Analysis of next-generation genomic data in cancer: Accomplishments and challenges

Human Molecular Genetics

Volumn 19, Issue R2, 2010, Pages

  Ding, Li ^a   Wendl, Michael C ^a   Koboldt, Daniel C ^a   Mardis, Elaine R ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER GENETICS; GENE DELETION; GENE DOSAGE; GENE INSERTION; GENE MUTATION; GENE REGULATORY NETWORK; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENOMICS; HUMAN; METHYLATION; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; DNA SEQUENCE; GENETICS; METHODOLOGY; NEOPLASM; REVIEW; STATISTICS;

GENOMICS; HUMANS; NEOPLASMS; SEQUENCE ANALYSIS, DNA;

EID: 78650791604     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddq391     Document Type: Article

References (54)

1. 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. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
2. Koboldt, D.C., Chen, K., Wylie, T., Larson, D.E., McLellan, M.D., Mardis, E.R., Weinstock, G.M., Wilson, R.K. and Ding, L. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25, 2283-2285.
3. Shen, Y., Wan, Z., Coarfa, C., Drabek, R., Chen, L., Ostrowski, E.A., Liu, Y., Weinstock, G.M., Wheeler, D.A., Gibbs, R.A. et al. (2010) A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res., 20, 273-280.
4. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
5. Li, R., Li, Y., Kristiansen, K. and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
6. Goya, R., Sun, M.G., Morin, R.D., Leung, G., Ha, G., Wiegand, K.C., Senz, J., Crisan, A., Marra, M.A., Hirst, M. et al. (2010) SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics, 26, 730-736.
7. Shah, S.P., Morin, R.D., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., Delaney, A., Gelmon, K., Guliany, R., Senz, J. et al. (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809-813.
8. Mardis, E.R., Ding, L., Dooling, D.J., Larson, D.E., McLellan, M.D., Chen, K., Koboldt, D.C., Fulton, R.S., Delehaunty, K.D., McGrath, S.D. et al. (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med., 361, 1058-1066.
9. Ding, L., Ellis, M.J., Li, S., Larson, D.E., Chen, K., Wallis, J.W., Harris, C.C., McLellan, M.D., Fulton, R.S., Fulton, L.L. et al. (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464, 999-1005.
10. Wood, L.D., Parsons, D.W., Jones, S., Lin, J., Sjoblom, T., Leary, R.J., Shen, D., Boca, S.M., Barber, T., Ptak, J. et al. (2007) The genomic landscapes of human breast and colorectal cancers. Science, 318, 1108-1113.
11. Ding, L., Getz, G., Wheeler, D.A., Mardis, E.R., McLellan, M.D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D.M., Morgan, M.B. et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455, 1069-1075.
12. 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.
13. Ye, K., Kosters, W.A. and Ijzerman, A.P. (2007) An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. Bioinformatics, 23, 687-693.
14. Bignell, G.R., Greenman, C.D., Davies, H., Butler, A.P., Edkins, S., Andrews, J.M., Buck, G., Chen, L., Beare, D., Latimer, C. et al. (2010) Signatures of mutation and selection in the cancer genome. Nature, 463, 893-898.
15. Beroukhim, R., Mermel, C.H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J.S., Dobson, J., Urashima, M. et al. (2010) The landscape of somatic copy-number alteration across human cancers. Nature, 463, 899-905.
16. Shih Ie, M., Sheu, J.J., Santillan, A., Nakayama, K., Yen, M.J., Bristow, R.E., Vang, R., Parmigiani, G., Kurman, R.J., Trope, C.G. et al. (2005) Amplification of a chromatin remodeling gene, Rsf-1/HBXAP, in ovarian carcinoma. Proc. Natl Acad. Sci. USA, 102, 14004-14009.
17. Leary, R.J., Cummins, J., Wang, T.L. and Velculescu, V.E. (2007) Digital karyotyping. Nat. Protoc., 2, 1973-1986.
18. Morozova, O. and Marra, M.A. (2008) From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. Biochem. Cell Biol., 86, 81-91.
19. Salani, R., Chang, C.L., Cope, L. and Wang, T.L. (2006) Digital karyotyping: an update of its applications in cancer. Mol. Diagn. Ther., 10, 231-237.
20. Wang, T.L., Maierhofer, C., Speicher, M.R., Lengauer, C., Vogelstein, B., Kinzler, K.W. and Velculescu, V.E. (2002) Digital karyotyping. Proc. Natl Acad. Sci. USA, 99, 16156-16161.
21. Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32.
22. McKernan, K.J., Peckham, H.E., Costa, G.L., McLaughlin, S.F., Fu, Y., Tsung, E.F., Clouser, C.R., Duncan, C., Ichikawa, J.K., Lee, C.C. et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res., 19, 1527-1541.
23. 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.
24. Campbell, P.J., Stephens, P.J., Pleasance, E.D., O'Meara, S., Li, H., Santarius, T., Stebbings, L.A., Leroy, C., Edkins, S., Hardy, C. et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet., 40, 722-729.
25. 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.
26. Zhang, Q., Ding, L., Larson, D.E., Koboldt, D.C., McLellan, M.D., Chen, K., Shi, X., Kraja, A., Mardis, E.R., Wilson, R.K. et al. (2010) CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics, 26, 464-469.
27. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N. and Stratton, M.R. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
28. Raphael, B.J., Volik, S., Collins, C. and Pevzner, P.A. (2003) Reconstructing tumor genome architectures. Bioinformatics, 19(Suppl. 2), ii162-ii171.
29. Raphael, B.J., Volik, S., Yu, P., Wu, C., Huang, G., Linardopoulou, E.V., Trask, B.J., Waldman, F., Costello, J., Pienta, K.J. et al. (2008) A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol., 9, R59.
30. Volik, S., Raphael, B.J., Huang, G., Stratton, M.R., Bignel, G., Murnane, J., Brebner, J.H., Bajsarowicz, K., Paris, P.L., Tao, Q. et al. (2006) Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res., 16, 394-404.
31. Volik, S., Zhao, S., Chin, K., Brebner, J.H., Herndon, D.R., Tao, Q., Kowbel, D., Huang, G., Lapuk, A., Kuo, W.L. et al. (2003) End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA, 100, 7696-7701.
32. Bignell, G.R., Santarius, T., Pole, J.C., Butler, A.P., Perry, J., Pleasance, E., Greenman, C., Menzies, A., Taylor, S., Edkins, S. et al. (2007) Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res., 17, 1296-1303.
33. Clark, M.J., Homer, N., O'Connor, B.D., Chen, Z., Eskin, A., Lee, H., Merriman, B. and Nelson, S.F. (2010) U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet., 6, e1000832.
34. Pleasance, E.D., Cheetham, R.K., Stephens, P.J., McBride, D.J., Humphray, S.J., Greenman, C.D., Varela, I., Lin, M.L., Ordonez, G.R., Bignell, G.R. et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191-196.
35. Pleasance, E.D., Stephens, P.J., O'Meara, S., McBride, D.J., Meynert, A., Jones, D., Lin, M.L., Beare, D., Lau, K.W., Greenman, C. et al. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 463, 184-190.
36. Lee, W., Jiang, Z., Liu, J., Haverty, P.M., Guan, Y., Stinson, J., Yue, P., Zhang, Y., Pant, K.P., Bhatt, D. et al. (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature, 465, 473-477.
37. Sindi, S., Helman, E., Bashir, A. and Raphael, B.J. (2009) A geometric approach for classification and comparison of structural variants. Bioinformatics, 25, i222-i230.
38. 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. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
39. Smith, D.R., Quinlan, A.R., Peckham, H.E., Makowsky, K., Tao, W., Woolf, B., Shen, L., Donahue, W.F., Tusneem, N., Stromberg, M.P. et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res., 18, 1638-1642.
40. Ng, S.B., Turner, E.H., Robertson, P.D., Flygare, S.D., Bigham, A.W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E.E. et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272-276.
41. Sjoblom, T., Jones, S., Wood, L.D., Parsons, D.W., Lin, J., Barber, T.D., Mandelker, D., Leary, R.J., Ptak, J., Silliman, N. et al. (2006) The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268-274.
42. The Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
43. Parsons, D.W., Jones, S., Zhang, X., Lin, J.C., Leary, R.J., Angenendt, P., Mankoo, P., Carter, H., Siu, I.M., Gallia, G.L. et al. (2008) An integrated genomic analysis of human glioblastoma multiforme. Science, 321, 1807-1812.
44. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G.L., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C. et al. (2007) Patterns of somatic mutation in human cancer genomes. Nature, 446, 153-158.
45. Ley, T.J., Mardis, E.R., Ding, L., Fulton, B., McLellan, M.D., Chen, K., Dooling, D., Dunford-Shore, B.H., McGrath, S., Hickenbotham, M. et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66-72.
46. Clark, M.J., Homer, N., O'Connor, B.D., Chen, Z., Eskin, A., Lee, H., Merriman, B. and Nelson, S.F. (2010) U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet., 6, e1000832.
47. Stephens, P., Edkins, S., Davies, H., Greenman, C., Cox, C., Hunter, C., Bignell, G., Teague, J., Smith, R., Stevens, C. et al. (2005) A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat. Genet., 37, 590-592.
48. Rubin, A.F. and Green, P. (2009) Mutation patterns in cancer genomes. Proc. Natl Acad. Sci. USA, 106, 21766-21770.
49. Jones, S., Zhang, X., Parsons, D.W., Lin, J.C., Leary, R.J., Angenendt, P., Mankoo, P., Carter, H., Kamiyama, H., Jimeno, A. et al. (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science, 321, 1801-1806.
50. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic. Acids Res., 36, D480-D484.
51. Lin, J., Gan, C.M., Zhang, X., Jones, S., Sjoblom, T., Wood, L.D., Parsons, D.W., Papadopoulos, N., Kinzler, K.W., Vogelstein, B. et al. (2007) A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res., 17, 1304-1318.
52. Cerami, E., Demir, E., Schultz, N., Taylor, B.S. and Sander, C. (2010) Automated network analysis identifies core pathways in glioblastoma. PLoS ONE, 5, e8918.
53. Girvan, M. and Newman, M.E. (2002) Community structure in social and biological networks. Proc. Natl Acad. Sci. USA, 99, 7821-7826.
54. Vandin, F., Upfal, F. and Raphael, B.J. (2010) Algorithms for detecting significantly mutated pathways in cancer. Lect. Notes Comput. Sci., 6044, 506-521.