Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more?

American Journal of Medical Genetics

Volumn 134 A, Issue 3, 2005, Pages 259-267

  Bejjani, Bassem A ^a,b,c   Saleki, Reza ^a   Ballif, Blake C ^a   Rorem, Emily A ^a   Sundin, Kyle ^a   Theisen, Aaron ^c   Kashork, Catherine D ^a   Shaffer, Lisa G ^a,b,c  

^a Signature Genomic Laboratories LLC   (United States)

^b SACRED HEART MEDICAL CENTER   (United States)

^c WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Array CGH; Chromosomal imbalance; Diagnosis; FISH mapping; Targeted array

Indexed keywords

ACROCEPHALOSYNDACTYLY; ALAGILLE SYNDROME; ANEUPLOIDY; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BECKWITH WIEDEMANN SYNDROME; CAT CRY SYNDROME; CHONDRODYSPLASIA; CHROMOSOMAL LOCALIZATION; CHROMOSOME ABERRATION; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CLINICAL ARTICLE; CLINICAL FEATURE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DIGEORGE SYNDROME; DUCHENNE MUSCULAR DYSTROPHY; ETHNIC GROUP; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; HAPPY PUPPET SYNDROME; HEREDITARY MOTOR SENSORY NEUROPATHY; HOLOPROSENCEPHALY; HUMAN; ICHTHYOSIS; KALLMANN SYNDROME; KARYOTYPE; KIDNEY POLYCYSTIC DISEASE; MALE; MICROPHTHALMIA; MILLER DIEKER SYNDROME; MONOSOMY; NEPHRONOPHTHISIS; PELIZAEUS MERZBACHER DISEASE; PRADER WILLI SYNDROME; PRIORITY JOURNAL; RUBINSTEIN SYNDROME; SMITH MAGENIS SYNDROME; SOTOS SYNDROME; TUBEROUS SCLEROSIS; WAGR SYNDROME; WOLF HIRSCHHORN SYNDROME;

CELL LINE, TRANSFORMED; CHROMOSOME ABERRATIONS; CHROMOSOME DELETION; CHROMOSOME DISORDERS; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CYTOGENETIC ANALYSIS; DOUBLE-BLIND METHOD; FEMALE; GENE DUPLICATION; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; MALE; NUCLEIC ACID HYBRIDIZATION; POLYMORPHISM, GENETIC; REPRODUCIBILITY OF RESULTS;

EID: 16344393207     PISSN: 15524825     EISSN: None     Source Type: Journal    
DOI: 10.1002/ajmg.a.30621     Document Type: Article

References (30)

1. Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo WL, Gray JW, Pinkel D. 2000. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25:144-146.
2. Ballif BC, Kashork CD, Shaffer LG. 2000. The promise and pitfalls of telomere region-specific probes. Am J Hum Genet 67:1356-1359.
3. Ballif BC, Yu W, Shaw CA, Kashork CD, Shaffer LG. 2003. Monosomy 1p36 breakpoint junctions suggest pre-meiotic breakage-fusion-bridge cycles are involved in generating terminal deletions. Hum Mol Genet 12:2153-2165.
4. Bentz M, Plesch A, Stilgenbauer S, Dohner H, Lichter P. 1998. Minimal sizes of deletions detected by comparative genomic hybridization. Genes Chromosomes Cancer 21:172-175.
5. Bruder CE, Hirvela C, Tapia-Paez I, Fransson I, Segraves R, Hamilton G, Zhang XX, Evans DG, Wallace AJ, Baser ME, Zucman-Rossi J, Hergersberg M, Boltshauser E, Papi L, Rouleau GA, Poptodorov G, Jordanova A, Rask-Andersen H, Kluwe L, Mautner V, Sainio M, Hung G, Mathiesen T, Moller C, Pulst SM, Harder H, Heiberg A, Honda M, Niimura M, Sahlen S, Blennow E, Albertson DG, Pinkel D, Dumanski JP. 2001. High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH. Hum Mol Genet 10:271-282.
6. Buckley PG, Mantripragada KK, Benetkiewicz M, Tapia-Paez I, Diaz De Stahl T, Rosenquist M, Ali H, Jarbo C, De Bustos C, Hirvela C, Sinder Wilen B, Fransson I, Thyr C, Johnsson BI, Bruder CE, Menzel U, Hergersberg M, Mandahl N, Blennow E, Wedell A, Beare DM, Collins JE, Dunham I, Albertson D, Pinkel D, Bastian BC, Faruqi AF, Lasken RS, Ichimura K, Collins VP, Dumanski JP. 2002. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet 11:3221-3229.
7. Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP. 2003. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 36:361-374.
8. Ghaffari SR, Boyd E, Tolmie JL, Crow YJ, Trainer AH, Connor JM. 1998. A new strategy for cryptic telomeric translocation screening in patients with idiopathic mental retardation. J Med Genet 35:225-233.
9. Hodgson G, Hager JH, Volik S, Hariono S, Wernick M, Moore D, Nowak N, Albertson DG, Pinkel D, Collins C, Hanahan D, Gray JW. 2001. Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat Genet 29:459-464.
10. Hui AB, Lo KW, Yin XL, Poon WS, Ng HK. 2001. Detection of multiple gene amplifications in glioblastoma multiforme using array-based comparative genomic hybridization. Lab Invest 81:717-723.
11. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36:949-951.
12. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL. 2004. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299-303.
13. Joly G, Lapierre JM, Ozilou C, Gosset P, Aurias A, de Blois MC, Prieur M, Raoul O, Colleaux L, Munnich A, Romana S, Vekemans M, Turleau C, 2001. Comparative genomic hybridisation in mentally retarded patients with dysmorphic features and a normal karyotype. Clin Genet 60:212-219.
14. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818-821.
15. Kallioniemi OP, Kallioniemi A, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. 1993. Comparative genomic hybridization: A rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol 4:41-46.
16. Kirchhoff M, Gerdes T, Maahr J, Rose H, Bentz M, Dohner H, Lundsteen C. 1999. Deletions below 10 megabasepairs are detected in comparative genomic hybridization by standard reference intervals. Genes Chromosomes Cancer 25:410-413.
17. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
18. Ligon AH, Beaudet AL, Shaffer LG. 1997. Simultaneous, multilocus FISH analysis for detection of microdeletions in the diagnostic evaluation of developmental delay and mental retardation. Am J Hum Genet 61:51-59.
19. Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE. 2004. BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J Med Genet 41:175-182.
20. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. 1998. High resolution analysis of DNA copy-number variation using comparative genomic hybridication to microarrays. Nat Genet 20:207-211.
21. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science 305:525-528.
22. Shaffer LG, McCaskill C, Han JY, Choo KH, Cutillo DM, Donnenfeld AE, Weiss L, Van Dyke DL. 1994. Molecular characterization of de novo secondary trisomy 13. Am J Hum Genet 55:968-974.
23. Shaffer LG, Ledbetter DH, Lupski JR. 2001. Molecular cytogenetics of contiguous gene syndromes: Mechanisms and consequences of gene dosage imbalance. In: Scriver CR, Beaudet AL, Sly WS, Valle D, Childs B, Kinzler KW, Vogelstein B, editors. Metabolic and molecular basis of inherited disease. New York: McGraw Hill. 1291-1324.
24. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG. 2001. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29:263-264.
25. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P. 1997. Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399-407.
26. Veltman JA, Schoenmakers EF, Bussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG. 2002. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet 70:1269-1276.
27. Veltman JA, Jonkers Y, Nuijten I, Janssen I, van der Vliet W, Huys E, Vermeesch J, Van Buggenhout G, Fryns JP, Admiraal R, Terhal P, Lacombe D, van Kessel AG, Smeets D, Schoenmakers EF, van Ravenswaaij-Arts CM. 2003. Definition of a critical region on chromosome 18 for congenital aural atresia by array CGH. Am J Hum Genet 72:1578-1584.
28. Vissers LE, de Vries BB, Osoegawa K, Janssen IM, Feuth T, Choy CO, Straatman H, van der Vliet W, Huys EH, van Rijk A, Smeets D, van Ravenswaaij-Arts CM, Knoers NV, van der Burgt I, de Jong PJ, Brunner HG, van Kessel AG, Schoenmakers EF, Veltman JA. 2003. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 73:1261-1270.
29. Wessendorf S, Fritz B, Wrobel G, Nessling M, Lampel S, Goettel D, Kuepper M, Joos S, Hopman T, Kokocinski F, Dohner H, Bentz M, Schwaenen C, Lichter P. 2002. Automated screening for genomic imbalances using matrix-based comparative genomic hybridization. Lab Invest 82:47-60.
30. Yu W, Ballif BC, Kashork CD, Heilstedt HA, Howard LA, Cai WW, White LD, Liu W, Beaudet AL, Bejjani BA, Shaw CA, Shaffer LG. 2003. Development of a comparative genomic hybridization microarray and demonstration of it utility with 25 well-characterized 1p36 deletions. Hum Mol Genet 12:2145-2152.