Custom oligonucleotide array-based CGH: A reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes

European Journal of Human Genetics

Volumn 21, Issue 9, 2013, Pages 977-987

  Vasson, Aurélie ^a   Leroux, Céline ^a   Orhant, Lucie ^a   Boimard, Mathieu ^a   Toussaint, Aurélie ^a   Leroy, Chrystel ^a   Commere, Virginie ^a   Ghiotti, Tiffany ^a   Deburgrave, Nathalie ^a   Saillour, Yoann ^b   Atlan, Isabelle ^a   Fouveaut, Corinne ^a   Beldjord, Cherif ^a,b   Valleix, Sophie ^a,b   Leturcq, France ^a,b   Dodé, Catherine ^a,b   Bienvenu, Thierry ^a,b   Chelly, Jamel ^a,b   Cossée, Mireille ^a,b  

^a MONTPELLIER UNIVERSITY HOSPITAL   (France)

^b INSTITUT COCHIN   (France)

Author keywords

CGH array; CNMs; complex rearrangements; copy number mutations; oligonucleotide probes

Indexed keywords

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DIAGNOSTIC VALUE; EXON; FEMALE; GENE DELETION; GENE DUPLICATION; GENE REARRANGEMENT; GENETIC DISORDER; GENETIC HETEROGENEITY; HUMAN; MOLECULAR DIAGNOSIS; MOSAICISM; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE BASED COMPARATIVE GENOMIC HYBRIDIZATION ARRAY; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL;

CASE-CONTROL STUDIES; COMPARATIVE GENOMIC HYBRIDIZATION; CYSTIC FIBROSIS; DNA COPY NUMBER VARIATIONS; EXONS; FEMALE; GENE DUPLICATION; GENETIC COUNSELING; GENETIC TESTING; HEMOPHILIA A; HUMANS; KALLMANN SYNDROME; MALE; RETT SYNDROME; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 84882456841     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2012.279     Document Type: Article

References (35)

1. Quemener S, Chen JM, Chuzhanova N et al: Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci. Hum Mutat 2010; 31: 421-428.
2. Deburgrave N, Daoud F, Llense S et al: Protein- and mRNA-based phenotype-genotype correlations in DMD/BMD with point mutations and molecular basis for BMD with nonsense and frameshift mutations in the DMD gene. Hum Mutat 2007; 28: 183-195.
3. Tuffery-Giraud S, Beroud C, Leturcq F et al: Genotype-phenotype analysis in 2,405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase. Hum Mutat 2009; 30: 934-945.
4. Ferec C, Casals T, Chuzhanova N et al: Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms. Eur J Human Genet 2006; 14: 567-576.
5. Casilli F, Di Rocco ZC, Gad S et al: Rapid detection of novel BRCA1 rearrangements in high-risk breast-ovarian cancer families using multiplex PCR of short fluorescent fragments. Hum Mutat 2002; 20: 218-226.
6. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002; 30: e57.
7. White S, Kalf M, Liu Q et al: Comprehensive detection of genomic duplications and deletions in the DMD gene, by use of multiplex amplifiable probe hybridization. Am J Hum Genet 2002; 71: 365-374.
8. del Gaudio D, Yang Y, Boggs BA et al: Molecular diagnosis of Duchenne/Becker muscular dystrophy: enhanced detection of dystrophin gene rearrangements by oligonucleotide array-comparative genomic hybridization. Hum Mutat 2008; 29: 1100-1107.
9. Audrezet MP, Chen JM, Raguenes O et al: Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms. Hum Mutat 2004; 23: 343-357.
10. Hegde MR, Chin EL, Mulle JG, Okou DT, Warren ST, Zwick ME: Microarray-based mutation detection in the dystrophin gene. Hum Mutat 2008; 29: 1091-1099.
11. Vissers LE, Veltman JA, van Kessel AG, Brunner HG: Identification of disease genes by whole genome CGH arrays. Hum Mol Genet 2005; 14(Spec No. 2): R215-R223.
12. Bovolenta M, Neri M, Fini S et al: A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies. BMC Genomics 2008; 9: 572.
13. Saillour Y, Cossee M, Leturcq F et al: Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method. Hum Mutat 2008; 29: 1083-1090.
14. Wong LJ, Dimmock D, Geraghty MT et al: Utility of oligonucleotide array-based comparative genomic hybridization for detection of target gene deletions. Clin Chem 2008; 54: 1141-1148.
15. Staaf J, Torngren T, Rambech E et al: Detection and precise mapping of germline rearrangements in BRCA1, BRCA2, MSH2, and MLH1 using zoom-in array comparative genomic hybridization (aCGH). Hum Mutat 2008; 29: 555-564.
16. Piluso G, Dionisi M, Del Vecchio Blanco F et al: Motor chip: a comparative genomic hybridization microarray for copy-number mutations in 245 neuromuscular disorders. Clin Chem 2011; 57: 1584-1596.
17. Trabelsi M, Kavian N, Daoud F et al: Revised spectrum of mutations in sarcoglycanopathies. Eur J Human Genet 2008; 16: 793-803.
18. Manilal S, Recan D, Sewry CA et al: Mutations in Emery-Dreifuss muscular dystrophy and their effects on emerin protein expression. Hum Mol Genet 1998; 7: 855-864.
19. Vencesla A, Baena M, Garrido RP et al: F8 gene dosage defects in atypical patients with severe haemophilia A. Haemophilia 2012; 18: 708-713.
20. Van Esch H, Bauters M, Ignatius J et al: Duplication of the MECP2 region is a frequent cause of severe mental retardation and progressive neurological symptoms in males. Am J Hum Genet 2005; 77: 442-453.
21. Hardwick SA, Reuter K, Williamson SL et al: Delineation of large deletions of the MECP2 gene in Rett syndrome patients, including a familial case with a male proband. Eur J Human Genet 2007; 15: 1218-1229.
22. Nemos C, Lambert L, Giuliano F et al: Mutational spectrum of CDKL5 in early-onset encephalopathies: a study of a large collection of French patients and review of the literature. Clin Genet 2009; 76: 357-371.
23. Papa FT, Mencarelli MA, Caselli R et al: A 3 Mb deletion in 14q12 causes severe mental retardation, mild facial dysmorphisms and Rett-like features. Am J Med Genet A 2008; 146A: 1994-1998.
24. Ariani F, Hayek G, Rondinella D et al: FOXG1 is responsible for the congenital variant of Rett syndrome. Am J Hum Genet 2008; 83: 89-93.
25. Borg I, Freude K, Kubart S et al: Disruption of Netrin G1 by a balanced chromosome translocation in a girl with Rett syndrome. Eur J Human Genet 2005; 13: 921-927.
26. Shoichet SA, Duprez L, Hagens O et al: Truncation of the CNS-expressed JNK3 in a patient with a severe developmental epileptic encephalopathy. Hum Genet 2006; 118: 559-567.
27. Hammond LS, Macias MM, Tarleton JC, Shashidhar Pai G: Fragile X syndrome and deletions in FMR1: new case and review of the literature. Am J Med Genet 1997; 72: 430-434.
28. Sahoo T, Theisen A, Marble M et al: Microdeletion of Xq28 involving the AFF2 (FMR2) gene in two unrelated males with developmental delay. Am J Med Genet A 2011; 155A: 3110-3115.
29. Kato M, Das S, Petras K et al: Mutations of ARX are associated with striking pleiotropy and consistent genotype-phenotype correlation. Hum Mutat 2004; 23: 147-159.
30. Haverfield EV, Whited AJ, Petras KS, Dobyns WB, Das S: Intragenic deletions and duplications of the LIS1 and DCX genes: a major disease-causing mechanism in lissencephaly and subcortical band heterotopia. Eur J Human Genet 2009; 17: 911-918.
31. Lo Nigro C, Chong CS, Smith AC, Dobyns WB, Carrozzo R, Ledbetter DH: Point mutations and an intragenic deletion in LIS1, the lissencephaly causative gene in isolated lissencephaly sequence and Miller-Dieker syndrome. Hum Mol Genet 1997; 6: 157-164.
32. Dode C, Hardelin JP: Kallmann syndrome. Eur J Human Genet 2009; 17: 139-146.
33. Hardelin JP, Levilliers J, Young J et al: Xp22.3 deletions in isolated familial Kallmann's syndrome. J Clin Endocrinol Metab 1993; 76: 827-831.
34. Bassi MT, Schiaffino MV, Renieri A et al: Cloning of the gene for ocular albinism type 1 from the distal short arm of the X chromosome. Nat Genet 1995; 10: 13-19.
35. Ishmukhametova A, Van Kien PK, Mechin D et al: Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene. Eur J Human Genet 2012; 20: 1096-1100.