Using microarray-based molecular cytogenetic methods to identify chromosome abnormalities

Pediatric Annals

Volumn 38, Issue 8, 2009, Pages 440-447

  Shaffer, Lisa G ^a   Bejjani, Bassem A ^a  

^a PerkinElmer   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; OLIGONUCLEOTIDE;

BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; DOWN SYNDROME; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN; MICROARRAY ANALYSIS; REVIEW; ARTICLE; CHROMOSOME BANDING PATTERN; CHROMOSOME DELETION;

CHROMOSOME ABERRATIONS; CHROMOSOME BANDING; CHROMOSOME DELETION; IN SITU HYBRIDIZATION, FLUORESCENCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 70349769951     PISSN: 00904481     EISSN: None     Source Type: Journal    
DOI: 10.3928/00904481-20090723-08     Document Type: Review

References (53)

1. Tolarová MM, Cervenka J. Classifi cation and birth prevalence of orofacial clefts. Am J Med Genet. 1998;75(2):126-137. (Pubitemid 28034487)
2. Harris J, Robert E, Källén B. Epidemiology of choanal atresia with special reference to the CHARGE association. Pediatrics. 1997;99(3):363-367. (Pubitemid 27176006)
3. Källén B, Tornqvist K. The epidemiology of anophthalmia and microphthalmia in Sweden. Eur J Epidemiol. 2005;20(4):345-350.
4. Shevell M, Ashwal S, Donley D, et al. Practice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society. Neurology. 2003;60(3):367-380.
5. Xu J, Zwaigenbaum L, Szatmari P, Scherer SW. Molecular cytogenetics of autism. Curr Genomics. 2004;5:347-364.
6. Flint J, Wilkie AO, Buckle VJ, Winter RM, Holland AJ, McDermid HE. The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation. Nat Genet. 1995;9(2):132-140.
7. A complete set of human telomeric probes and their clinical application. National Institutes of Health and Institute of Molecular Medicine collaboration. Nat Genet. 1996;14(1):86-89.
8. Rodríguez L, Martinez-Fernández ML, Mansilla E, et al. Screening for subtelomeric chromosome alteration in a consecutive series of newborns with congenital defects. Clin Dysmorphol. 2008;17(1):5-12.
9. Ballif BC, Kashork CD, Shaffer LG. The promise and pitfalls of telomere region-specific probes. Am J Hum Genet. 2000;67(5):1356-1359.
10. Ravnan JB, Tepperberg JH, Papenhausen P, et al. 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. 2006;43(6):478-489.
11. Ballif BC, Sulpizio SG, Lloyd RM, et al. The clinical utility of enhanced subtelomeric coverage in array CGH. Am J Med Genet A. 2007;143A(16):1850-1857.
12. Shaffer LG, Bejjani BA, Torchia B, Kirkpatrick S, Coppinger J, Ballif BC. The identification of microdeletion syndromes and other chromosome abnormalities: Cytogenetic methods of the past, new technologies for the future. Am J Med Genet C Semin Med Genet. 2007;145C(4):335-345.
13. Shaffer LG, Beaudet AL, Brothman AR, et al; Working Group of the Laboratory Quality Assurance Committee of the American College of Medical Genetics. Microarray analysis for constitutional cytogenetic abnormalities. Genet Med. 2007;9(9):654-662.
14. de Vries BB, Pfundt R, Leisink M, et al. Diagnostic genome profi ling in mental retardation. Am J Hum Genet. 2005;77(4):606-616.
15. Friedman JM, Baross A, Delaney AD, et al. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 2006;79(3):500-513.
16. Thuresson AC, Bondeson ML, Edeby C, et al. Whole-genome array-CGH for detection of submicroscopic chromosomal imbalances in children with mental retardation. Cytogenet Genome Res. 2007;118(1):1-7.
17. Krepischi-Santos AC, Vianna-Morgante AM, Jehee FS, et al. Whole-genome array-CGH screening in undiagnosed syndromic patients: old syndromes revisited and new alterations. Cytogenet Genome Res. 2006;115(3-4):254-261.
18. Sharp AJ, Hansen S, Selzer RR, et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet. 2006;38(9):1038-1042.
19. Aston E, Whitby H, Maxwell T, et al. Comparison of targeted and whole genome analysis of postnatal specimens using a commercially available array based comparative genomic hybridisation (aCGH) microarray platform. J Med Genet. 2008;45(5):268-274.
20. Lu X, Shaw CA, Patel A, et al. Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS ONE. 2007;2(3):e327.
21. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet. 2004;36(9):949-951.
22. Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science. 2004;305(5683):525-528.
23. Mencarelli MA, Katzaki E, Papa FT, et al. Private inherited microdeletion/microduplications: implications in clinical practice. Eur J Med Genet. 2008;51(5):409-416.
24. Shaffer LG, Kashork CD, Saleki R, et al. Targeted genomic microarray analysis for identifi cation of chromosome abnormalities in 1500 consecutive clinical cases. J Pediatr. 2006;149(1):98-102.
25. Shevell MI, Bejjani BA, Srour M, Rorem EA, Hall N, Shaffer LG. Array comparative genomic hybridization in global developmental delay. Am J Med Genet B Neuropsychiatr Genet. 2008;147B(7):1101-1108.
26. Shaffer LG, Coppinger J, Alliman S, et al. Comparison of microarray-based detection rates for cytogenetic abnormalities in prenatal and neonatal specimens. Prenat Diagn. 2008;28(9):789-795.
27. Thorland EC, Gonzales PR, Gliem TJ, Wiktor AE, Ketterling RP. Comprehensive validation of array comparative genomic hybridization platforms: how much is enough? Genet Med. 2007;9(9):632-641.
28. Bejjani BA, Saleki R, Ballif BC, et al. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am J Med Genet A. 2005;134(3):259-267.
29. Ballif BC, Rorem EA, Sundin K, et al. Detection of low-level mosaicism by array CGH in routine diagnostic specimens. Am J Med Genet A. 2006;140(24):2757-2767.
30. Gribble SM, Prigmore E, Burford DC, et al. The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J Med Genet. 2005;42(1):8-16.
31. Baptista J, Mercer C, Prigmore E, et al. Breakpoint mapping and array CGH in translocations: comparison of a phenotypically normal and an abnormal cohort. Am J Hum Genet. 2008;82(4):927-936.
32. De Gregori M, Ciccone R, Magini P, et al. Cryptic deletions are a common finding in "balanced" reciprocal and complex chromosome rearrangements: a study of 59 patients. J Med Genet. 2007;44(12):750-762.
33. Sismani C, Kitsiou-Tzeli S, Ioannides M, et al. Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype. Mol Cytogenet. 2008;1(1):15.
34. Ballif BC, Hornor SA, Sulpizio SG, et al. Development of a high-density pericentromeric region BAC clone set for the detection and characterization of small supernumerary marker chromosomes by array CGH. Genet Med. 2007;9(3):150-162.
35. Ballif BC, Hornor SA, Jenkins E, et al. Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-p12.2. Nat Genet. 2007;39(9):1071-1073.
36. Shaffer LG, Theisen A, Bejjani BA, et al. The discovery of microdeletion syndromes in the post-genomic era: review of the methodology and characterization of a new 1q41q42 microdeletion syndrome. Genet Med. 2007;9(9):607-616.
37. Lybaek H, Øyen N, Fauske L, Houge G. A 2.1 Mb deletion adjacent but distal to a 14q21q23 paracentric inversion in a family with spherocytosis and severe learning difficulties. Clin Genet. 2008;74(6):553-559.
38. Mulatinho M, Llerena J, Leren TP, Rao PN, Quintero-Rivera F. Deletion (1)(p32.2-p32.3) detected by array-CGH in a patient with developmental delay/mental retardation, dysmorphic features and low cholesterol: A new microdeletion syndrome? Am J Med Genet A. 2008;146A(17):2284-2290.
39. Van Vooren S, Coessens B, De Moor B, Moreau Y, Vermeesch JR. Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes. Genet Med. 2007;9(9):642-649.
40. Vissers LE, de Vries BB, Osoegawa K, et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet. 2003;73(6):1261-1270.
41. Shaw-Smith C, Redon R, Rickman L, et al. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet. 2004;41(4):241-248.
42. Tyson C, Harvard C, Locker R, et al. Submicroscopic deletions and duplications in individuals with intellectual disability detected by array-CGH. Am J Med Genet A. 2005;139(3):173-185.
43. Rosenberg C, Knijnenburg J, Bakker E, et al. Array-CGH detection of micro rearrangements in mentally retarded individuals: clinical signifi cance of imbalances present both in affected children and normal parents. J Med Genet. 2006;43(2):180-186.
44. Menten B, Maas N, Thienpont B, et al. Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports. J Med Genet. 2006;43(8):625-633.
45. Miyake N, Shimokawa O, Harada N, et al. BAC array CGH reveals genomic aberrations in idiopathic mental retardation. Am J Med Genet A. 2006;140(3):205-211.
46. Engels H, Brockschmidt A, Hoischen A, et al. DNA microarray analysis identifi es candidate regions and genes in unexplained mental retardation. Neurology. 2007;68(10):743-750.
47. Hoyer J, Dreweke A, Becker C, et al. Molecular karyotyping in patients with mental retardation using 100K single-nucleotide polymorphism arrays. J Med Genet. 2007;44(10):629-636.
48. Baris HN, Tan WH, Kimonis VE, Irons MB. Diagnostic utility of array-based comparative genomic hybridization in a clinical setting. Am J Med Genet A. 2007;143A(21):2523-2533.
49. Aradhya S, Manning MA, Splendore A, Cherry AM. Whole-genome array-CGH identifi es novel contiguous gene deletions and duplications associated with developmental delay, mental retardation, and dysmorphic features. Am J Med Genet A. 2007;143A(13):1431-1441.
50. Shen Y, Irons M, Miller DT, et al. Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin Chem. 2007;53(12):2051-2059.
51. Baldwin EL, Lee JY, Blake DM, et al. Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet Med. 2008;10(6):415-429.
52. Monfort S, Rosello M, Orellana C, et al. Detection of known and novel genomic rearrangements by array based comparative genomic hybridization: deletion of ZNF533 and duplication of CHARGE syndrome genes. J Med Genet. 2008;45(7):432-437.
53. Pickering DL, Eudy JD, Olney AH, et al. Array-based comparative genomic hybridization analysis of 1176 consecutive clinical genetics investigations. Genet Med. 2008;10(4):262-266.