Whole-genome CNV analysis: Advances in computational approaches

Frontiers in Genetics

Volumn 6, Issue MAR, 2015, Pages

  Pirooznia, Mehdi ^a   Goes, Fernando ^a   Zandi, Peter P ^a,b  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; ASSEMBLY BASED METHOD; CHROMOSOME BREAKAGE; COPY NUMBER VARIATION; EPIGENETICS; GENE MAPPING; GENE SEQUENCE; GENETIC PROCEDURES; GENETIC VARIABILITY; NEXT GENERATION SEQUENCING; POISSON DISTRIBUTION; READ DEPTH METHOD; READ PAIR METHOD; SPLIT READ METHOD; SUPPORT VECTOR MACHINE;

EID: 84927128250     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2015.00138     Document Type: Article

References (70)

1. Abel, H.J., and Duncavage, E.J. (2013). Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet 206, 432-440.
2. Abyzov, A., Urban, A.E., Snyder, M., and Gerstein, M. (2011). CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21, 974-984.
3. Alkan, C., Coe, B.P., and Eichler, E.E. (2011). Genome structural variation discovery and genotyping. Nat Rev Genet 12, 363-376.
4. Alkan, C., Kidd, J.M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J.O., Baker, C., Malig, M., Mutlu, O., Sahinalp, S.C., Gibbs, R.A., and Eichler, E.E. (2009). Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41, 1061-1067.
5. Alkodsi, A., Louhimo, R., and Hautaniemi, S. (2014). Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Brief Bioinform.
6. Bellos, E., Johnson, M.R., and Lj, M.C. (2012). cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data. Genome Biol 13, R120.
7. Benjamini, Y., and Speed, T.P. (2012). Summarizing and correcting the GC content bias in highthroughput sequencing. Nucleic Acids Res 40, e72.
8. 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., et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59.
9. Boeva, V., Zinovyev, A., Bleakley, K., Vert, J.P., Janoueix-Lerosey, I., Delattre, O., and Barillot, E. (2011). Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27, 268-269.
10. Castellani, C.A., Awamleh, Z., Melka, M.G., O'reilly, R.L., and Singh, S.M. (2014). Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. Twin Res Hum Genet 17, 108-120.
11. Chen, K., Wallis, J.W., Mclellan, M.D., Larson, D.E., Kalicki, J.M., Pohl, C.S., Mcgrath, S.D., Wendl, M.C., Zhang, Q., Locke, D.P., Shi, X., Fulton, R.S., Ley, T.J., Wilson, R.K., Ding, L., and Mardis, E.R. (2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6, 677-681.
12. 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.
13. Chu, C., Zhang, J., and Wu, Y. (2014). GINDEL: Accurate Genotype Calling of Insertions and Deletions from Low Coverage Population Sequence Reads. PLoS One 9, e113324.
14. Chung, B.H., Tao, V.Q., and Tso, W.W. (2014). Copy number variation and autism: new insights and clinical implications. J Formos Med Assoc 113, 400-408.
15. Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T.D., Barnes, C., Campbell, P., Fitzgerald, T., Hu, M., Ihm, C.H., Kristiansson, K., Macarthur, D.G., Macdonald, J.R., Onyiah, I., Pang, A.W., Robson, S., Stirrups, K., Valsesia, A., Walter, K., Wei, J., Wellcome Trust Case Control, C., Tyler-Smith, C., Carter, N.P., Lee, C., Scherer, S.W., and Hurles, M.E. (2010). Origins and functional impact of copy number variation in the human genome. Nature 464, 704- 712.
16. Cook, E.H., Jr., and Scherer, S.W. (2008). Copy-number variations associated with neuropsychiatric conditions. Nature 455, 919-923.
17. Duan, J., Zhang, J.G., Deng, H.W., and Wang, Y.P. (2013). Comparative studies of copy number variation detection methods for next-generation sequencing technologies. PLoS One 8, e59128.
18. Feuk, L., Carson, A.R., and Scherer, S.W. (2006). Structural variation in the human genome. Nat Rev Genet 7, 85-97.
19. Genomes Project, C., Abecasis, G.R., Altshuler, D., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., Hurles, M.E., and Mcvean, G.A. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.
20. Gillet-Markowska, A., Richard, H., Fischer, G., and Lafontaine, I. (2014). Ulysses: Accurate detection of low-frequency structural variations in large insert-size sequencing libraries. Bioinformatics.
21. Handsaker, R.E., Korn, J.M., Nemesh, J., and Mccarroll, S.A. (2011). Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet 43, 269-276.
22. Haraksingh, R.R., and Snyder, M.P. (2013). Impacts of variation in the human genome on gene regulation. J Mol Biol 425, 3970-3977.
23. Hart, S.N., Sarangi, V., Moore, R., Baheti, S., Bhavsar, J.D., Couch, F.J., and Kocher, J.P. (2013). SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations. PLoS One 8, e83356.
24. Hormozdiari, F., Alkan, C., Eichler, E.E., and Sahinalp, S.C. (2009). Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 19, 1270-1278.
25. 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.
26. Ivakhno, S., Royce, T., Cox, A.J., Evers, D.J., Cheetham, R.K., and Tavare, S. (2010). CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics 26, 3051-3058.
27. Janevski, A., Varadan, V., Kamalakaran, S., Banerjee, N., and Dimitrova, N. (2012). Effective normalization for copy number variation detection from whole genome sequencing. BMC Genomics 13 Suppl 6, S16.
28. Jiang, Y., Wang, Y., and Brudno, M. (2012). PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics 28, 2576-2583.
29. Kidd, J.M., Graves, T., Newman, T.L., Fulton, R., Hayden, H.S., Malig, M., Kallicki, J., Kaul, R., Wilson, R.K., and Eichler, E.E. (2010). A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143, 837-847.
30. Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.A., Mitterecker, A., Bodenhofer, U., and Hochreiter, S. (2012). cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res 40, e69.
31. Korbel, J.O., Abyzov, A., Mu, X.J., Carriero, N., Cayting, P., Zhang, Z., Snyder, M., and Gerstein, M.B. (2009). PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10, R23.
32. 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). Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426.
33. Layer, R.M., Chiang, C., Quinlan, A.R., and Hall, I.M. (2014). LUMPY: a probabilistic framework for structural variant discovery. Genome Biol 15, R84.
34. Le Scouarnec, S., and Gribble, S.M. (2012). Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity (Edinb) 108, 75-85.
35. Li, W., and Olivier, M. (2013). Current analysis platforms and methods for detecting copy number variation. Physiol Genomics 45, 1-16.
36. Li, X., Chen, S., Xie, W., Vogel, I., Choy, K.W., Chen, F., Christensen, R., Zhang, C., Ge, H., Jiang, H., Yu, C., Huang, F., Wang, W., Jiang, H., and Zhang, X. (2014). PSCC: sensitive and reliable populationscale copy number variation detection method based on low coverage sequencing. PLoS One 9, e85096.
37. Lindberg, M.R., Hall, I.M., and Quinlan, A.R. (2014). Population-based structural variation discovery with Hydra-Multi. Bioinformatics.
38. Liu, B., Morrison, C.D., Johnson, C.S., Trump, D.L., Qin, M., Conroy, J.C., Wang, J., and Liu, S. (2013). Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. Oncotarget 4, 1868-1881.
39. Macdonald, J.R., Ziman, R., Yuen, R.K., Feuk, L., and Scherer, S.W. (2014). The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res 42, D986-992.
40. Malhotra, D., and Sebat, J. (2012). CNVs: harbingers of a rare variant revolution in psychiatric genetics. Cell 148, 1223-1241.
41. Mardis, E.R. (2013). Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto Calif) 6, 287- 303.
42. Marschall, T., Hajirasouliha, I., and Schonhuth, A. (2013). MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics 29, 3143-3150.
43. Medvedev, P., Fiume, M., Dzamba, M., Smith, T., and Brudno, M. (2010). Detecting copy number variation with mated short reads. Genome Res 20, 1613-1622.
44. Medvedev, P., Stanciu, M., and Brudno, M. (2009). Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6, S13-20.
45. Miller, C.A., Hampton, O., Coarfa, C., and Milosavljevic, A. (2011). ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One 6, e16327.
46. Nguyen, H.T., Merriman, T.R., and Black, M.A. (2014). The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data. Front Genet 5, 248.
47. Nijkamp, J.F., Van Den Broek, M.A., Geertman, J.M., Reinders, M.J., Daran, J.M., and De Ridder, D. (2012). De novo detection of copy number variation by co-assembly. Bioinformatics 28, 3195- 3202.
48. O'dushlaine, C., Ripke, S., Ruderfer, D.M., Hamilton, S.P., Fava, M., Iosifescu, D.V., Kohane, I.S., Churchill, S.E., Castro, V.M., Clements, C.C., Blumenthal, S.R., Murphy, S.N., Smoller, J.W., and Perlis, R.H. (2014). Rare copy number variation in treatment-resistant major depressive disorder. Biol Psychiatry 76, 536-541.
49. Olson, H., Shen, Y., Avallone, J., Sheidley, B.R., Pinsky, R., Bergin, A.M., Berry, G.T., Duffy, F.H., Eksioglu, Y., Harris, D.J., Hisama, F.M., Ho, E., Irons, M., Jacobsen, C.M., James, P., Kothare, S., Khwaja, O., Lipton, J., Loddenkemper, T., Markowitz, J., Maski, K., Megerian, J.T., Neilan, E., Raffalli, P.C., Robbins, M., Roberts, A., Roe, E., Rollins, C., Sahin, M., Sarco, D., Schonwald, A., Smith, S.E., Soul, J., Stoler, J.M., Takeoka, M., Tan, W.H., Torres, A.R., Tsai, P., Urion, D.K., Weissman, L., Wolff, R., Wu, B.L., Miller, D.T., and Poduri, A. (2014). Copy number variation plays an important role in clinical epilepsy. Ann Neurol 75, 943-958.
50. Pinto, D., Pagnamenta, A.T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T.R., Correia, C., Abrahams, B.S., Almeida, J., Bacchelli, E., Bader, G.D., Bailey, A.J., Baird, G., Battaglia, A., Berney, T., Bolshakova, N., Bolte, S., Bolton, P.F., Bourgeron, T., Brennan, S., Brian, J., Bryson, S.E., Carson, A.R., Casallo, G., Casey, J., Chung, B.H., Cochrane, L., Corsello, C., Crawford, E.L., Crossett, A., Cytrynbaum, C., Dawson, G., De Jonge, M., Delorme, R., Drmic, I., Duketis, E., Duque, F., Estes, A., Farrar, P., Fernandez, B.A., Folstein, S.E., Fombonne, E., Freitag, C.M., Gilbert, J., Gillberg, C., Glessner, J.T., Goldberg, J., Green, A., Green, J., Guter, S.J., Hakonarson, H., Heron, E.A., Hill, M., Holt, R., Howe, J.L., Hughes, G., Hus, V., Igliozzi, R., Kim, C., Klauck, S.M., Kolevzon, A., Korvatska, O., Kustanovich, V., Lajonchere, C.M., Lamb, J.A., Laskawiec, M., Leboyer, M., Le Couteur, A., Leventhal, B.L., Lionel, A.C., Liu, X.Q., Lord, C., Lotspeich, L., Lund, S.C., Maestrini, E., Mahoney, W., Mantoulan, C., Marshall, C.R., Mcconachie, H., Mcdougle, C.J., Mcgrath, J., Mcmahon, W.M., Merikangas, A., Migita, O., Minshew, N.J., Mirza, G.K., Munson, J., Nelson, S.F., Noakes, C., Noor, A., Nygren, G., Oliveira, G., Papanikolaou, K., Parr, J.R., Parrini, B., Paton, T., Pickles, A., Pilorge, M., et al. (2010). Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368-372.
51. Rausch, T., Zichner, T., Schlattl, A., Stutz, A.M., Benes, V., and Korbel, J.O. (2012). DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339.
52. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M., Navin, N., Lucito, R., Healy, J., Hicks, J., Ye, K., Reiner, A., Gilliam, T.C., Trask, B., Patterson, N., Zetterberg, A., and Wigler, M. (2004). Large-scale copy number polymorphism in the human genome. Science 305, 525-528.
53. Sindi, S.S., Onal, S., Peng, L.C., Wu, H.T., and Raphael, B.J. (2012). An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol 13, R22.
54. Tan, R., Wang, Y., Kleinstein, S.E., Liu, Y., Zhu, X., Guo, H., Jiang, Q., Allen, A.S., and Zhu, M. (2014). An evaluation of copy number variation detection tools from whole-exome sequencing data. Hum Mutat 35, 899-907.
55. Teo, S.M., Pawitan, Y., Ku, C.S., Chia, K.S., and Salim, A. (2012). Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 28, 2711- 2718.
56. Trappe, K., Emde, A.K., Ehrlich, H.C., and Reinert, K. (2014). Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics.
57. Wang, J., Mullighan, C.G., Easton, J., Roberts, S., Heatley, S.L., Ma, J., Rusch, M.C., Chen, K., Harris, C.C., Ding, L., Holmfeldt, L., Payne-Turner, D., Fan, X., Wei, L., Zhao, D., Obenauer, J.C., Naeve, C., Mardis, E.R., Wilson, R.K., Downing, J.R., and Zhang, J. (2011). CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 8, 652-654.
58. Wang, L.Y., Abyzov, A., Korbel, J.O., Snyder, M., and Gerstein, M. (2009). MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res 19, 106-117.
59. Xi, R., Hadjipanayis, A.G., Luquette, L.J., Kim, T.M., Lee, E., Zhang, J., Johnson, M.D., Muzny, D.M., Wheeler, D.A., Gibbs, R.A., Kucherlapati, R., and Park, P.J. (2011). Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A 108, E1128-1136.
60. Xi, R., Kim, T.M., and Park, P.J. (2010). Detecting structural variations in the human genome using next generation sequencing. Brief Funct Genomics 9, 405-415.
61. Xi, R., Lee, S., and Park, P.J. (2012). A survey of copy-number variation detection tools based on highthroughput sequencing data. Curr Protoc Hum Genet Chapter 7, Unit7 19.
62. Xie, C., and Tammi, M.T. (2009). CNV-seq, a new method to detect copy number variation using highthroughput sequencing. BMC Bioinformatics 10, 80.
63. Ye, K., Schulz, M.H., Long, Q., Apweiler, R., and Ning, Z. (2009). Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871.
64. Yoon, S., Xuan, Z., Makarov, V., Ye, K., and Sebat, J. (2009). Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19, 1586-1592.
65. Zeitouni, B., Boeva, V., Janoueix-Lerosey, I., Loeillet, S., Legoix-Ne, P., Nicolas, A., Delattre, O., and Barillot, E. (2010). SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics 26, 1895-1896.
66. Zhang, J., Wang, J., and Wu, Y. (2012). An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. BMC Bioinformatics 13 Suppl 6, S6.
67. Zhang, Z.D., Du, J., Lam, H., Abyzov, A., Urban, A.E., Snyder, M., and Gerstein, M. (2011). Identification of genomic indels and structural variations using split reads. BMC Genomics 12, 375.
68. Zhao, M., Wang, Q., Wang, Q., Jia, P., and Zhao, Z. (2013). Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 14 Suppl 11, S1.
69. Zhou, J., Lemos, B., Dopman, E.B., and Hartl, D.L. (2011). Copy-number variation: the balance between gene dosage and expression in Drosophila melanogaster. Genome Biol Evol 3, 1014-1024.
70. Zhu, M., Need, A.C., Han, Y., Ge, D., Maia, J.M., Zhu, Q., Heinzen, E.L., Cirulli, E.T., Pelak, K., He, M., Ruzzo, E.K., Gumbs, C., Singh, A., Feng, S., Shianna, K.V., and Goldstein, D.B. (2012). Using ERDS to infer copy-number variants in high-coverage genomes. Am J Hum Genet 91, 408-421.