e105 Nucleic Acids Research, 2010, Vol. 38, No. 9 6. Wang,K., Li,M., Hadley,D., Liu,R., Glessner,J., Grant,S.F., Hakonarson,H. and Bucan,M. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res., 17, 1665–1674. 7. Hupe´ ,P., Stransky,N., Thiery,J.P., Radvanyi,F. and Barillot,E. (2004) Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics, 20, 3413–3422. 8. Olshen,A.B., Venkatraman,E.S., Lucito,R. and Wigler,M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557–572. 9. Fiegler,H., Redon,R., Andrews,D., Scott,C., Andrews,R., Carder,C., Clark,R., Dovey,O., Ellis,P., Feuk,L. et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res., 16, 1566–1574. 10. Lai,W.R., Johnson,M.D., Kucherlapati,R. and Park,P.J. (2005) Comparative analysis of algorithms for identifying ampliﬁcations and deletions in array CGH data. Bioinformatics, 21, 3763–3770. 11. 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. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444–454. 12. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M., Marshall,K.A. et al. (2009) NCBI GEO: archive for PAGE 14 OF 14 high-throughput functional genomic data. Nucleic Acids Res., 37, D885–D890. 13. Chiang,D.Y., Getz,G., Jaﬀe,D.B., O’Kelly,M.J., Zhao,X., Carter,S.L., Russ,C., Nusbaum,C., Meyerson,M. and Lander,E.S. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99–103. 14. Blauw,H.M., Veldink,J.H., van Es,M.A., Van Vught,P.W., Saris,C.G., van der,Z.B., Franke,L., Burbach,J.P., Wokke,J.H., Ophoﬀ,R.A. et al. (2008) Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen. Lancet Neurol., 7, 319–326. 15. Glessner,J.T., Wang,K., Cai,G., Korvatska,O., Kim,C.E., Wood,S., Zhang,H., Estes,A., Brune,C.W., Bradﬁeld,J.P. et al. (2009) Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature, 459, 569–573. 16. Vrijenhoek,T., Buizer-Voskamp,J.E., van,d.S.I., Strengman,E., Sabatti,C., van Geurts,K.A., Brunner,H.G., Ophoﬀ,R.A. and Veltman,J.A. (2008) Recurrent CNVs disrupt three candidate genes in schizophrenia patients. Am. J. Hum. Genet., 83, 504–510. 17. Fiegler,H., Geigl,J.B., Langer,S., Rigler,D., Porter,K., Unger,K., Carter,N.P. and Speicher,M.R. (2007) High resolution array-CGH analysis of single cells. Nucleic Acids Res., 35, e15. 18. Pugh,T.J., Delaney,A.D., Farnoud,N., Flibotte,S., Griﬃth,M., Li,H.I., Qian,H., Farinha,P., Gascoyne,R.D. and Marra,M.A. (2008) Impact of whole genome ampliﬁcation on analysis of copy number variants. Nucleic Acids Res., 36, e80.