Online resources for genomic structural variation

Methods in Molecular Biology

Volumn 838, Issue , 2012, Pages 273-289

  Sneddon, Tam P ^a   Church, Deanna M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Copy number variant; Database of Genomic Variants; dbVar; DGVa; Insertion deletion; Structural variation

Indexed keywords

ARTICLE; AUTISM; BASE PAIRING; CHROMOSOME ABERRATION; CHROMOSOME INVERSION; COPY NUMBER VARIATION; GENE DELETION; GENE DOSAGE; GENE DUPLICATION; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; INTERNET; METHODOLOGY; NEOPLASM; PHENOTYPE; SEQUENCE ALIGNMENT;

AUTISTIC DISORDER; BASE PAIRING; CHROMOSOME ABERRATIONS; CHROMOSOME INVERSION; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; GENE DELETION; GENE DOSAGE; GENE DUPLICATION; GENETIC VARIATION; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; NEOPLASMS; PHENOTYPE; SEQUENCE ALIGNMENT;

EID: 84856249711     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-507-7_13     Document Type: Article

References (93)

1. Lupski, J. R., de Oca-Luna, R. M., Slaugenhaupt, S., Pentao, L., Guzzetta, V., Trask, B. J., Saucedo-Cardenas, O., Barker, D. F., Killian, J. M., Garcia, C. A., Chakravarti, A., and Patel, P. I. (1991) DNA duplication associated with Charcot-Marie-Tooth disease type 1A, Cell 66, 219-232. (Pubitemid 121001361)
2. Koolen, D. A., Vissers, L. E., Pfundt, R., de Leeuw, N., Knight, S. J., Regan, R., Kooy, R. F., Reyniers, E., Romano, C., Fichera, M., Schinzel, A., Baumer, A., Anderlid, B. M., Schoumans, J., Knoers, N. V., van Kessel, A. G., Sistermans, E. A., Veltman, J. A., Brunner, H. G., and de Vries, B. B. (2006) A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism, Nat Genet 38, 999-1001. (Pubitemid 44325923)
3. Shaw-Smith, C., Pittman, A. M., Willatt, L., Martin, H., Rickman, L., Gribble, S., Curley, R., Cumming, S., Dunn, C., Kalaitzopoulos, D., Porter, K., Prigmore, E., Krepischi-Santos, A. C., Varela, M. C., Koiffmann, C. P., Lees, A. J., Rosenberg, C., Firth, H. V., de Silva, R., and Carter, N. P. (2006) Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability, Nat Genet 38, 1032-1037. (Pubitemid 44325928)
4. 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(7), 667-675 (Pubitemid 351240746)
5. Gonzalez, E., Kulkarni, H., Bolivar, H., Mangano, A., Sanchez, R., Catano, G., Nibbs, R. J., Freedman, B. I., Quinones, M. P., Bamshad, M. J., Murthy, K. K., Rovin, B. H., Bradley, W., Clark, R. A., Anderson, S. A., OConnell R, J., Agan, B. K., Ahuja, S. S., Bologna, R., Sen, L., Dolan, M. J., and Ahuja, S. K. (2005) The influence of CCL3L1 genecontaining segmental duplications on HIV-1/AIDS susceptibility, Science 307, 1434-1440. (Pubitemid 40321934)
6. Fanciulli, M., Norsworthy, P. J., Petretto, E., Dong, R., Harper, L., Kamesh, L., Heward, J. M., Gough, S. C., de Smith, A., Blakemore, A. I., Froguel, P., Owen, C. J., Pearce, S. H., Teixeira, L., Guillevin, L., Graham, D. S., Pusey, C. D., Cook, H. T., Vyse, T. J., and Aitman, T. J. (2007) FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity, Nat Genet 39, 721-723. (Pubitemid 46848593)
7. Fellermann, K., Stange, D. E., Schaeffeler, E., Schmalzl, H., Wehkamp, J., Bevins, C. L., Reinisch, W., Teml, A., Schwab, M., Lichter, P., Radlwimmer, B., and Stange, E. F. (2006) A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon, American journal of human genetics 79, 439-448. (Pubitemid 44384253)
8. Hollox, E. J., Huffmeier, U., Zeeuwen, P. L., Palla, R., Lascorz, J., Rodijk-Olthuis, D., van de Kerkhof, P. C., Traupe, H., de Jongh, G., den Heijer, M., Reis, A., Armour, J. A., and Schalkwijk, J. (2008) Psoriasis is associated with increased beta-defensin genomic copy number, Nat Genet 40, 23-25.
9. Huse, K., Taudien, S., Groth, M., Rosenstiel, P., Szafranski, K., Hiller, M., Hampe, J., Junker, K., Schubert, J., Schreiber, S., Birkenmeier, G., Krawczak, M., and Platzer, M. (2008) Genetic Variants of the Copy Number Polymorphic beta-Defensin Locus Are Associated with Sporadic Prostate Cancer, Tumour Biol 29, 83-92.
10. Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E., and Pritchard, J. K. (2006) A high-resolution survey of deletion polymorphism in the human genome, Nat Genet 38, 75-81. (Pubitemid 43011885)
11. Cooper, G. M., Nickerson, D. A., and Eichler, E. E. (2007) Mutational and selective effects on copy-number variants in the human genome, Nat Genet 39, S22-29. (Pubitemid 47014473)
12. Cutler, G., Marshall, L. A., Chin, N., Baribault, H., and Kassner, P. D. (2007) Significant gene content variation characterizes the genomes of inbred mouse strains, Genome research 17, 1743-1754. (Pubitemid 351359998)
13. Graubert, T. A., Cahan, P., Edwin, D., Selzer, R. R., Richmond, T. A., Eis, P. S., Shannon, W. D., Li, X., McLeod, H. L., Cheverud, J. M., and Ley, T. J. (2007) A high-resolution map of segmental DNA copy number variation in the mouse genome, PLoS Genet 3, e3.
14. Nguyen, D. Q., Webber, C., and Ponting, C. P. (2006) Bias of selection on human copy-number variants, PLoS Genet 2, e20.
15. Wong, K. K., deLeeuw, R. J., Dosanjh, N. S., Kimm, L. R., Cheng, Z., Horsman, D. E., MacAulay, C., Ng, R. T., Brown, C. J., Eichler, E. E., and Lam, W. L. (2007) A comprehensive analysis of common copy-number variations in the human genome, American journal of human genetics 80, 91-104. (Pubitemid 46047653)
16. (2003) The International HapMap Project, Nature 426, 789-796.
17. Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., Marth, G., Sherry, S., Mullikin, J. C., Mortimore, B. J., Willey, D. L., Hunt, S. E., Cole, C. G., Coggill, P. C., Rice, C. M., Ning, Z., Rogers, J., Bentley, D. R., Kwok, P. Y., Mardis, E. R., Yeh, R. T., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R. H., McPherson, J. D., Gilman, B., Schaffner, S., Van Etten, W. J., Reich, D., Higgins, J., Daly, M. J., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M. C., Linton, L., Lander, E. S., and Altshuler, D. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms, Nature 409, 928-933. (Pubitemid 32165347)
18. NCBI -http://www.ncbi.nlm.nih.gov/.
19. HuRef Project -http://huref.jcvi.org/.
20. MapViewer -http://www.ncbi.nlm.nih.gov/mapview/.
21. Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y. J., Makhijani, V., Roth, G. T., Gomes, X., Tartaro, K., Niazi, F., Turcotte, C. L., Irzyk, G. P., Lupski, J. R., Chinault, C., Song, X. Z., Liu, Y., Yuan, Y., Nazareth, L., Qin, X., Muzny, D. M., Margulies, M., Weinstock, G. M., Gibbs, R. A., and Rothberg, J. M. (2008) The complete genome of an individual by massively parallel DNA sequencing, Nature 452, 872-876. (Pubitemid 351550870)
22. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., Guo, Y., Feng, B., Li, H., Lu, Y., Fang, X., Liang, H., Du, Z., Li, D., Zhao, Y., Hu, Y., Yang, Z., Zheng, H., Hellmann, I., Inouye, M., Pool, J., Yi, X., Zhao, J., Duan, J., Zhou, Y., Qin, J., Ma, L., Li, G., Yang, Z., Zhang, G., Yang, B., Yu, C., Liang, F., Li, W., Li, S., Li, D., Ni, P., Ruan, J., Li, Q., Zhu, H., Liu, D., Lu, Z., Li, N., Guo, G., Zhang, J., Ye, J., Fang, L., Hao, Q., Chen, Q., Liang, Y., Su, Y., San, A., Ping, C., Yang, S., Chen, F., Li, L., Zhou, K., Zheng, H., Ren, Y., Yang, L., Gao, Y., Yang, G., Li, Z., Feng, X., Kristiansen, K., Wong, G. K., Nielsen, R., Durbin, R., Bolund, L., Zhang, X., Li, S., Yang, H., and Wang, J. (2008) The diploid genome sequence of an Asian individual, Nature 456, 60-65.
23. Ahn, S. M., Kim, T. H., Lee, S., Kim, D., Ghang, H., Kim, D. S., Kim, B. C., Kim, S. Y., Kim, W. Y., Kim, C., Park, D., Lee, Y. S., Kim, S., Reja, R., Jho, S., Kim, C. G., Cha, J. Y., Kim, K. H., Lee, B., Bhak, J., and Kim, S. J. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socioethnic group, Genome research 19, 1622-1629.
24. Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., Boutell, J. M., Bryant, J., Carter, R. J., Keira Cheetham, R., Cox, A. J., Ellis, D. J., Flatbush, M. R., Gormley, N. A., Humphray, S. J., Irving, L. J., Karbelashvili, M. S., Kirk, S. M., Li, H., Liu, X., Maisinger, K. S., Murray, L. J., Obradovic, B., Ost, T., Parkinson, M. L., Pratt, M. R., Rasolonjatovo, I. M., Reed, M. T., Rigatti, R., Rodighiero, C., Ross, M. T., Sabot, A., Sankar, S. V., Scally, A., Schroth, G. P., Smith, M. E., Smith, V. P., Spiridou, A., Torrance, P. E., Tzonev, S. S., Vermaas, E. H., Walter, K., Wu, X., Zhang, L., Alam, M. D., Anastasi, C., Aniebo, I. C., Bailey, D. M., Bancarz, I. R., Banerjee, S., Barbour, S. G., Baybayan, P. A., Benoit, V. A., Benson, K. F., Bevis, C., Black, P. J., Boodhun, A., Brennan, J. S., Bridgham, J. A., Brown, R. C., Brown, A. A., Buermann, D. H., Bundu, A. A., Burrows, J. C., Carter, N. P., Castillo, N., Chiara, E. C. M., Chang, S., Neil Cooley, R., Crake, N. R., Dada, O. O., Diakoumakos, K. D., Dominguez-Fernandez, B., Earnshaw, D. J., Egbujor, U. C., Elmore, D. W., Etchin, S. S., Ewan, M. R., Fedurco, M., Fraser, L. J., Fuentes Fajardo, K. V., Scott Furey, W., George, D., Gietzen, K. J., Goddard, C. P., Golda, G. S., Granieri, P. A., Green, D. E., Gustafson, D. L., Hansen, N. F., Harnish, K., Haudenschild, C. D., Heyer, N. I., Hims, M. M., Ho, J. T., Horgan, A. M., Hoschler, K., Hurwitz, S., Ivanov, D. V., Johnson, M. Q., James, T., Huw Jones, T. A., Kang, G. D., Kerelska, T. H., Kersey, A. D., Khrebtukova, I., Kindwall, A. P., Kingsbury, Z., Kokko-Gonzales, P. I., Kumar, A., Laurent, M. A., Lawley, C. T., Lee, S. E., Lee, X., Liao, A. K., Loch, J. A., Lok, M., Luo, S., Mammen, R. M., Martin, J. W., McCauley, P. G., McNitt, P., Mehta, P., Moon, K. W., Mullens, J. W., Newington, T., Ning, Z., Ling Ng, B., Novo, S. M., ONeill, M. J., Osborne, M. A., Osnowski, A., Ostadan, O., Paraschos, L. L., Pickering, L., Pike, A. C., Pike, A. C., Chris Pinkard, D., Pliskin, D. P., Podhasky, J., Quijano, V. J., Raczy, C., Rae, V. H., Rawlings, S. R., Chiva Rodriguez, A., Roe, P. M., Rogers, J., Rogert Bacigalupo, M. C., Romanov, N., Romieu, A., Roth, R. K., Rourke, N. J., Ruediger, S. T., Rusman, E., Sanches-Kuiper, R. M., Schenker, M. R., Seoane, J. M., Shaw, R. J., Shiver, M. K., Short, S. W., Sizto, N. L., Sluis, J. P., Smith, M. A., Ernest Sohna Sohna, J., Spence, E. J., Stevens, K., Sutton, N., Szajkowski, L., Tregidgo, C. L., Turcatti, G., Vandevondele, S., Verhovsky, Y., Virk, S. M., Wakelin, S., Walcott, G. C., Wang, J., Worsley, G. J., Yan, J., Yau, L., Zuerlein, M., Rogers, J., Mullikin, J. C., Hurles, M. E., McCooke, N. J., West, J. S., Oaks, F. L., Lundberg, P. L., Klenerman, D., Durbin, R., and Smith, A. J. (2008) Accurate whole human genome sequencing using reversible terminator chemistry, Nature 456, 53-59.
25. Kim, J. I., Ju, Y. S., Park, H., Kim, S., Lee, S., Yi, J. H., Mudge, J., Miller, N. A., Hong, D., Bell, C. J., Kim, H. S., Chung, I. S., Lee, W. C., Lee, J. S., Seo, S. H., Yun, J. Y., Woo, H. N., Lee, H., Suh, D., Lee, S., Kim, H. J., Yavartanoo, M., Kwak, M., Zheng, Y., Lee, M. K., Park, H., Kim, J. Y., Gokcumen, O., Mills, R. E., Zaranek, A. W., Thakuria, J., Wu, X., Kim, R. W., Huntley, J. J., Luo, S., Schroth, G. P., Wu, T. D., Kim, H., Yang, K. S., Park, W. Y., Kim, H., Church, G. M., Lee, C., Kingsmore, S. F., and Seo, J. S. (2009) A highly annotated whole-genome sequence of a Korean individual, Nature 460, 1011-1015.
26. The Copy Number Variation (CNV) Project -http://www.sanger.ac.uk/humgen/ cnv/.
27. 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., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, 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. (Pubitemid 44809057)
28. UCSC Genome Browser -http://genome. ucsc.edu/.
29. Ensembl Genome Browser -http://www. ensembl.org/.
30. Human Genome Structural Variation Project -http://hgsv.washington.edu/.
31. Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen, E., Zerr, T., Yamada, N. A., Tsang, P., Newman, T. L., Tuzun, E., Cheng, Z., Ebling, H. M., Tusneem, N., David, R., Gillett, W., Phelps, K. A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J. D., Korn, J. M., McCarroll, S. A., Altshuler, D. A., Peiffer, D. A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D. A., Mullikin, J. C., Wilson, R. K., Bruhn, L., Olson, M. V., Kaul, R., Smith, D. R., and Eichler, E. E. (2008) Mapping and sequencing of structural variation from eight human genomes, Nature 453, 56-64. (Pubitemid 351630326)
32. Tuzun, E., Sharp, A. J., Bailey, J. A., Kaul, R., Morrison, V. A., Pertz, L. M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D., Olson, M. V., and Eichler, E. E. (2005) Fine-scale structural variation of the human genome, Nat Genet 37, 727-732. (Pubitemid 41754889)
33. 1000 Genomes Project -http://www. 1000genomes.org.
34. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing, Nature 467, 1061-1073.
35. Mills, R.E., Walter, K., Stewart, C.et. al. (2011) Mapping copy number variation by populationscale genome sequencing, Nature 470, 59-65.
36. The Copy Number Variation project at the Childrens Hospital of Philadelphia (CHOP) -http://cnv.chop.edu/.
37. Shaikh, T. H., Gai, X., Perin, J. C., Glessner, J. T., Xie, H., Murphy, K., OHara, R., Casalunovo, T., Conlin, L. K., DArcy, M., Frackelton, E. C., Geiger, E. A., Haldeman-Englert, C., Imielinski, M., Kim, C. E., Medne, L., Annaiah, K., Bradfi eld, J. P., Dabaghyan, E., Eckert, A., Onyiah, C. C., Ostapenko, S., Otieno, F. G., Santa, E., Shaner, J. L., Skraban, R., Smith, R. M., Elia, J., Goldmuntz, E., Spinner, N. B., Zackai, E. H., Chiavacci, R. M., Grundmeier, R., Rappaport, E. F., Grant, S. F., White, P. S., and Hakonarson, H. (2009) Highresolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications, Genome research 19, 1682-1690.
38. Chromosome Anomaly Collection -http://www.ngrl.org.uk/Wessex/collection/ index. htm.
39. Snijders, A. M., Nowak, N. J., Huey, B., Fridlyand, J., Law, S., Conroy, J., Tokuyasu, T., Demir, K., Chiu, R., Mao, J. H., Jain, A. N., Jones, S. J., Balmain, A., Pinkel, D., and Albertson, D. G. (2005) Mapping segmental and sequence variations among laboratory mice using BAC array CGH, Genome research 15, 302-311. (Pubitemid 40309395)
40. Guryev, V., Saar, K., Adamovic, T., Verheul, M., van Heesch, S. A., Cook, S., Pravenec, M., Aitman, T., Jacob, H., Shull, J. D., Hubner, N., and Cuppen, E. (2008) Distribution and functional impact of DNA copy number variation in the rat, Nat Genet 40, 538-545. (Pubitemid 351601223)
41. Lee, A. S., Gutierrez-Arcelus, M., Perry, G. H., Vallender, E. J., Johnson, W. E., Miller, G. M., Korbel, J. O., and Lee, C. (2008) Analysis of copy number variation in the rhesus macaque genome identifi es candidate loci for evolutionary and human disease studies, Hum Mol Genet 17(8), 1127-1136. (Pubitemid 351494184)
42. Fortna, A., Kim, Y., MacLaren, E., Marshall, K., Hahn, G., Meltesen, L., Brenton, M., Hink, R., Burgers, S., Hernandez-Boussard, T., Karimpour-Fard, A., Glueck, D., McGavran, L., Berry, R., Pollack, J., and Sikela, J. M. (2004) Lineagespecific gene duplication and loss in human and great ape evolution, PLoS Biol 2, E207.
43. Goidts, V., Armengol, L., Schempp, W., Conroy, J., Nowak, N., Muller, S., Cooper, D. N., Estivill, X., Enard, W., Szamalek, J. M., Hameister, H., and Kehrer-Sawatzki, H. (2006) Identifi cation of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization, Hum Genet 119, 185-198.
44. Locke, D. P., Segraves, R., Carbone, L., Archidiacono, N., Albertson, D. G., Pinkel, D., and Eichler, E. E. (2003) Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization, Genome research 13, 347-357. (Pubitemid 36395392)
45. Perry, G. H., Tchinda, J., McGrath, S. D., Zhang, J., Picker, S. R., Caceres, A. M., Iafrate, A. J., Tyler-Smith, C., Scherer, S. W., Eichler, E. E., Stone, A. C., and Lee, C. (2006) Hotspots for copy number variation in chimpanzees and humans, Proceedings of the National Academy of Sciences of the United States of America 103, 8006-8011. (Pubitemid 43801043)
46. Wilson, G. M., Flibotte, S., Missirlis, P. I., Marra, M. A., Jones, S., Thornton, K., Clark, A. G., and Holt, R. A. (2006) Identifi cation by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla, Genome research 16, 173-181. (Pubitemid 43200265)
47. AtSFP -The SIGnAL Arabidopsis SNP, Deletion and SFP Database -http://signal. salk.edu/cgi-bin/AtSFP.
48. Borevitz, J. O., Hazen, S. P., Michael, T. P., Morris, G. P., Baxter, I. R., Hu, T. T., Chen, H., Werner, J. D., Nordborg, M., Salt, D. E., Kay, S. A., Chory, J., Weigel, D., Jones, J. D., and Ecker, J. R. (2007) Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana, Proceedings of the National Academy of Sciences of the United States of America 104, 12057-12062. (Pubitemid 47185629)
49. Wang, J., He, X., Ruan, J., Dai, M., Chen, J., Zhang, Y., Hu, Y., Ye, C., Li, S., Cong, L., Fang, L., Liu, B., Li, S., Wang, J., Burt, D. W., Wong, G. K., Yu, J., Yang, H., and Wang, J. (2005) ChickVD: a sequence variation database for the chicken genome, Nucleic acids research 33, D438-441. (Pubitemid 40207911)
50. Chicken Variation Database (ChickVD) -http://chicken.genomics.org.cn/.
51. Copy Number Variations across Vertebrate genomes (CNVVdb) -http://cnvvdb.genomics. sinica.edu.tw/.
52. Chen, F. C., Chen, Y. Z., and Chuang, T. J. (2009) CNVVdb: a database of copy number variations across vertebrate genomes, Bioinformatics (Oxford, England) 25, 1419-1421.
53. Database of Genomic Variants -http://projects. tcag.ca/variation/.
54. UCSC liftover tool -http://genome.ucsc.edu/cgi-bin/hgLiftOver.
55. AnEUploidy Project -http://www.aneuploidy. eu/.
56. CAD (Chromosome Abnormality Database) -http://www.ukcad.org.uk./cocoon/ ukcad/
57. ECARUCA (The European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations) -http://www. ecaruca.net/.
58. DECIPHER (DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources) -https://decipher.sanger. ac.uk/.
59. Database of Mental Retardation Associated CNVs -http://bioinfo.ut.ee/ dbcard/.
60. The Autism Chromosome Rearrangement Database -http://projects.tcag.ca/ autism/.
61. Autism CNV Database -http://projects.tcag. ca/autism-500k/.
62. Szatmari, P., Paterson, A. D., Zwaigenbaum, L., Roberts, W., Brian, J., Liu, X. Q., Vincent, J. B., Skaug, J. L., Thompson, A. P., Senman, L., Feuk, L., Qian, C., Bryson, S. E., Jones, M. B., Marshall, C. R., Scherer, S. W., Vieland, V. J., Bartlett, C., Mangin, L. V., Goedken, R., Segre, A., Pericak-Vance, M. A., Cuccaro, M. L., Gilbert, J. R., Wright, H. H., Abramson, R. K., Betancur, C., Bourgeron, T., Gillberg, C., Leboyer, M., Buxbaum, J. D., Davis, K. L., Hollander, E., Silverman, J. M., Hallmayer, J., Lotspeich, L., Sutcliffe, J. S., Haines, J. L., Folstein, S. E., Piven, J., Wassink, T. H., Sheffi eld, V., Geschwind, D. H., Bucan, M., Brown, W. T., Cantor, R. M., Constantino, J. N., Gilliam, T. C., Herbert, M., Lajonchere, C., Ledbetter, D. H., Lese-Martin, C., Miller, J., Nelson, S., Samango-Sprouse, C. A., Spence, S., State, M., Tanzi, R. E., Coon, H., Dawson, G., Devlin, B., Estes, A., Flodman, P., Klei, L., McMahon, W. M., Minshew, N., Munson, J., Korvatska, E., Rodier, P. M., Schellenberg, G. D., Smith, M., Spence, M. A., Stodgell, C., Tepper, P. G., Wijsman, E. M., Yu, C. E., Roge, B., Mantoulan, C., Wittemeyer, K., Poustka, A., Felder, B., Klauck, S. M., Schuster, C., Poustka, F., Bolte, S., Feineis-Matthews, S., Herbrecht, E., Schmotzer, G., Tsiantis, J., Papanikolaou, K., Maestrini, E., Bacchelli, E., Blasi, F., Carone, S., Toma, C., Van Engeland, H., de Jonge, M., Kemner, C., Koop, F., Langemeijer, M., Hijmans, C., Staal, W. G., Baird, G., Bolton, P. F., Rutter, M. L., Weisblatt, E., Green, J., Aldred, C., Wilkinson, J. A., Pickles, A., Le Couteur, A., Berney, T., McConachie, H., Bailey, A. J., Francis, K., Honeyman, G., Hutchinson, A., Parr, J. R., Wallace, S., Monaco, A. P., Barnby, G., Kobayashi, K., Lamb, J. A., Sousa, I., Sykes, N., Cook, E. H., Guter, S. J., Leventhal, B. L., Salt, J., Lord, C., Corsello, C., Hus, V., Weeks, D. E., Volkmar, F., Tauber, M., Fombonne, E., Shih, A., and Meyer, K. J. (2007) Mapping autism risk loci using genetic linkage and chromosomal rearrangements, Nat Genet 39, 319-328. (Pubitemid 46328498)
63. Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., Shago, M., Moessner, R., Pinto, D., Ren, Y., Thiruvahindrapduram, B., Fiebig, A., Schreiber, S., Friedman, J., Ketelaars, C. E., Vos, Y. J., Ficicioglu, C., Kirkpatrick, S., Nicolson, R., Sloman, L., Summers, A., Gibbons, C. A., Teebi, A., Chitayat, D., Weksberg, R., Thompson, A., Vardy, C., Crosbie, V., Luscombe, S., Baatjes, R., Zwaigenbaum, L., Roberts, W., Fernandez, B., Szatmari, P., and Scherer, S. W. (2008) Structural variation of chromosomes in autism spectrum disorder, American journal of human genetics 82, 477-488.
64. Autism Genetic Database -http://wren.bcf. ku.edu/.
65. The Cancer Genome Project -http://www. sanger.ac.uk/genetics/CGP/.
66. COSMIC -http://www.sanger.ac.uk/genetics/CGP/cosmic/.
67. The Cancer Genome Atlas -http://cancergenome. nih.gov/.
68. TCGA Data Portal -http://tcga-data.nci.nih. gov/tcga/homepage.htm.
69. Progenetix -www.progenetix.net/.
70. Baudis, M., and Cleary, M. L. (2001) Progenetix.net: an online repository for molecular cytogenetic aberration data, Bioinformatics (Oxford, England) 17, 1228-1229. (Pubitemid 33735351)
71. Cancer Chromosomes -http://www.ncbi.nlm. nih.gov/cancerchromosomes.
72. Knutsen, T., Gobu, V., Knaus, R., Padilla-Nash, H., Augustus, M., Strausberg, R. L., Kirsch, I. R., Sirotkin, K., and Ried, T. (2005) The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence, Genes, chromosomes & cancer 44, 52-64. (Pubitemid 41060196)
73. McCarroll, S. A., Hadnott, T. N., Perry, G. H., Sabeti, P. C., Zody, M. C., Barrett, J. C., Dallaire, S., Gabriel, S. B., Lee, C., Daly, M. J., and Altshuler, D. M. (2006) Common deletion polymorphisms in the human genome, Nat Genet 38, 86-92. (Pubitemid 43011887)
74. NimbleGen -http://www.nimblegen.com.
75. Illumina -http://www.illumina.com.
76. Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., Taillon, B. E., Chen, Z., Tanzer, A., Saunders, A. C., Chi, J., Yang, F., Carter, N. P., Hurles, M. E., Weissman, S. M., Harkins, T. T., Gerstein, M. B., Egholm, M., and Snyder, M. (2007) Pairedend mapping reveals extensive structural variation in the human genome, Science 318, 420-426. (Pubitemid 47614521)
77. BreakPtr -http://breakptr.gersteinlab.org.
78. CNAG -http://www.genome.umin.jp/CNAGtop2.html.
79. http://www.sanger.ac.uk/resources/software/cnvfi nder/.
80. dChip -http://biosun1.harvard.edu/complab/dchip/.
81. http://www.genome.rcast.u-tokyo.ac.jp/CNV/gemca-details.html.
82. PennCNV -http://www.neurogenome.org/cnv/penncnv/.
83. VariationHunter -http://compbio.cs.sfu.ca/strvar.htm.
84. GEO (Gene Expression Omnibus) -http://www.ncbi.nlm.nih.gov/geo/.
85. ArrayExpress -http://www.ebi.ac.uk/array express/.
86. Trace Archive -http://www.ncbi.nlm.nih. gov/Traces/trace.cgi.
87. Short Read Archive (SRA) -http://trace.ncbi. nlm.nih.gov/Traces/sra/sra. cgi.
88. Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., Lin, Y., MacDonald, J. R., Pang, A. W., Shago, M., Stockwell, T. B., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S. A., Busam, D. A., Beeson, K. Y., McIntosh, T. C., Remington, K. A., Abril, J. F., Gill, J., Borman, J., Rogers, Y. H., Frazier, M. E., Scherer, S. W., Strausberg, R. L., and Venter, J. C. (2007) The diploid genome sequence of an individual human, PLoS Biol 5, e254.
89. dbGaP -http://www.ncbi.nlm.nih.gov/gap.
90. European Genome-phenome Archive (EGA) -http://www.ebi.ac.uk/ega/.
91. dbVar -http://www.ncbi.nlm.nih.gov/dbvar/.
92. DGVa -http://www.ebi.ac.uk/dgva/
93. 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. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies, American journal of human genetics 86, 749-764.