CANOES: Detecting rare copy number variants from whole exome sequencing data

Nucleic Acids Research

Volumn 42, Issue 12, 2014, Pages

  Backenroth, Daniel ^a,b   Homsy, Jason ^c,d   Murillo, Laura R ^e   Glessner, Joe ^f   Lin, Edwin ^a   Brueckner, Martina ^g   Lifton, Richard ^g,h   Goldmuntz, Elizabeth ⁱ   Chung, Wendy K ^a   Shen, Yufeng ^a,b  

^a New York Presbyterian Morgan Stanley Children's Hospital   (United States)

^b Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^f CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^g YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h YALE UNIVERSITY   (United States)

ⁱ UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; GUANINE;

ACCURACY; ARTICLE; BINOMIAL DISTRIBUTION; CANOES ALGORITHM; COPY NUMBER VARIATION; EXOME; EXON; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ASSOCIATION; HIDDEN MARKOV MODEL; INTERMETHOD COMPARISON; KERNEL METHOD; MICROARRAY ANALYSIS; POISSON DISTRIBUTION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEX CHROMOSOME; XHMM ALGORITHM; Y CHROMOSOME;

ALGORITHMS; DNA COPY NUMBER VARIATIONS; EXOME; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 84903977447     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku345     Document Type: Article

References (22)

1. Coe, B.P., Girirajan, S., Eichler, E.E. (2012) A genetic model for neurodevelopmental disease. Curr. Opin. Neurobiol., 22, 829-836.
2. Wheeler, E., Huang, N., Bochukova, E.G., Keogh, J.M., Lindsay, S., Garg, S., Henning, E., Blackburn, H., Loos, R.J.F., Wareham, N.J. et al. (2013) Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. Nat. Genet., 45, 513-517.
3. International Schizophrenia Consortium. (2008) Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature, 455, 237-241.
4. Buxbaum, J.D., Daly, M.J., Devlin, B., Lehner, T., Roeder, K., State, M.W. (2012) The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders. Neuron, 76, 1052-1056.
5. Rovelet-Lecrux, A., Legallic, S., Wallon, D., Flaman, J.-M., Martinaud, O., Bombois, S., Rollin-Sillaire, A., Michon, A., Le Ber, I., Pariente, J. et al. (2012) A genome-wide study reveals rare CNVs exclusive to extreme phenotypes of Alzheimer disease. Eur. J. Hum. Genet., 20, 613-617.
6. Pylkäs, K., Vuorela, M., Otsukka, M., Kallioniemi, A., Jukkola-Vuorinen, A., Winqvist, R. (2012) Rare copy number variants observed in hereditary breast cancer cases disrupt genes in estrogen signaling and TP53 tumor suppression network. PLoS Genet., 8, e1002734.
7. Girirajan, S., Campbell, C.D., Eichler, E.E. (2011) Human copy number variation and complex genetic disease. Annu. Rev. Genet., 45, 203-226.
8. Girirajan, S., Dennis, M.Y., Baker, C., Malig, M., Coe, B.P., Campbell, C.D., Mark, K., Vu, T.H., Alkan, C., Cheng, Z. et al. (2013) Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. Am. J. Hum. Genet., 92, 221-237.
9. Krumm, N., Sudmant, P.H., Ko, A., O'Roak, B.J., Malig, M., Coe, B.P., NHLBI Exome Sequencing Project, N.NHLBI Exome Sequencing Project, N., Quinlan, A.R., Nickerson, D.A., Eichler, E.E. (2012) Copy number variation detection and genotyping from exome sequence data. Genome Res., 1525-1532.
10. Fromer, M., Moran, J.L., Chambert, K., Banks, E., Bergen, S.E., Ruderfer, D.M., Handsaker, R.E., McCarroll, S.A., O'Donovan, M.C., Owen, M.J. et al. (2012) Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am. J. Hum. Genet., 91, 597-607.
11. Clark, M.J., Chen, R., Lam, H.Y.K., Karczewski, K.J., Chen, R., Euskirchen, G., Butte, A.J., Snyder, M. (2011) Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol., 29, 908-914.
12. Sathirapongsasuti, J.F., Lee, H., Horst, B.A.J., Brunner, G., Cochran, A.J., Binder, S., Quackenbush, J., Nelson, S.F. (2011) Exome sequencing-based copy-number variation and loss of heterozygosity detection: exome CNV. Bioinformatics, 27, 2648-2654.
13. Plagnol, V., Curtis, J., Epstein, M., Mok, K., Stebbings, E., Grigoriadou, S., Wood, N.W., Hambleton, S., Burns, S.O., Thrasher, A. et al. (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics, 28, 2747-2754.
14. Anders, S., Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
15. Love, M.I., Myšičková, A., Sun, R., Kalscheuer, V., Vingron, M., Haas, S.A. (2011) Modeling read counts for CNV detection in exome sequencing data. Stat. Appl. Genet. Mol. Biol., 10.
16. Ramachandran, A., Micsinai, M., Pe'er, I. (2011), BIBM Workshops, pp. 87-93.
17. Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F.A., Hakonarson, H., 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.
18. Brennecke, P., Anders, S., Kim, J.K., Kolodziejczyk, A.A., Zhang, X., Proserpio, V., Baying, B., Benes, V., Teichmann, S.A., Marioni, J.C. et al. (2013) Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods, 10, 1093-1095.
19. Zaidi, S., Choi, M., Wakimoto, H., Ma, L., Jiang, J., Overton, J.D., Romano-Adesman, A., Bjornson, R.D., Breitbart, R.E., Brown, K.K. et al. (2013) De novo mutations in histone-modifying genes in congenital heart disease. Nature, 498, 220-223.
20. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Maller, J., Sklar, P., de Bakker, P.I.W., Daly, M.J. et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
21. Pinheiro, L.B., Coleman, V.A., Hindson, C.M., Herrmann, J., Hindson, B.J., Bhat, S., Emslie, K.R. (2011) Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal. Chem., 84, 1003-1011.
22. Soemedi, R., Wilson, Ian, J., Bentham, J., Darlay, R., Töpf, A., Zelenika, D., Cosgrove, C., Setchfield, K., Thornborough, C., Granados-Riveron, J. et al. (2012) Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease. Am. J. Hum. Genet., 91, 489-501.