Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation

BMC Medical Genomics

Volumn 8, Issue 1, 2015, Pages

  Mittal, Vinay K ^a   McDonald, John F ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE TRANSPORTER 1;

ARTICLE; CANCER GROWTH; CLINICAL ARTICLE; CONTROLLED STUDY; FARP1 GENE; FEMALE; GENE; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUSION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GERMLINE MUTATION; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; OVARY CANCER; PRIORITY JOURNAL; RP127O53 GENE; SLC15A1 GENE; SOMATIC MUTATION; ZNF643 GENE; CHROMOSOMAL MAPPING; CHROMOSOME BREAKAGE; DISEASE COURSE; DNA SEQUENCE; GENETIC VARIATION; GENETICS; INTRON; OVARY TUMOR; SYSTEM ANALYSIS;

CHROMOSOME BREAKAGE; CHROMOSOME MAPPING; DISEASE PROGRESSION; FEMALE; GENE EXPRESSION PROFILING; GENE FUSION; GENETIC VARIATION; HUMANS; INTRONS; OVARIAN NEOPLASMS; SEQUENCE ANALYSIS, DNA; SYSTEMS INTEGRATION;

EID: 84988603266     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/s12920-015-0118-9     Document Type: Article

References (51)

1. Lupski JR, Stankiewicz P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 2005;1:e49.
2. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191-6.
3. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Can. 2004;4:177-83.
4. Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458:719-24.
5. Edwards PA. Fusion genes and chromosome translocations in the common epithelial cancers. J Path. 2010;220:244-54.
6. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007;318:420-6.
7. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009;462:1005-10.
8. Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, et al. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Gen Res. 2011;21:665-75.
9. Rabbitts TH. Chromosomal translocations in human cancer. Nature. 1994;372:143-9.
10. Rowley JD. Chromosome translocations: dangerous liaisons revisited. Nat Rev Can. 2001;1:245-50.
11. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Can. 2007;7:233-45.
12. Nowell PC. The minute chromosome (Phl) in chronic granulocytic leukemia. Blut. 1962;8:65-6.
13. Rowley JD. Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature. 1973;243:290-3.
14. Lugo TG, Pendergast AM, Muller AJ, Witte ON. Tyrosine kinase activity and transformation potency of Bcr-Abl oncogene products. Science. 1990;247:1079-82.
15. Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol. 2008;4:e1000051.
16. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008;40:722-9.
17. Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Meth. 2009;6:S13-20.
18. Murphy SJ, Cheville JC, Zarei S, Johnson SH, Sikkink RA, Kosari F, et al. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer. DNA Res. 2012;19:395-406.
19. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, et al. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Gen Res. 2010;20:623-35.
20. Jiao X, Rosenlund M, Hooper SD, Tellgren-Roth C, He L, Fu Y, et al. Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing. PLoS ONE. 2011;6:e22250.
21. Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, et al. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Gen Res. 2013;2013(23):762-76.
22. Li H, Wang J, Mor G, Sklar J. A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science. 2008;321:1357-61.
23. The Cancer Genome Atlas. [TCGA, http://cancergenome.nih.gov/] data portal [https://tcga-data.nci.nih.gov/tcga/].
24. Picard Tools. [http://broadinstitute.github.io/picard/].
25. BamToFastQ program. [http://genome.sph.umich.edu/wiki/BamUtil].
26. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012;9:357-9.
27. Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-ne P, Nicolas A, et al. SVDetect: a tool to identify genomic structural variations from pairedend and mate-pair sequencing data. Bioinformatics. 2010;26:1895-6.
28. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, et al. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009;10:R23.
29. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Gen Res. 2009;19:1117-23.
30. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, et al. De novo assembly and analysis of RNA-seq data. Nat Meth. 2010;7:909-12.
31. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Gen Res. 2008;18:821-9.
32. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
33. Mittal VK, McDonald JF. R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nuc Acids Res. 2012;40:e67.
34. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Gen Res. 2001;11:1725-9.
35. TrimGalore. [http://www.bioinformatics.babraham.ac.uk/projects/trim-galore/].
36. Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 2011;12:R72.
37. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, et al. The Ensembl genome database project. Nuc Acids Res. 2002;30:38-41.
38. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC Table Browser data retrieval tool. Nuc Acids Res. 2004;32:D493-496.
39. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Devel. 2011;25:1915-27.
40. Affymetrix Expression Consol. [http://www.affymetrix.com/estore/browse/level-seven-software-products-only.jsp?productId=131414#1-1].
41. O'Donovan PJ, Livingston DM. BRCA1 and BRCA2: breast/ovarian cancer susceptibility gene products and participants in DNA double-strand break repair. Carcinogenesis. 2010;31:961-7.
42. Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nuc Acids Res. 2012;40:D302-305.
43. Clucas J, Valderrama F. ERM proteins in cancer progression. J Cell Sci. 2014;127:267-75.
44. Nakayama K, Nakayama N, Davidson B, Sheu JJ, Jinawath N, Santillan A, et al. A BTB/POZ protein, NAC-1, is related to tumor recurrence and is essential for tumor growth and survival. Proc Natl Acad Sci U S A. 2006;103:18739-44.
45. Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, et al. Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clin Can Res. 2012;18:5806-15.
46. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, et al. Origins and functional impact of copy number variation in the human genome. Nature. 2010;464:704-12.
47. O'Huallachain M, Karczewski KJ, Weissman SM, Urban AE, Snyder MP. Extensive genetic variation in somatic human tissues. Proc Natl Acad Sci U S A. 2012;109:18018-23.
48. Salzman J, Marinelle RJ, Wang PL, Green AE, Nielsen JS, Nelson BH, et al. ESRRA-Ciiorf20 is a recurrent gene fusion in serous ovarian carcinoma. PLoS Biol. 2011;9:e1001156.
49. Kannan K, Coarfa C, Rajapahshe K, Hawkins SM, Matzuk MM, Milosavljevic A, et al. CDKN2D-WDFY2 is a cancer-specific gene recurrent in high-grade serous ovarian carcinoma. PLoS Genet. 2014;10:e1004216.
50. Bueno MJ, Perez de Castro I, Gomez de Cedron M, Santos J, Calin GA, Cigudosa JC, et al. Genetic and epigenetic silencing of microRNA-203 enhances ABL1 and BCR-ABL1 oncogene expression. Cancer Cell. 2008;13:496-506.
51. Nambiar M, Raghavan SC. Chromosomal translocations among the healthy human population: implications in oncogenesis. Cell Mol Life Sci. 2013;70:1381-92.