Oligonucleotide microarrays for clinical diagnosis of copy number variation and zygosity status

Current Protocols in Human Genetics

Volumn , Issue SUPPL.74, 2012, Pages

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

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

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

Indexed keywords

GENOMIC DNA; OLIGONUCLEOTIDE;

ACCURACY; ARTICLE; CHROMOSOME ANALYSIS; CHROMOSOME BANDING PATTERN; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA ISOLATION; DNA MICROARRAY; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC VARIABILITY; GENOME ANALYSIS; HOMOZYGOSITY; HUMAN; KARYOTYPE; MALE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; RELIABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; ZYGOSITY; CHILD; CHROMOSOME ABERRATION; DEVELOPMENTAL DISORDER; DIAGNOSTIC PROCEDURE; GENE DOSAGE; GENETICS; MENTAL DEFICIENCY; METHODOLOGY; GENETIC DISORDER; KARYOTYPING;

CHILD; CHROMOSOME ABERRATIONS; DEVELOPMENTAL DISABILITIES; GENE DOSAGE; HUMANS; MENTAL RETARDATION; MOLECULAR DIAGNOSTIC TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VARIATION (GENETICS); CHROMOSOME BANDING; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; GENETIC DISEASES, INBORN; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 49149131938     PISSN: 19348266     EISSN: 19348258     Source Type: Journal    
DOI: 10.1002/0471142905.hg0812s74     Document Type: Article

References (30)

1. Baldwin, E.L., Lee, J.Y., Blake, D.M., Bunke, B.P., Alexander, C.R., Kogan, A.L., Ledbetter, D.H., and Martin, C.L. 2008. Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotidemicroarray. Genet. Med. 10:415-429.
2. Eichler, E.E. 2006. Widening the spectrum of human genetic variation. Nat. Genet. 38:911.
3. 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.
4. 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.
5. Itsara, A., Cooper, G.M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R.M., Myers, R.M., Ridker, P.M., Chasman, D.I., Mefford, H., Ying, P., Nickerson, D.A., and Eichler, E.E. 2009. Population analysis of large copy number variants and hotspots of human genetic disease. Am. J. Hum. Genet. 84:148-161.
6. 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.
7. Kearney, H.M., South, S.T., Wolff, D.J., Lamb, A., Hamosh, A., and Rao, K.W. 2011a. American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet. Med. 13:676-679.
8. Kearney, H.M., Thorland, E.C., Brown, K.K., Quintero-Rivera, F., and South, S.T. 2011b. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet. Med. 13:680-685.
9. 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., andAburatani, H. 2006. Genome-wide detection of human copy number variations using highdensity DNA oligonucleotide arrays. Genome Res. 16:1575-1584.
10. Lee, C., Iafrate, A.J., and Brothman, A.R. 2007. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat. Genet. 39:S48-S54.
11. Manning, M. and Hudgins, L. 2007. Use of arraybased technology in the practice of medical genetics. Genet. Med. 9:650-653.
12. Manning, M., and Hudgins, L. 2010. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet.Med. 12:742-745.
13. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., de Bakker, P.I., Maller, J.B., Kirby, A., Elliott, A.L., Parkin, M., Hubbell, E., Webster, T., Mei, R., Veitch, J., Collins, P.J., Handsaker, R., Lincoln, S., Nizzari, M., Blume, J., Jones, K.W., Rava, R., Daly, M.J., Gabriel, S.B., and Altshuler, D. 2008. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40:1166-1174.
14. Miller, D.T., Adam, M.P., Aradhya, S., Biesecker, L.G., Brothman, A.R., Carter, N.P., Church, D.M., Crolla, J.A., Eichler, E.E., Epstein, C.J., Faucett, W.A., Feuk, L., Friedman, J.M., Hamosh, A., Jackson, L., Kaminsky, E.B., Kok, K., Krantz, I.D., Kuhn, R.M., Lee, C., Ostell, J.M., Rosenberg, C., Scherer, S.W., Spinner, N.B., Stavropoulos, D.J., Tepperberg, J.H., Thorland, E.C., Vermeesch, J.R., Waggoner, D.J., Watson, M.S., Martin, C.L., and Ledbetter, D.H. 2010. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Genet. 86:749-764.
15. Ravnan, J.B., Tepperberg, J.H., Papenhausen, P., Lamb, A.N., Hedrick, J., Eash, D., Ledbetter, D.H., and Martin, C.L. 2006. 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. 43:478-489.
16. 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.
17. Sagoo, G.S., Butterworth, A.S., Sanderson, S., Shaw-Smith, C., Higgins, J.P., and Burton, H. 2009. Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic reviewandmetaanalysis of 19 studies and 13,926 subjects. Genet. Med. 11:139-146.
18. 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.
19. 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.
20. Shaikh, T.H. 2007. Oligonucleotide arrays for highresolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet. Med. 9:617-625.
21. 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.
22. Shen, Y. and Wu, B.L. 2009. Microarray-based genomic DNA profiling technologies in clinical molecular diagnostics (Review) Clin. Chem. 55:659-669.
23. 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.
24. Shen, Y., Dies, K.A., Holm, I.A., Bridgemohan, C., Sobeih, M.M., Caronna, E.B., Miller, K.J., Frazier, J.A., Silverstein, I., Picker, J., Weissman, L., Raffalli, P., Jeste, S., Demmer, L.A., Peters, H.K., Brewster, S.J., Kowalczyk, S.J., Rosen-Sheidley, B., McGowan, C., Duda, A.W. 3rd, Lincoln, S.A., Lowe, K.R., Schonwald, A., Robbins, M., Hisama, F., Wolff, R., Becker, R., Nasir, R., Urion, D.K., Milunsky, J.M., Rappaport, L., Gusella, J.F., Walsh, C.A., Wu, B.L., Miller, D.T.; Autism Consortium Clinical Genetics/DNA Diagnostics Collaboration. 2010. Clinical genetic testing for patientswith autism spectrum disorders. Pediatrics 125:e727-e735.
25. 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 theChild Neurology Society. Neurology 60:367-380.
26. 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.
27. VanVooren, 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.
28. Vermeesch, J.R., Fiegler, H., de Leeuw, N., Szuhai, K., Schoumans, J., Ciccone, R., Speleman, F., 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.
29. 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., de Jong, P.J., Brunner, H.G., van Kessel, A.G., Schoenmakers, E.F., and Veltman, J.A. 2003. Arraybased comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities.Am. J.Hum.Genet. 73:1261-1270.
30. Weiss, L.A., Shen, Y., Korn, J.M., Arking, D.E., Miller, D.T., Fossdal, R., Saemundsen, E., 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, P., Wu, B.L., and Daly, M.J. 2008. Association between Microdeletion and Microduplication at 16p11.2 and Autism. N. Engl. J. Med. 358:667-675.