Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays

Journal of Molecular Diagnostics

Volumn 18, Issue 3, 2016, Pages 336-349

  Sims, David J ^a   Harrington, Robin D ^a   Polley, Eric C ^b   Forbes, Thomas D ^a   Mehaffey, Michele G ^a   McGregor, Paul M ^a   Camalier, Corinne E ^a   Harper, Kneshay N ^a   Bouk, Courtney H ^a   Das, Biswajit ^a   Conley, Barbara A ^b   Doroshow, James H ^b   Williams, P Mickey ^a   Lih, Chih Jian ^a  

^a FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; PLASMID DNA;

ARTICLE; BIOINFORMATICS; CELL LINE; CONTROL PLASMID SPIKED IN GENOME ASSAY; CONTROLLED STUDY; DNA BARCODING; GENE DOSAGE; GENE FREQUENCY; GENETIC PROCEDURES; GENOME ANALYSIS; HAPLOTYPE MAP; NEXT GENERATION SEQUENCING; NONHUMAN; PLASMID; TANDEM REPEAT; WHOLE EXOME SEQUENCING; BIOLOGY; GENETIC SCREENING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; QUALITY CONTROL; REPRODUCIBILITY; STANDARD; STANDARDS; WORKFLOW;

COMPUTATIONAL BIOLOGY; DNA BARCODING, TAXONOMIC; GENETIC TESTING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PLASMIDS; QUALITY CONTROL; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; WORKFLOW;

EID: 84963954565     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2015.11.008     Document Type: Article

References (22)

1. I. Schrijver, N. Aziz, D.H. Farkas, M. Furtado, A.F. Gonzalez, T.C. Greiner, W.W. Grody, T. Hambuch, L. Kalman, J.A. Kant, R.D. Klein, D.G. Leonard, I.M. Lubin, R. Mao, N. Nagan, V.M. Pratt, M.E. Sobel, K.V. Voelkerding, and J.S. Gibson Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology J Mol Diagn 14 2012 525 540
2. J. Xuan, Y. Yu, T. Qing, L. Guo, and L. Shi Next-generation sequencing in the clinic: promises and challenges Cancer Lett 340 2013 284 295
3. B. Tran, J.E. Dancey, S. Kamel-Reid, J.D. McPherson, P.L. Bedard, A.M. Brown, T. Zhang, P. Shaw, N. Onetto, L. Stein, T.J. Hudson, B.G. Neel, and L.L. Siu Cancer genomics: technology, discovery, and translation J Clin Oncol 30 2012 647 660
4. F. Andre, E. Mardis, M. Salm, J.C. Soria, L.L. Siu, and C. Swanton Prioritizing targets for precision cancer medicine Ann Oncol 25 2014 2295 2303
5. H.L. Rehm, S.J. Bale, P. Bayrak-Toydemir, J.S. Berg, K.K. Brown, J.L. Deignan, M.J. Friez, B.H. Funke, M.R. Hegde, and E. Lyon ACMG clinical laboratory standards for next-generation sequencing Genet Med 15 2013 733 747
6. A.S. Gargis, L. Kalman, M.W. Berry, D.P. Bick, D.P. Dimmock, T. Hambuch, and et al. Assuring the quality of next-generation sequencing in clinical laboratory practice Nat Biotechnol 30 2012 1033 1036
7. J.M. Zook, B. Chapman, J. Wang, D. Mittelman, O. Hofmann, W. Hide, and M. Salit Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls Nat Biotechnol 32 2014 246 251
8. S. Pant, R. Weiner, and M.J. Marton Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics Front Oncol 4 2014 78
9. R.R. Singh, K.P. Patel, M.J. Routbort, N.G. Reddy, B.A. Barkoh, B. Handal, R. Kanagal-Shamanna, W.O. Greaves, L.J. Medeiros, K.D. Aldape, and R. Luthra Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes J Mol Diagn 15 2013 607 622
10. D. Dias-Santagata, S. Akhavanfard, S.S. David, K. Vernovsky, G. Kuhlmann, S.L. Boisvert, H. Stubbs, U. McDermott, J. Settleman, E.L. Kwak, J.W. Clark, S.J. Isakoff, L.V. Sequist, J.A. Engelman, T.J. Lynch, D.A. Haber, D.N. Louis, L.W. Ellisen, D.R. Borger, and A.J. Iafrate Rapid targeted mutational analysis of human tumours: a clinical platform to guide personalized cancer medicine EMBO Mol Med 2 2010 146 158
11. S.C. Baker, S.R. Bauer, R.P. Beyer, J.D. Brenton, B. Bromley, J. Burrill, and et al. The External RNA Controls Consortium: a progress report Nat Methods 2 2005 731 734
12. C.-J. Lih, D.J. Sims, R.D. Harrington, E.C. Polley, Y. Zhao, M.G. Mehaffey, T.D. Forbes, B. Das, V. Datta, K.N. Harper, C.H. Bouk, L.V. Rubinstein, R.M. Simon, B.A. Conley, A.P. Chen, S. Kummar, J.H. Doroshow, and P.M. Williams Analytical validation and application of a targeted next generation sequencing mutation detection assay for use in treatment assignment in the NCI-MPACT trial (NCT01827384) J Mol Diagn 18 2016 51 67
13. H. Li, and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 26 2010 589 595
14. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
15. H. Thorvaldsdottir, J.T. Robinson, and J.P. Mesirov Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Brief Bioinform 14 2013 178 192
16. R Development Core Team R: a language and environment for statistical computing 2014 R Foundation for Statistical Computing Vienna, Austria
17. H. Wickham ggplot2: Elegant Graphics for Data Analysis 2009 Springer-Verlag New York
18. C.J. Clopper, and E.S. Pearson The use of confidence or fiducial limits illustrated in the case of the binomial Biometrika 26 1934 404 413
19. A.V. Roschke, G. Tonon, K.S. Gehlhaus, N. McTyre, K.J. Bussey, S. Lababidi, D.A. Scudiero, J.N. Weinstein, and I.R. Kirsch Karyotypic complexity of the NCI-60 drug-screening panel Cancer Res 63 2003 8634 8647
20. D.M. Stults, M.W. Killen, B.J. Shelton, and A.J. Pierce Recombination phenotypes of the NCI-60 collection of human cancer cells BMC Mol Biol 12 2011 23
21. M. Sausen, J. Phallen, V. Adleff, S. Jones, R.J. Leary, M.T. Barrett, V. Anagnostou, S. Parpart-Li, D. Murphy, Q. Kay Li, C.A. Hruban, R. Scharpf, J.R. White, P.J. O'Dwyer, P.J. Allen, J.R. Eshleman, C.B. Thompson, D.S. Klimstra, D.C. Linehan, A. Maitra, R.H. Hruban, L.A. Diaz Jr., D.D. Von Hoff, J.S. Johansen, J.A. Drebin, and V.E. Velculescu Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients Nat Commun 6 2015 7686
22. Z. Piotrowska, M.J. Niederst, C.A. Karlovich, H.A. Wakelee, J.W. Neal, M. Mino-Kenudson, L. Fulton, A.N. Hata, E.L. Lockerman, A. Kalsy, S. Digumarthy, A. Muzikansky, M. Raponi, A.R. Garcia, H.E. Mulvey, M.K. Parks, R.H. DiCecca, D. Dias-Santagata, A.J. Iafrate, A.T. Shaw, A.R. Allen, J.A. Engelman, and L.V. Sequist Heterogeneity underlies the emergence of EGFRT790 wild-type clones following treatment of T790M-positive cancers with a third-generation EGFR inhibitor Cancer Discov 5 2015 713 722