FACTERA: A practical method for the discovery of genomic rearrangements at breakpoint resolution

Bioinformatics

Volumn 30, Issue 23, 2014, Pages 3390-3393

  Newman, Aaron M ^a   Bratman, Scott V ^a,b   Stehr, Henning ^c   Lee, Luke J ^a,c   Liu, Chih Long ^a   Diehn, Maximilian ^a,b,c   Alizadeh, Ash A ^a,c  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

^c STANFORD CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CHROMOSOME ABERRATION; CHROMOSOME BREAKAGE; CHROMOSOME MAP; COMPUTER PROGRAM; DNA SEQUENCE; GENE FUSION; GENE TRANSLOCATION; GENETICS; GENOMICS; HUMAN; LUNG TUMOR; NON SMALL CELL LUNG CANCER; PROCEDURES;

ALGORITHMS; CARCINOMA, NON-SMALL-CELL LUNG; CHROMOSOME ABERRATIONS; CHROMOSOME BREAKPOINTS; CHROMOSOME MAPPING; GENE FUSION; GENOMICS; HUMANS; LUNG NEOPLASMS; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSLOCATION, GENETIC;

EID: 84930726139     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu549     Document Type: Article

References (19)

1. Bergethon, K. et al. (2012) ROS1 rearrangements define a unique molecular class of lung cancers. J. Clin. Oncol., 30, 863-870.
2. Chen, K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
3. Druker, B.J. et al. (1996) Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat. Med., 2, 561-566.
4. Govindan, R. et al. (2012) Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell, 150, 1121-1134.
5. Hart, S.N. et al. (2013) SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations. PLoS One, 8, e83356.
6. Imielinski, M. et al. (2012) Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell, 150, 1107-1120.
7. Kwak, E.L. et al. (2010) Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N. Engl. J. Med., 363, 1693-1703.
8. Leary, R.J. et al. (2010) Development of personalized tumor biomarkers using massively parallel sequencing. Sci. Transl. Med., 2, 20ra14.
9. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
10. McBride, D.J. et al. (2010) Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes Chromosomes Cancer, 49, 1062-1069.
11. McDermott, U. et al. (2008) Genomic alterations of anaplastic lymphoma kinase may sensitize tumors to anaplastic lymphoma kinase inhibitors. Cancer Res., 68, 3389-3395.
12. Newman, A.M. et al. (2014) An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med., 20, 548-554.
13. Nowell, P.C. and Hungerford, D.A. (1960) A minute chromosome in human chronic granulocytic leukemia. Science, 142, 1497.
14. Rausch, T. et al. (2012) DELLY: structural variant discovery by integrated pairedend and split-read analysis. Bioinformatics, 28, i333-i339.
15. Schroder, J. et al. (2014) Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. Bioinformatics, 30, 1064-1072.
16. Tomlins, S.A. et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science, 310, 644-648.
17. Tsujimoto, Y. et al. (1984) Cloning of the chromosome breakpoint of neoplastic B cells with the t(14;18) chromosome translocation. Science, 226, 1097-1099.
18. Vaishnavi, A. et al. (2013) Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer. Nat. Med., 19, 1469-1472.
19. Wang, J. et al. (2011) CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat. Methods, 8, 652-654.