NFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

Genome Research

Volumn 22, Issue 11, 2012, Pages 2250-2261

  McPherson, Andrew ^a   Wu, Chunxiao ^b   Wyatt, Alexander W ^b   Shah, Sohrab ^c   Collins, Colin ^b   Sahinalp, S Cenk ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b VANCOUVER PROSTATE CENTRE   (Canada)

^c BRITISH COLUMBIA CANCER RESEARCH CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

ALGORITHM; ARTICLE; BREAST CANCER; CANCER CELL CULTURE; CELL FUNCTION; COMPLEX GENOMIC REARRANGEMENT; GENE EXPRESSION; GENE FUSION; GENE REARRANGEMENT; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; MOLECULAR MECHANICS; PRIMARY TUMOR; PRIORITY JOURNAL; PROSTATE TUMOR; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; BREAST NEOPLASMS; CELL LINE, TUMOR; CHROMOSOME BREAKAGE; DNA, NEOPLASM; FEMALE; GENE FUSION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; NEOPLASMS; PROSTATIC NEOPLASMS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; TRANSLOCATION, GENETIC;

EID: 84868332770     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.136572.111     Document Type: Article

References (31)

1. Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, et al. 2011. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res 39: e100. doi:10.1093/nar/ gkr362.
2. Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. 2008. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol 4: e1000051. doi:10.1371/journal. pcbi.1000051.
3. Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, Robinson J, Verhaak RG, Sougnez C, et al. 2010. Integrative analysis of the melanoma transcriptome. Genome Res 20:413-427.
4. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, et al. 2011. The genomic complexity of primary human prostate cancer. Nature 470:214-220.
5. Bignell GR, Santarius T, Pole JC, Butler AP, 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.
6. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. 2009. BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677-681.
7. Dave SS, Fu K, Wright GW, Lam LT, Kluin P, Boerma EJ, Greiner TC, Weisenburger DD, Rosenwald A, Ott G, et al. 2006. Molecular diagnosis of Burkitt's lymphoma. N Engl J Med 354:2431-2442.
8. Galante P, Parmigiani R, Zhao Q, Caballero O, de Souza J, Navarro F, Gerber A, Nicolás M, Salim A, Silva A, et al. 2011. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res 39:6056-6068.
9. Greenman CD, Pleasance ED, Newman S, Yang F, Fu B, Nik-Zainal S, Jones D, Lau KW, Carter N, Edwards PA, et al. 2011. Estimation of rearrangement phylogeny for cancer genomes. Genome Res 22:346-361.
10. Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. 2009. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 19:1270-1278.
11. Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. 2011. Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Res 21:2203-2212.
12. Langmead B, Salzberg S. 2012. Fast gapped-read alignment with bowtie 2. Nat Methods 9:357-359.
13. Lin C, Yang L, Tanasa B, Hutt K, Ju B, Ohgi K, Zhang J, Rose D, Fu X, Glass C, et al. 2009. Nuclear receptor-induced chromosomal proximity and dna breaks underlie specific translocations in cancer. Cell 139:1069-1083.
14. McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun M, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, et al. 2011a. deFuse: An algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 7: e1001138. doi:10.1371/journal.pcbi.1001138.
15. McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp C, et al. 2011b. Comrad: Detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics 27:1481-1488.
16. Mitelman F, Johansson B, Mertens F. 2007. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7:233-245.
17. Nambiar M, Raghavan S. 2011. How does DNA break during chromosomal translocations? Nucleic Acids Res 39:5813-5825.
18. Ozery-Flato M, Shamir R. 2009. Sorting cancer karyotypes by elementary operations. J Comput Biol 16:1445-1460.
19. Pevzner P. 2000. Computational molecular biology: An algorithmic approach (Computational Molecular Biology). MIT Press, Cambridge, MA.
20. Raphael BJ, Pevzner PA. 2004. Reconstructing tumor amplisomes. Bioinformatics 20:265-273.
21. Raphael BJ, Volik S, Collins C, Pevzner PA. 2003. Reconstructing tumor genome architectures. Bioinformatics 19:162-171.
22. Shah S, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, et al. 2012. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486:395-399.
23. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, et al. 2009. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462:1005-1010.
24. Stephens P, Greenman C, Fu B, Yang F, Bignell G, Mudie L, Pleasance E, Lau K, Beare D, Stebbings L, et al. 2011. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:27-40.
25. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, et al. 2005. Fine-scale structural variation of the human genome. Nat Genet 37:727-732.
26. Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo WL, et al. 2003. End-sequence profiling: Sequence-based analysis of aberrant genomes. Proc Natl Acad Sci 100:7696-7701.
27. Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, et al. 2011. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 8:652-654.
28. Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJM, Zhao Y, et al. 2012a. Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosomes Cancer. doi:10.1002/gcc.21999.
29. Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, et al. 2012b. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol 227:53-61.
30. Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, et al. 2009. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci 106:1886-1891.
31. Zhao Q, Kirkness E, Caballero O, Galante P, Parmigiani R, Edshall L, Kuan S, Ye Z, Levy S, Vasconcelos A, et al. 2010. Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.Genome Biol 11: R114. doi:10.1186/gb-2010-11-11-r114.