1 gene: Implications for genotype-phenotype correlations in neurofibromatosis type 1? Hum Mutat 1997; 9: 458-464.
23. Rasmussen SA, Colman SD, Ho VT et al: Constitutional and mosaic large NF1 gene deletions in neurofibromatosis type 1. J Med Genet 1998; 35: 468-471.
24. Kluwe L, Siebert R, Gesk S et al: Screening of 500 unselected neurofibromatosis 1 patients for deletions of the NF1 gene. Hum Mutat 2004; 23: 111-116.
25. Dorschner MO, Sybert VP, Weaver M, Pletcher BA, Stephens K: NF1 microdeletion breakpoints are clustered at flanking repetitive sequences. Hum Mol Genet 2000; 9: 35-46.
26. Jenne DE, Tinschert S, Reimann H et al: Molecular characterization and gene content of breakpoint boundaries in patients with neurofibromatosis type 1 with 17q11.2 microdeletions. Am J Hum Genet 2001; 69: 516-527.
27. López-Correa C, Dorschner M, Brems H et al: Recombination hotspot in NF1 microdeletion patients. Hum Mol Genet 2001; 10: 1387-1392.
28. Jenne DE, Tinschert S, Dorschner MO, Hameister H, Stephens K, Kehrer-Sawatzki H: Complete physical map and gene content of the human NF1 tumor suppressor region in human and mouse. Genes Chromosomes Cancer 2003; 37: 111-120.
29. De Raedt T, Brems H, Lopez-Correa C, Vermeesch JR, Marynen P, Legius E: Genomic organization and evolution of the NF1 microdeletion region. Genomics 2004; 84: 346-360.
30. Forbes SH, Dorschner MO, Le R, Stephens K: Genomic context of paralogous recombination hotspots mediating recurrent NF1 region microdeletion. Genes Chromosomes Cancer 2004; 41: 12-25.
31. De Raedt T, Stephens M, Heyns I: Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet 2006; 38: 1419-1423.
32. Petek E, Jenne DE, Smolle J et al: Mitotic recombination mediated by the JJAZF1 (KIAA0160) gene causing somatic mosaicism and a new type of constitutional NF1 microdeletion in two children of a mosaic female with only few manifestations. J Med Genet 2003; 40: 520-525.
33. Kehrer-Sawatzki H, Kluwe L, Sandig C et al: High frequency of mosaicism among patients with neurofibromatosis type 1 (NF1) with microdeletions caused by somatic recombination of the JJAZ1 gene. Am J Hum Genet 2004; 75: 410-423.
34. Steinmann K, Cooper DN, Kluwe L et al: Type-2 NF1 deletions are highly unusual by virtue of the absence of non-allelic homologous recombination hotspots and an apparent preference for female mitotic recombination. Am J Hum Genet 2007; 81: 1201-1220.
35. Kehrer-Sawatzki H, Kluwe L, Funsterer C, Mautner VF: Extensively high load of internal tumors determined by whole body MRI scanning in a patient with neurofibromatosis type 1 and a non-LCR-mediated 2-Mb deletion in 17q11.2. Hum Genet 2005; 116: 466-475.
36. Kehrer-Sawatzki H, Schmid E, Fünsterer C, Kluwe L, Mautner VF: Absence of cutaneous neurofibromas in an NF1 patient with an atypical deletion partially overlapping the classical 1.4 Mb microdeleted region. Am J Med Genet 2007, (in press).
37. Mantripragada KK, Thuresson AC, Piotrowski A et al: Identification of novel deletion breakpoints bordered by segmental duplications in the NF1 locus using high resolution array-CGH. J Med Genet 2006; 43 28-38.
38. Lander ES, Linton LM, Birren B, et al, International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921.
39. López-Correa C, Brems H, Lazaro C, Marynen P, Legius E: Unequal meiotic crossover: A frequent cause of NF1 microdeletions. Am J Hum Genet 2000; 66: 1969-1974.
40. Wimmer K, Yao S, Claes K et al: Spectrum of single- and multiexon NF1 copy number changes in a cohort of 1100 unselected NF1 patients. Genes Chromosomes Cancer 2006; 45: 265-276.
41. Kehrer-Sawatzki H, Tinschert S, Jenne DE: Heterogeneity of breakpoints in non-LCR-mediated large constitutional deletions of the 17q11.2 NF1 tumour suppressor region. J Med Genet 2003; 40: E116.
42. Inoue K, Lupski JR: Molecular mechanisms for genomic disorders. Annu Rev Genomics Hum Genet 2002; 3: 199-242.
43. Stankiewicz PG Inoue K, Bi W et al: Genomic disorders: genome architecture results in susceptibility to DNA rearrangements causing common human traits. Cold Spring Harb Symp Quant Biol 2003; 68 445-454.
44. Stankiewicz P, Lupski JR: Genome architecture, rearrangements and genomic disorders. Trends Genet 2002; 18: 74-82.
45. Lupski JR: Hotspots of homologous recombination in tNe human genome: not all homologous sequences are equal. Genome Biol 2004; 5: 242.
46. Shaw CJ, Lupski JR: Implications of human genome architecture for rearrangement-based disorders: The genomic basis of disease. Hum Mol Genet 2004; 13 (Spec no 1): R57-R64.
47. Lupski JR, StMnkiewicz P: Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 2005; 1: E49.
48. Amos-Landgraf JM, Ji Y, Gottlieb W et al: Chromosome breakage in the Prader-Willi and Angelman syndromes involves recombination between large, transcribed repeats at proximal and distal breakpoints. Am J Hum Genet 1999; 65: 370-386.
49. Shaikh TH, Kurahashi H, Saitta SC et al: Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: Genomic organization and deletion endpoint analysis. Hum Mol Genet 2000; 9: 489-501.
50. Park SS, Stankiewicz P, Bi W et al: Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs. Genome Res 2002; 12: 729-738.
51. Antonell A, de Luis O, Domingo-Roura X, Perez-Jurado LA: Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23. Genome Res 2005; 15: 1179-1188.
52. Kurotaki N, Stankiewicz P, Wakui K, Niikawa N, Lupski JR: Sotos syndrome common deletion is mediated by directly oriented subunits within inverted Sos-REP low-copy repeats. Hum Mol Genet 2005; 14: 535-542.
53. Samonte RV, Eichler EE: Segmental duplications and the evolution of the primate genome. Nat Rev Genet 2002; 3: 65-72.
54. Osborne LR, Li M, Pober B et al: A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nat Genet 2001; 29: 321-325.
55. Gimelli G, Pujana MA, Patricelli MG et al: Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet 2003; 12: 849-858.
56. Visser R, Shimokawa O, Harada N et al: Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. Am J Hum Genet 2005; 76: 52-67.
57. Barber JC, Cross IE, Douglas F, Nicholson JC, Moore KJ, Browne CE: Neurofibromatosis pseudogene amplification underlies euchromatic cytogenetic duplications and triplications of proximal 15q. Hum Genet 1998; 103: 600-607.