A short primer on the functional analysis of copy number variation for biomedical scientists

Methods in Molecular Biology

Volumn 628, Issue , 2010, Pages 119-135

  Barnes, Michael R ^a   Breen, Gerome ^a  

^a NONE

Author keywords

Bioinformatics; CNV; Copy number; Deletion; Duplication; Genome; Variation

Indexed keywords

NERVE CELL ADHESION MOLECULE; NERVE PROTEIN; NRXN1 PROTEIN, HUMAN;

COPY NUMBER VARIATION; GENETICS; HUMAN; HUMAN GENOME; REVIEW; SCHIZOPHRENIA;

CELL ADHESION MOLECULES, NEURONAL; DNA COPY NUMBER VARIATIONS; GENOME, HUMAN; HUMANS; NERVE TISSUE PROTEINS; SCHIZOPHRENIA;

EID: 77952579118     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-367-1_7     Document Type: Review

References (37)

1. 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 identifes candidate loci for evolutionary and human disease studies. Hum. Mol. Genet., 17, 1127-1136.
2. Henrichsen, C.N., Chaignat, E. and Reymond, A. (2009) Copy number variants, diseases and gene expression. Hum. Mol. Genet., 18, R1-R8.
3. Freeman, J.L., Perry, G.H., Feuk, L., Redon, R., McCarroll, S.A., Altshuler, D.M., et al. (2006) Copy number variation: new insights in genome diversity. Genome Res., 16, 949-961.
4. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature, 447, 661-678.
5. McDermid, H.E. and Morrow, B.E. (2002) Genomic disorders on 22q11. Am. J. Hum. Genet., 70, 1077-1088.
6. Walsh, T., McClellan, J.M., McCarthy, S.E., Addington, A.M., Pierce, S.B., Cooper, G.M., et al. (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 320, 539-543.
7. Pritchard, J.K. (2001) Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet., 69, 124-137.
8. Stefansson, H., Rujescu, D., Cichon, S., Pietilainen, O.P., Ingason, A., Steinberg, S., et al. (2008) Large recurrent microdeletions associated with schizophrenia. Nature, 455, 232-236.
9. Scherer, S.W., Lee, C., Birney, E., Altshuler, D.M., Eichler, E.E., Carter, N.P., Hurles, M.E. and Feuk, L. (2007) Challenges and standards in integrating surveys of structural variation. Nat. Genet., 39, S7-S15.
10. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
11. Emanuel, B.S. and Saitta, S.C. (2007) From microscopes to microarrays: dissecting recurrent chromosomal rearrangements. Nat. Rev. Genet., 8, 869-883.
12. Khaja, R., Zhang, J., MacDonald, J.R., He, Y., Joseph-George, A.M., Wei, J., et al. (2006) Genome assembly comparison identifes structural variants in the human genome. Nat. Genet., 38, 1413-1418.
13. Fredman, D., White, S.J., Potter, S., Eichler, E.E., Den Dunnen, J.T. and Brookes, A.J. (2004) Complex SNP-related sequence variation in segmental genome duplications. Nat. Genet., 36, 861-866.
14. Shen, F., Huang, J., Fitch, K.R., Truong, V.B., Kirby, A., Chen, W., et al. (2008) Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes. BMC Genet., 9, 27.
15. Peiffer, D.A. and Gunderson, K.L. (2009) Design of tag SNP whole genome genotyping arrays. Methods Mol. Biol., 529, 51-61.
16. Colella, S., Yau, C., Taylor, J.M., Mirza, G., Butler, H., Clouston, P., Bassett, A.S., Seller, A., Holmes, C.C. and Ragoussis, J. (2007) QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res., 35, 2013-2025.
17. 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.
18. Lin, C.H., Huang, M.C., Li, L.H., Wu, J.Y., Chen, Y.T. and Fann, C.S. (2008) Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling. Hum. Mutat., 29, 1055-1062.
19. Xu, B., Roos, J.L., Levy, S., van Rensburg, E.J., Gogos, J.A. and Karayiorgou, M. (2008) Strong association of de novo copy number mutations with sporadic schizophrenia. Nat. Genet., 40, 880-885.
20. Marshall, C.R., Noor, A., Vincent, J.B., Lionel, A.C., Feuk, L., Skaug, J., et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet., 82, 477-488.
21. Yau, C. and Holmes, C.C. (2008) CNV discovery using SNP genotyping arrays. Cytogenet. Genome Res., 123, 307-312.
22. Casilli, F., Di Rocco, Z.C., Gad, S., Tournier, I., Stoppa-Lyonnet, D., Frebourg, T. and Tosi, M. (2002) Rapid detection of novel BRCA1 rearrangements in high-risk breast-ovarian cancer families using multiplex PCR of short fuorescent fragments. Hum. Mutat., 20, 218-226.
23. Wu, Y.L., Savelli, S.L., Yang, Y., Zhou, B., Rovin, B.H., Birmingham, D.J., Nagaraja, H.N., Hebert, L.A. and Yu, C.Y. (2007) Sensitive and specifc real-time polymerase chain reaction assays to accurately determine copy number variations (CNVs) of human complement C4A, C4B, C4-long, C4-short, and RCCX modules: elucidation of C4 CNVs in 50 consanguineous subjects with defned HLA genotypes. J. Immunol., 179, 3012-3025.
24. Sellner, L.N. and Taylor, G.R. (2004) MLPA and MAPH: new techniques for detection of gene deletions. Hum. Mutat., 23, 413-419.
25. Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., et al. (2007) Strong association of de novo copy number mutations with autism. Science, 316, 445-449.
26. Pugh, T.J., Delaney, A.D., Farnoud, N., Flibotte, S., Griffth, M., Li, H.I., Qian, H., Farinha, P., Gascoyne, R.D. and Marra, M.A. (2008) Impact of whole genome amplifca-tion on analysis of copy number variants. Nucleic Acids Res., 36, e80.
27. Bediaga, N.G., Alfonso-Sanchez, M.A., de Renobales, M., Rocandio, A.M., Arroyo, M. and de Pancorbo, M.M. (2008) GSTT1 and GSTM1 gene copy number analysis in paraf-fn-embedded tissue using quantitative realtime PCR. Anal. Biochem., 378, 221-223.
28. Cukier, H.N., Pericak-Vance, M.A., Gilbert, J.R. and Hedges, D.J. (2009) Sample degradation leads to false-positive copy number variation calls in multiplex real-time poly-merase chain reaction assays. Anal. Biochem., 386, 288-290.
29. Curtis, D., Vine, A.E. and Knight, J. (2008) Study of regions of extended homozygosity provides a powerful method to explore haplo-type structure of human populations. Ann. Hum. Genet., 72, 261-278.
30. Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J. and Eichler, E.E. (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res., 11, 1005-1017.
31. Silva, A.L. and Romao, L. (2009) The mammalian nonsense-mediated mRNA decay pathway: to decay or not to decay! Which players make the decision? FEBS Lett., 583, 499-505.
32. Pan, Q., Shai, O., Lee, L.J., Frey, B.J. and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
33. Rujescu, D., Ingason, A., Cichon, S., Pietilainen, O.P., Barnes, M.R., Toulopoulou, T., et al. (2009) Disruption of the neurexin 1 gene is associated with schizophrenia. Hum. Mol. Genet., 18, 988-996.
34. Rowen, L., Young, J., Birditt, B., Kaur, A., Madan, A., Philipps, D.L., et al. (2002) Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics, 79, 587-597.
35. Beglopoulos, V., Montag-Sallaz, M., Rohlmann, A., Piechotta, K., Ahmad, M., Montag, D. and Missler, M. (2005) Neurexophilin 3 is highly localized in cortical and cerebellar regions and is functionally important for sensorimotor gating and motor coordination. Mol. Cell Biol., 25, 7278-7288.
36. Liu, Q., Dinu, I., Adewale, A.J., Potter, J.D. and Yasui, Y. (2007) Comparative evaluation of gene-set analysis methods. BMC Bioinformatics, 8, 431.
37. Baranzini, S.E., Galwey, N.W., Wang, J., Khankhanian, P., Lindberg, R., Pelletier, D., et al. (2009) Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum. Mol. Genet. 18, 2078-2090.