Detection and calibration of microdeletions and microduplications by array-based comparative genomic hybridization and its applicability to clinical genetic testing

Genetics in Medicine

Volumn 7, Issue 4, 2005, Pages 264-271

  Wong, Andrew ^a   Martin, Christa Lese ^a   Heretis, Konstantina ^a   Ruffalo, Teresa ^b   Wilber, Kim ^b   King, Walter ^b   Ledbetter, David H ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ABBOTT LABORATORIES   (United States)

Author keywords

Array based CGH; FISH; Molecular cytogenetics; Molecular rulers; Telomere

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; CALIBRATION; CHROMOSOME 10Q; CHROMOSOME 16P; CHROMOSOME 17P; CHROMOSOME 1P; CHROMOSOME 22Q; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME REARRANGEMENT; COMPARATIVE GENOMIC HYBRIDIZATION; DNA PROBE; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCATION; GENETIC ANALYSIS; GENETIC SCREENING; GENOME ANALYSIS; GENOME SIZE; HIGH THROUGHPUT SCREENING; HUMAN; INTERPHASE; MAJOR CLINICAL STUDY; MALE; MENTAL DEFICIENCY; RETROSPECTIVE STUDY; TELOMERE;

CHROMOSOME ABERRATIONS; CYTOGENETIC ANALYSIS; EVALUATION STUDIES; GENETIC SCREENING; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MENTAL RETARDATION; NUCLEIC ACID HYBRIDIZATION; RETROSPECTIVE STUDIES; TELOMERE;

EID: 18344389362     PISSN: 10983600     EISSN: None     Source Type: Journal    
DOI: 10.1097/01.GIM.0000160076.14102.EC     Document Type: Article

References (40)

1. Biesecker LG. The end of the beginning of chromosome ends. Am J Med Genet 2002;107:263-266.
2. Knight SJ, Regan R, Nicod A et al. Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet 1999;354:1676-1681.
3. Slavotinek A, Rosenberg M, Knight S et al. Screening for submicroscopic chromosome rearrangements in children with idiopathic mental retardation using microsatellite markers for the chromosome telomeres. J Med Genet 1999;36:405-411.
4. Sismani C, Armour JA, Flint J, Girgalli C, Regan R, Patsalis PC. Screening for subtelomeric chromosome abnormalities in children with idiopathic mental retardation using multiprobe telomeric FISH and the new MAPH telomeric assay. Eur J Hum Genet 2001;9:527-532.
5. Rooms L, Reyniers E, van Luijk R et al. Subtelomeric deletions detected in patients with idiopathic mental retardation using multiplex ligation-dependent probe amplification (MLPA). Hum Mutat 2004;23:17-21.
6. Knight SJ, Lese CM, Precht KS et al. An optimized set of human telomere clones for studying telomere integrity and architecture. Am J Hum Genet 2000;67:320-332.
7. Wong AC, Ning Y, Flint J, et al. Molecular characterization of a 130-kb terminal microdeletion at 22q in a child with mild mental retardation. Am J Hum Genet 1997;60:113-120.
8. Pinkel D, Segraves R, Sudar D et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998;20:207-211.
9. Gunn SR, Mohammed M, Reveles XT et al. Molecular characterization of a patient with central nervous system dysmyelination and cryptic unbalanced translocation between chromosomes 4q and 18q. Am J Med Genet 2003;120A:127-135.
10. Ki A, Rauen KA, Black LD et al. Ring 21 chromosome and a satellited 1p in the same patient: novel origin for an ectopic NOR. Am J Med Genet 2003;120A:365-369.
11. Veltman JA, Jonkers Y, Nuijten I et al. Definition of a Critical Region on Chromosome 18 for Congenital Aural Atresia by ArrayCGH. Am J Hum Genet 2003;72:1578-1584.
12. 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;73:1261-1270.
13. Buckley PG, Mantripragada KK, Benetkiewicz M et al. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet 2002;11:3221-3229.
14. Veltman JA, Schoenmakers EF, Eussen BH et al. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet 2002;70:1269-1276.
15. Harada N, Hatchwell E, Okamoto N et al. Subtelomere specific microarray based comparative genomic hybridisation: a rapid detection system for cryptic rearrangements in idiopathic mental retardation. J Med Genet 2004;41:130-136.
16. Wilson HL, Wong AC, Shaw SR et al. Molecular characterisation of the 22q13 deletion syndrome supports the role of haploinsufficiency of SHANK3/PROSAP2 in the major neurological symptoms. J Med Genet 2003;40:575-584.
17. Cardoso C, Leventer RJ, Ward HL et al. Refinement of a 400-kb critical region allows genotypic differentiation between isolated lissencephaly, Miller-Dicker syndrome, and other phenotypes secondary to deletions of 17p13.3. Am J Hum Genet 2003;72:918-930.
18. Macina RA, Negorev DG, Spais C, Ruthig LA, Hu XL, Riethman HC. Sequence organization of the human chromosome 2q telomere. Hum Mol Genet 1994;3:1847-1853.
19. van Geel M, Dickson MC, Beck AF et al. Genomic analysis of human chromosome 10q and 4q telomeres suggests a common origin. Genomics 2002;79:210-217.
20. Wilkie AO, Higgs DR, Rack KA et al. Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16. Cell 1991;64:595-606.
21. Martin CL, Waggoner DJ, Wong A et al. "Molecular rulers" for calibrating phenotypic effects of telomere imbalance. J Med Genet 2002;39:734-740.
22. Chen YZ, Hayashi Y, Wu IG et al. A BAC-based STS-content map spanning a 35-Mb region of human chromosome 1p35-p36. Genomics 2001;74:55-70.
23. Daniels RJ, Peden JF, Lloyd C et al. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. Hum Mol Genet 2001;10:339-352.
24. Doggett NA, Goodwin LA, Tesmer JG et al. An integrated physical map of human chromosome 16. Nature 1995;377:335-365.
25. Dunham I, Shimizu N, Roe B et al. The DNA sequence of human chromosome 22. Nature 1999;402;489-495.
26. Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001;29:263-264.
27. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36:949-951.
28. Sebat J, Lakshmi B, Troge J et al. Large-scale copy number polymorphism in the human genome. Science 2004;305:525-528.
29. McDermid HE, Duncan AM, Brasch KR et al. Characterization of the supernumerary chromosome in cat eye syndrome. Science 1986;232:646-648.
30. McTaggart KE, Budarf ML, Driscoll DA, Emanuel BS, Ferreira P, McDermid HE. Cat eye syndrome chromosome breakpoint clustering: identification of two intervals also associated with 22q11 deletion syndrome breakpoints. Cytogenet Cell Genet 1998;81:222-228.
31. Lindsay EA, Shaffer LG, Carrozzo R, Greenberg F, Baldini A. De novo tandem duplication of chromosome segment 22q11-q12: clinical, cytogenetic, and molecular characterization. Am J Med Genet 1995;56:296-299.
32. Knoll JH, Asamoah A, Pletcher BA, Wagstaff J. Interstitial duplication of proximal 22q: phenotypic overlap with cat eye syndrome. Am J Med Genet 1995;55:221-224.
33. Reiss JA, Weleber RG, Brown MG, Bangs CD, Lovrien EW, Magenis RE. Tandem duplication of proximal 22q: a cause of cat-eye syndrome. Am J Med Genet 1985;20:165-171.
34. Yu W, Ballif BC, Kashork CD, et al. Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized 1p36 deletions. Hum Mol Genet 2003;12:2145-2152.
35. Schaeffer AJ, Chung J, Heretis K, Wong A, Ledbetter DH, Lese Martin C. Comparative genomic hybridization-array analysis enhances the detection of aneuploidies and submicroscopic imbalances in spontaneous miscarriages. Am J Hum Genet 2004;74:1168-1174.
36. Veltman JA, Yntema HG, Lugtenberg D et al. High resolution profiling of X chromosomal aberrations by array comparative genomic hybridisation. J Med Genet 2004;41:425-432.
37. Collins FS, Green ED, Guttmacher AE, Guyer MS. A vision for the future of genomics research. Nature 2003;422:835-847.
38. Ishkanian AS, Malloff CA, Watson SK, et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004;36:299-303.
39. Smirnov DA, Burdick JT, Morley M, Cheung VG. Method for manufacturing whole-genome microarrays by rolling circle amplification. Genes Chromosomes Cancer 2004;40:72-77.
40. Greshock J, Naylor TL, Margolin A et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004;14:179-187.