Oligonucleotide microarrays for clinical diagnosis of copy number variation

Current Protocols in Human Genetics

Volumn , Issue SUPPL. 58, 2008, Pages

  Miller, David T ^a,b   Shen, Yiping ^a,b,c   Wu, Bai Lin ^a,b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

ACGH; Array CGH; CNV; Copy number variant; Genomic imbalance; Molecular diagnostics

Indexed keywords

ANEUPLOIDY; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CYTOGENETICS; DIAGNOSTIC ACCURACY; DNA DETERMINATION; DNA MICROARRAY; FAMILIAL DISEASE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE NUMBER; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; INTERMETHOD COMPARISON; KARYOTYPE; PRIORITY JOURNAL; REVIEW; VALIDITY;

BACTERIA (MICROORGANISMS);

EID: 58749091659     PISSN: 19348266     EISSN: 19348258     Source Type: Journal    
DOI: 10.1002/0471142905.hg0812s58     Document Type: Review

References (33)

1. Bejjani, B.A. and Shaffer, L.G. 2006. Application of array-based comparative genomic hybridization to clinical diagnostics. J. Mol. Diagn. 8:528-533.
2. Bejjani, B.A., Saleki, R., Ballif, B.C., Rorem, E.A., Sundin, K., Theisen, A., Kashork, C.D., and Shaffer, L.G. 2005a. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am. J. Med. Genet. A. 134:259-267.
3. Bejjani, B.A., Theisen, A.P., Ballif, B.C., and Shaffer, L.G. 2005b. Array-based comparative genomic hybridization in clinical diagnosis. Expert. Rev. Mol. Diagn. 5:421-429.
4. Cheung, S.W., Shaw, C.A., Yu, W., Li, J., Ou, Z., Patel, A., Yatsenko, S.A., Cooper, M.L., Furman, P., Stankiewicz, P., Lupski, J.R., Chinault, A.C., and Beaudet, A.L. 2005. Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet. Med. 7:422-432.
5. de Vries, B.B., Pfundt, R., Leisink, M., Koolen, D.A., Vissers, L.E., Janssen, I.M., Reijmersdal, S., Nillesen, W.M., Huys, E.H., Leeuw, N., Smeets, D., Sistermans, E.A., Feuth, T., van Ravenswaaij-Arts, C.M., van Kessel, A.G., Schoenmakers, E.F., Brunner, H.G., and Veltman, J.A. 2005. Diagnostic genome profiling in mental retardation. Am. J. Hum. Genet. 77:606-616.
6. Eichler, E.E. 2006. Widening the spectrum of human genetic variation. Nat. Genet. 38:911.
7. Fan, Y.S., Jayakar, P., Zhu, H., Barbouth, D., Sacharow, S., Morales, A., Carver, V., Benke, P., Mundy, P., and Elsas, L.J. 2007. Detection of pathogenic gene copy number variations in patients with mental retardation by genomewide oligonucleotide array comparative genomic hybridization. Hum. Mutat. 28:1124-1132.
8. Friedman, J.M., Baross, A., Delaney, A.D., Ally, A., Arbour, L., Armstrong, L., Asano, J., Bailey, D.K., Barber, S., Birch, P., Brown-John, M., Cao, M., Chan, S., Charest, D.L., Farnoud, N., Fernandes, N., Flibotte, S., Go, A., Gibson, W.T., Holt, R.A., Jones, S.J., Kennedy, G.C., Krzywinski, M., Langlois, S., Li, H.I., McGillivray, B.C., Nayer, T., Pugh, T.J., Rajcan-Separovic, E., Schein, J.E., Schnerch, A., Siddiqui, A., Van Allen, M.I., Wilson, G., Yong, S.L., Zahir, F., Eydoux, P., and Marra, M.A. 2006. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am. J. Hum. Genet. 79:500-513.
9. Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W., and Lee, C. 2004. Detection of large-scale variation in the human genome. Nat. Genet. 36:949-951.
10. Jacquemont, M.L., Sanlaville, D., Redon, R., Raoul, O., Cormier-Daire, V., Lyonnet, S., Amiel, J., Le Merrer, M., Heron, D., de Blois, M.C., Prieur, M., Vekemans, M., Carter, N.P., Munnich, A., Colleaux, L., and Philippe, A. 2006. Arraybased comparative genomic hybridisation identifies high frequency of cryptic chromosomal rearrangements in patients with syndromic autism spectrum disorders. J. Med. Genet. 43:843-849.
11. Komura, D., Shen, F., Ishikawa, S., Fitch, K.R., Chen, W., Zhang, J., Liu, G., Ihara, S., Nakamura, H., Hurles, M.E., Lee, C., Scherer, S.W., Jones, K.W., Shapero, M.H., Huang, J., and Aburatani, H. 2006. Genome-wide detection of human copy number variations using highdensity DNA oligonucleotide arrays. Genome Res. 16:1575-1584.
12. Krzywinski, M., Bosdet, I., Smailus, D., Chiu, R., Mathewson, C., Wye, N., Barber, S., Brown-John, M.,Chan, S.,Chand, S.,Cloutier, A.,Girn, N., Lee, D., Masson, A., Mayo, M., Olson, T., Pahdoh, P., Prabhu, A.-L., Schoenmakers, E., Tsai, M., Albertson, D., Lam, W., Choy, C.-O., Osoegawa, K., Zhao, S., de Jong, P.J., Schein, J., Jones, S., Marra, M.A. 2004. A set of BAC clones spanning the human genome. Nucleic Acids Res. 32:3651-3660.
13. Lee, C., Iafrate, A.J., and Brothman, A.R. 2007. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat. Genet. 39:S48-54.
14. Lugtenberg, D., Veltman, J.A., and van Bokhoven, H. 2007. High-resolution genomic microarrays for X-linked mental retardation. Genet. Med. 9:560-565.
15. Manning, M. and Hudgins, L. 2007. Use of arraybased technology in the practice of medical genetics. Genet. Med. 9:650-653.
16. Osoegawa, K., Mammoser, A.G., Wu, C., Frengen, E., Zeng, C., Catanese, J.J., and de Jong, P.J. 2001. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 11:483-496.
17. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo,W.L., Chen, C., Zhai,Y., Dairkee, S.H., Ljung, B.M.,Gray, J.W., and Albertson, D.G. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20:207-211.
18. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Carson, A.R., Chen, W., Cho, E.K., Dallaire, S., Freeman, J.L., Gonzalez, J.R., Gratacos, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J.R., Marshall, C.R., Mei, R., Montgomery, L., Nisimura, K., Okamura, K., Shen, F., Somerville, M.J., Tchinda, J., Valesia, A., Woodward, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengo, L., Conrad, D.F., Estivill, X., Tyler-Smith, C., Carter,N.P., Aburatani, H., Lee, C., Jones, K.W., Scherer, S.W., and Hurles, M.E. 2006. Global variation in copy number in the human genome. Nature 444:444-454.
19. Schoumans, J., Ruivenkamp, C., Holmberg, E., Kyllerman, M., Anderlid, B.M., and Nordenskjold, M. 2005. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). J. Med. Genet. 42:699-705.
20. Sebat, J.,Lakshmi,B., Malhotra,D.,Troge, J., Lese-Martin, C, Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., Leotta, A., Pai, D., Zhang, R., Lee, Y.-H., Hicks, J., Spence, S.J., Lee, A.T., Puura, K., Lehtimaki, T., Ledbetter, D., Gregersen, P.K., Bregman, J., Sutcliffe, J.S., Jobanputra,V., Chung,W.,Warburton, D.,King, M.-C., Skuse, D., Geschwind, D.H., Gilliam, T.C., Ye, K., and Wigler, M. 2007. Strong association of de novo copy number mutations with autism. Science 316:445-449.
21. Shaffer, L.G. 2005. American College of Medical Genetics guideline on the cytogenetic evaluation of the individual with developmental delay or mental retardation. Genet. Med. 7:650-654.
22. Shaffer. L.G., Beaudet, A.L., Brothman, A.R., Hirsch, B., Levy, B., Martin, C.L., Mascarello, J.T., and Rao, K.W. 2007. Microarray analysis for constitutional cytogenetic abnormalities. Genet. Med. 9:654-662
23. Shaikh, T.H. 2007. Oligonucleotide arrays for highresolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet. Med. 9:617-625.
24. Shaw-Smith, C., Redon, R., Rickman, L., Rio, M., Willatt, L., Fiegler, H., Firth, H., Sanlaville, D., Winter, R., Colleaux, L., Bobrow, M., and Carter, N.P. 2004. 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. 41:241-248.
25. Shen,Y., Irons,M., Miller, D.T., Cheung, S.W., Lip, V., Sheng, X., Tomaszewicz, K., Shao, H., Fang, H., Tang, H.S., Irons,M.,Walsh, C.A., Platt. O., Gusella, J.F., and Wu, B.L. 2007. Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin. Chem. 53:2051-2059.
26. Shevell, M., Ashwal, S., Donley, D., Flint, J., Gingold, M., Hirtz, D., Majnemer, A., Noetzel, M., and Sheth, R.D. 2003. 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 60:367-380.
27. Stankiewicz, P. and Beaudet, A.L. 2007. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr. Opin. Genet. Dev. 17:182-192.
28. Thorland, E.C., Gonzales, P.R., Gliem, T.J.,Wiktor, A.E., and Ketterling, R.P. 2007. Comprehensive validation of array comparative genomic hybridization platforms: How much is enough? Genet. Med. 9:632-641.
29. Van Vooren, S., Coessens, B., De Moor,B., Moreau, Y., and Vermeesch, J.R. 2007. Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: Suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes. Genet. Med. 9:642-649.
30. Vermeesch, J.R., Fiegler, H., de Leeuw, N., Szuhai, K., Schoumans, J., Ciccone, R., Speleman, Rauch, A., Clayton-Smith, J., Van Ravenswaaij, C., Sanlaville, D., Patsalis, P.C., Firth, H., Devriendt, K., and Zuffardi, O. 2007. Guidelines for molecular karyotyping in constitutional genetic diagnosis. Eur. J. Hum. Genet. 15:1105-1114.
31. Vissers, L.E., de Vries, B.B., Osoegawa, K., Janssen, I.M., Feuth, T., Choy, C.O., Straatman, H., Van Der Vliet, W., Huys, E.H., van Rijk, A., Smeets, D., van Ravenswaaij-Arts, C.M., Knoers, N.V., Van Der Burgt, I., Jong, P.J., Brunner, H.G., van Kessel, A.G., Schoenmakers, E.F., and Veltman, J.A. 2003. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am. J. Hum. Genet. 73:1261-1270.
32. Weiss, L.A., Shen, Y., Korn, J.M., Arking, D. Miller, D.T., Fossdal, R., Saemundsen, Stefansson, H., Ferreira, M.A., Green, T., Platt, O.S., Ruderfer, D.M., Walsh, C.A., Altshuler, D., Chakravarti, A., Tanzi, R.E., Stefansson, K., Santangelo, S.L., Gusella, J.F., Sklar, Wu, B.L., and Daly, M.J. 2008. Association between Microdeletion and Microduplication 16p11.2 and Autism. N. Engl. J. Med. 358:667-675.
33. Ylstra, B., Van Den Ijssel, P., Carvalho, B., Brakenhoff, R.H., and Meijer, G.A. 2006. BAC to the future! or oligonucleotides: A perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34:445-450.