An integrated framework for reporting clinically relevant biomarkers from paired tumor/normal genomic and transcriptomic sequencing data in support of clinical trials in personalized medicine

Pacific Symposium on Biocomputing

Volumn , Issue , 2015, Pages 56-67

  Nasser, Sara ^a   Kurdolgu, Ahmet A ^a   Izatt, Tyler ^a   Aldrich, Jessica ^a   Russell, Megan L ^a   Christoforides, Alexis ^a   Tembe, Wiabhav ^a   Keifer, Jeffery A ^a   Corneveaux, Jason J ^a   Byron, Sara A ^a   Forman, Karen M ^b   Zuccaro, Clarice ^b   Keats, Jonathan J ^a   Lorusso, Patricia M ^c   Carpten, John D ^a   Trent, Jeffrey M ^a   Craig, David W ^a  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^b WAYNE STATE UNIVERSITY   (United States)

^c YALE CANCER CENTER   (United States)

Author keywords

Genomic Testing; Next Gen Sequencing Analysis; Personalized Medicine

Indexed keywords

BIOMARKERS; CLINICAL RESEARCH; GENE EXPRESSION; GENE THERAPY; RELATIONAL DATABASE SYSTEMS; TUMORS;

CHROMOSOMAL REARRANGEMENT; COMPUTATIONAL ARCHITECTURE; COMPUTATIONAL FRAMEWORK; INSERTIONS AND DELETIONS; NEXT-GEN SEQUENCING; PERFORMANCE MEASUREMENTS; PERSONALIZED MEDICINES; POSITIVE PREDICTIVE VALUES;

DIAGNOSIS;

TUMOR MARKER;

BIOLOGY; CLINICAL TRIAL (TOPIC); GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC VARIATION; GENETICS; GENOMICS; HUMAN; MOLECULARLY TARGETED THERAPY; NEOPLASMS; PERSONALIZED MEDICINE; PROCEDURES;

BIOMARKERS, TUMOR; CLINICAL TRIALS AS TOPIC; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENOMICS; HUMANS; MOLECULAR TARGETED THERAPY; NEOPLASMS; PRECISION MEDICINE;

EID: 84971233871     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (23)

1. P. B. Chapman, A. Hauschild, C. Robert, J. B. Haanen, P. Ascierto, J. Larkin, R. Dummer, C. Garbe, A. Testori, M. Maio, D. Hogg, P. Lorigan, C. Lebbe, T. Jouary, D. Schadendorf, A. Ribas, S. J. O'Day, J. A. Sosman, J. M. Kirkwood, A. M. M. Eggermont, B. Dreno, K. Nolop, J. Li, B. Nelson, J. Hou, R. J. Lee, K. T. Flaherty, G. A. McArthur and BRIM-3 Study Group, N Engl J Med 364, 2507 (Jun 2011).
2. M. J. Borad and et al, PLoS Genet 10, p. e1004135 (Feb 2014).
3. G. J.Weiss, W. S. Liang, M. J. Demeure, J. A. Kiefer, G. Hostetter, T. Izatt, S. Sinari, A. Christo-forides, J. Aldrich, A. Kurdoglu, L. Phillips, H. Benson, R. Reiman, A. Baker, V. Marsh, D. D. Von Hoff, J. D. Carpten and D. W. Craig, PLoS One 8, p. e76438 (2013).
4. U. Food and D. Administration, Paving the way for personalized medicine: Fda's role in a new era of medical product development:fda's role in a new era of medical product development.
5. C. for Medicare and M. Services, Clinical laboratory improvement amendments.
6. M.-P. Schapranow, Analyze Genomes, tech. rep., Hasso Plattner Institute.
7. C. A. Del Vecchio, C. P. Giacomini, H. Vogel, K. C. Jensen, T. Florio, A. Merlo, J. R. Pollack and A. J. Wong, Oncogene 32, 2670 (May 2013).
8. Filemaker pro (2013).
9. H. Li, arXiv 1303, p. 3997 (2013).
10. K. Cibulskis, M. S. Lawrence, S. L. Carter, A. Sivachenko, D. Jaé, C. Sougnez, S. Gabriel, M. Meyerson, E. S. Lander and G. Getz, Nat Biotechnol 31, 213 (Mar 2013).
11. C. T. Saunders, W. S. W. Wong, S. Swamy, J. Becq, L. J. Murray and R. K. Cheetham, Bioin-formatics 28, 1811 (Jul 2012).
12. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly and M. A. DePristo, Genome Res 20, 1297 (Sep 2010).
13. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin and 1000 Genome Project Data Processing Subgroup, Bioinformatics 25, 2078 (Aug 2009).
14. L. T. Ben Alex Ben Alex, Spring security (July 2014).
15. E. D. Pleasance and et al, Nature 463, 191 (Jan 2010).
16. L. Tang and X.-H. Zhou, Stat Med 32, 620 (Feb 2013).
17. E. T. Wang, R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S. F. Kingsmore, G. P. Schroth and C. B. Burge, Nature 456, 470 (Nov 2008).
18. M. W. Pedersen, M. Meltorn, L. Damstrup and H. S. Poulsen, Ann Oncol 12, 745 (Jun 2001).
19. J. L. Munoz, V. Rodriguez-Cruz, S. J. Greco, V. Nagula, K. W. Scotto and P. Rameshwar, Mol Cancer Ther (Jul 2014).
20. Y. Katz, E. T. Wang, E. M. Airoldi and C. B. Burge, Nat Methods 7, 1009 (Dec 2010).
21. C. Trapnell, B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. van Baren, S. L. Salzberg, B. J. Wold and L. Pachter, Nat Biotechnol 28, 511 (May 2010).
22. R. Patro, S. M. Mount and C. Kingsford, Nat Biotechnol 32, 462 (May 2014).
23. B. J. Haas, A. Papanicolaou, M. Yassour, M. Grabherr, P. D. Blood, J. Bowden, M. B. Couger, D. Eccles, B. Li, M. Lieber, M. D. Macmanes, M. Ott, J. Orvis, N. Pochet, F. Strozzi, N. Weeks, R. Westerman, T. William, C. N. Dewey, R. Henschel, R. D. Leduc, N. Friedman and A. Regev, Nat Protoc 8, 1494 (Aug 2013).