Bellerophon: A hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data

BMC Bioinformatics

Volumn 14, Issue SUPPL.5, 2013, Pages

  Hayes, Matthew ^a   Li, Jing ^a  

^a Case Western Reserve University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETTER PERFORMANCE; BREAK-POINTS; HIGH SENSITIVITY; HYBRID METHOD; NEXT-GENERATION SEQUENCING; PROSTATE CANCERS; SIMULATED DATASETS; STRUCTURAL VARIATIONS;

ALGORITHMS; DISEASES;

FORECASTING;

BELLEROPHON;

ALGORITHM; ARTICLE; BASE PAIRING; CHROMOSOME BREAKAGE; COMPUTER PROGRAM; DNA SEQUENCE; GENE TRANSLOCATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MALE; PROSTATE TUMOR; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE PAIRING; CHROMOSOME BREAKPOINTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; PROSTATIC NEOPLASMS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSLOCATION, GENETIC;

EID: 84876130408     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S5-S6     Document Type: Article

References (22)

1. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marhshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal R, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. Global variation in copy number in the human genome. Nature 2006, 444:444-454. 10.1038/nature05329, 2669898, 17122850.
2. 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 TC, Trask B, Patterson N, Zetterberg A, Wigler M. Large-Scale Copy Number Polymorphism in the Human Genome. Science 2004, 305:525-528. 10.1126/science.1098918, 15273396.
3. O'Connor C. Human chromosome translocations and cancer. Nat Educ 2008, 1.
4. Mitelman F, Johansson B, Mertens F. The impace of translocations and gene fusions in cancer causation. Nature Reviews Cancer 2007, 7:233-245. 10.1038/nrc2091, 17361217.
5. Nowell P, Hungerford D. A minute chromosome in chronic granulocytic leukemia. Science 1960, 132:1497.
6. Stephens P, McBride D, Lin M, Varela I, Pleasance E, Simpson J, Stebbings L, Leroy C, Edkins S, Mudie L, Greenman C, Jia M, Latimer C, Teague J, Lau K, Burton J, Quail M, Swerdlow H, Churcher C, Natrajan R, Sieuwerts A, Martens J, Silver D, Langerod A, Russnes H, Foekens J, Reis-Filho J, van't V, Richardson A, Borresen-Dale A, Campbell P, Futreal PA, Stratton MR. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 2009, 462:1005-1010. 10.1038/nature08645, 3398135, 20033038.
7. Mardis E. The impact of next-generation sequence technology on genetics. Trends Genet 2009, 24:133-141.
8. Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24:142-149. 10.1016/j.tig.2007.12.006, 2680276, 18262676.
9. Chen K, Wallis JW, McLellan MD, Larson D, Kalicki J, Pohl C, McGrath S, Wendl M, Zhang Q, Locke D, Shi X, Fulton R, Ley T, Wilson R, Ding L, Mardis E. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2009, 6:677-681. 10.1038/nmeth.1363, 19668202.
10. Sindi S, Helman E, Bashir A, Raphael B. A geometric approach for classification and comparison of structural variants. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
11. Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-ne P, Nicolas A, Delattre O, Barillot E. SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics 2010, 26:1895-1896. 10.1093/bioinformatics/btq293, 2905550, 20639544.
12. Wang J, Mullighan C, Easton J, Roberts S, Heatley S, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer J, Naeve C, Mardis E, Wilson R, Downing J, Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 2011, 8:652-654. 10.1038/nmeth.1628, 3527068, 21666668.
13. Keane TM, Wong K, Adams DJ. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics 2013, 29.
14. Rausch T, Zichner T, Schalttl A, Stutz A, Benes V, Korbel J. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 2012, 28. 3436805, 22962449.
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMTools. Bioinformatics 2009, 25:222-230. 10.1093/bioinformatics/btp208, 2723002, 19505943.
16. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
17. Kent W. The BLAST-Like Alignment Tool. Genome Res 2002, 12:656-664. 187518, 11932250.
18. Gardner R, Sutherland G. Chromosome Abnormalities and Genetic Counseling 1989, Oxford, UK: Oxford University Press.
19. Tomlins S, Bjartell A, Chinnaiyan A, Jenster G, Nam R, Rubin M, Schalken J. ETS gene fusions in prostate cancer: from discovery to daily clinical practice. Eur Urol 2009, 56:275-286. 10.1016/j.eururo.2009.04.036, 19409690.
20. Howarth K, Pole J, Beavis JC, Batty EM, Newman S, Bignell GR, Edwards PA. Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles. Genome Res 2011, 21:525-534. 10.1101/gr.114116.110, 3065700, 21252201.
21. Berger MM, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esqueva R, Pueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger LA, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA. The genomic complexity of primary human prostate cancer. Nature 2011, 470:214-220. 10.1038/nature09744, 3075885, 21307934.
22. Hayes M, Pyon YS, Li J. A Model-Based Clustering Method for Genomic Structural Variant Prediction and Genotyping Using Paired-End Sequencing Data. PLOS ONE 2012, 7. 3531386, 23300804.