Next-generation sequencing in clinical molecular diagnostics of cancer: Advantages and challenges

Cancers

Volumn 7, Issue 4, 2015, Pages 2023-2036

  Luthra, Rajyalakshmi ^a   Chen, Hui ^a   Roy Chowdhuri, Sinchita ^a   Singh, R Rajesh ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

Cancer genomics; Guidelines; Molecular diagnostics; Mutation; Next generation sequencing

Indexed keywords

ANALYTIC METHOD; CANCER DIAGNOSIS; CANCER GENETICS; CONTROLLED STUDY; COPY NUMBER VARIATION; DIAGNOSTIC TEST ACCURACY STUDY; EXON; GENE MUTATION; GENETIC MARKER; HAPLOTYPE MAP; HIGH THROUGHPUT SCREENING; HUMAN; LIMIT OF DETECTION; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; REVIEW; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION;

EID: 84945177579     PISSN: None     EISSN: 20726694     Source Type: Journal    
DOI: 10.3390/cancers7040874     Document Type: Review

References (49)

1. Roychowdhury, S.; Chinnaiyan, A.M. Translating genomics for precision cancer medicine. Annu. Rev. Genomics Hum. Genet. 2014, 15, 395–415.
2. Previati, M.; Manfrini, M.; Galasso, M.; Zerbinati, C.; Palatini, J.; Gasparini, P.; Volinia, S. Next generation analysis of breast cancer genomes for precision medicine. Cancer Lett. 2013, 339, 1–7.
3. Prados, M.D.; Byron, S.A.; Tran, N.L.; Phillips, J.J.; Molinaro, A.M.; Ligon, K.L.; Wen, P.Y.; Kuhn, J.G.; Mellinghoff, I.K.; de Groot, J.F.; et al. Toward precision medicine in glioblastoma: The promise and the challenges. Neuro Oncol. 2015, 17, 1051–1063.
4. Richer, A.L.; Friel, J.M.; Carson, V.M.; Inge, L.J.; Whitsett, T.G. Genomic profiling toward precision medicine in non-small cell lung cancer: Getting beyond EGFR. Pharmgenomics Pers. Med. 2015, 8, 63–79.
5. Intlekofer, A.M.; Younes, A. Precision therapy for lymphoma—Current state and future directions. Nat. Rev. Clin. Oncol. 2014, 11, 585–596.
6. Roper, N.; Stensland, K.D.; Hendricks, R.; Galsky, M.D. The landscape of precision cancer medicine clinical trials in the United States. Cancer Treat. Rev. 2015, 41, 385–390.
7. Mardis, E.R.; Ding, L.; Dooling, D.J.; Larson, D.E.; McLellan, M.D.; Chen, K.; Koboldt, D.C.; Fulton, R.S.; Delehaunty, K.D.; McGrath, S.D.; et al Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 2009, 361, 1058–1066.
8. Mardis, E.R.; Wilson, R.K. Cancer genome sequencing: A review. Hum. Mol. Genet. 2009, 18, R163–R168.
9. Jennings, L.; van Deerlin, V.M.; Gulley, M.L. Recommended principles and practices for validating clinical molecular pathology tests. Arch. Pathol. Lab. Med. 2009, 133, 743–755.
10. Aziz, N.; Zhao, Q.; Bry, L.; Driscoll, D.K.; Funke, B.; Gibson, J.S.; Grody, W.W.; Hegde, M.R.; Hoeltge, G.A.; Leonard, D.G.; et al College of American Pathologists’ Laboratory Standards for Next-Generation Sequencing Clinical Tests. Arch. Pathol. Lab. Med. 2015, 139, 481–493.
11. Rehm, H.L.; Bale, S.J.; Bayrak-Toydemir, P.; Berg, J.S.; Brown, K.K.; Deignan, J.L.; Friez, M.J.; Funke, B.H.; Hegde, M.R.; Lyon, E.; et al ACMG clinical laboratory standards for next-generation sequencing. Genet. Med. 2013, 15, 733–747.
12. Schrijver, I.; Aziz, N.; Farkas, D.H.; Furtado, M.; Gonzalez, A.F.; Greiner, T.C.; Grody, W.W.; Hambuch, T.; Kalman, L.; Kant, J.A. ; et al Opportunities and challenges associated with clinical diagnostic genome sequencing: A report of the Association for Molecular Pathology. J. Mol. Diagn. 2012, 14, 525–540.
13. Gargis, A.S.; Kalman, L.; Berry, M.W.; Bick, D.P.; Dimmock, D.P.; Hambuch, T.; Lu, F.; Lyon, E.; Voelkerding, K.V.; Zehnbauer, B.A.; et al Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat. Biotechnol. 2012, 30, 1033–1036.
14. Beadling, C.; Neff, T.L.; Heinrich, M.C.; Rhodes, K.; Thornton, M.; Leamon, J.; Andersen, M.; Corless, C.L. Combining highly multiplexed PCR with semiconductor-based sequencing for rapid cancer genotyping. J. Mol. Diagn. 2013, 15, 171–176.
15. Hagemann, I.S.; Devarakonda, S.; Lockwood, C.M.; Spencer, D.H.; Guebert, K.; Bredemeyer, A.J.; Al-Kateb, H.; Nguyen, T.T.; Duncavage, E.J.; Cottrell, C.E.; et al Clinical next-generation sequencing in patients with non-small cell lung cancer. Cancer 2014, 121, 631–639.
16. Lin, M.T.; Mosier, S.L.; Thiess, M.; Beierl, K.F.; Debeljak, M.; Tseng, L.H.; Chen, G.; Yegnasubramanian, S.; Ho, H.; Cope, L.; et al Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. Am. J. Clin. Pathol. 2014, 141, 856–866.
17. Luthra, R.; Patel, K.P.; Reddy, N.G.; Haghshenas, V.; Routbort, M.J.; Harmon, M.A.; Barkoh, B.A.; Kanagal-Shamanna, R.; Ravandi, F.; Cortes, J.E. ; et al Next-generation sequencing-based multigene mutational screening for acute myeloid leukemia using MiSeq: Applicability for diagnostics and disease monitoring. Haematologica 2014, 99, 465–473.
18. Singh, R.R.; Patel, K.P.; Routbort, M.J.; Aldape, K.; Lu, X.; Manekia, J.; Abraham, R.; Reddy, N.G.; Barkoh, B.A.; Veliyathu, J.; et al Clinical massively parallel next-generation sequencing analysis of 409 cancer-related genes for mutations and copy number variations in solid tumours. Br. J. Cancer 2014, 111, 2014–2023.
19. Singh, R.R.; Patel, K.P.; Routbort, M.J.; Reddy, N.G.; Barkoh, B.A.; Handal, B.; Kanagal-Shamanna, R.; Greaves, W.O.; Medeiros, L.J.; Aldape, K.D.; et al Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes. J. Mol. Diagn. 2013, 15, 607–622.
20. Kanagal-Shamanna, R.; Portier, B.P.; Singh, R.R.; Routbort, M.J.; Aldape, K.D.; Handal, B.A.; Rahimi, H.; Reddy, N.G.; Barkoh, B.A.; Mishra, B.M.; et al Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: Promises and challenges for routine clinical diagnostics. Mod. Pathol. 2014, 27, 314–327.
21. Lorenzi, P.L.; Reinhold, W. C.; Varma, S.; Hutchinson, A.A.; Pommier, Y.; Chanock, S.J.; Weinstein, J.N. DNA fingerprinting of the NCI-60 cell line panel. Mol. Cancer Ther. 2009, 8, 713–724.
22. International HapMap Consortium. The International HapMap Project 2003, 426, 789–796.
23. Han, S.J.; Rutledge, W.C.; Molinaro, A.M.; Chang, S.M.; Clarke, J.L.; Prados, M.D.; Taylor, J.W.; Berger, M.S.; Butowski, N.A. The Effect of Timing of Concurrent Chemoradiation in Patients with Newly Diagnosed Glioblastoma. Neurosurgery 2015, 77, 248–253.
24. Metzker, M.L. Sequencing technologies—The next generation. Nat. Rev. Genet. 2010, 11, 31–46.
25. Pareek, C.S.; Smoczynski, R.; Tretyn, A. Sequencing technologies and genome sequencing. J. Appl. Genet. 2011, 52, 413–435.
26. Chaisson, M.J.; Huddleston, J.; Dennis, M.Y.; Sudmant, P.H.; Malig, M.; Hormozdiari, F.; Antonacci, F.; Surti, U.; Sandstrom, R.; Boitano, M.; et al Resolving the complexity of the human genome using single-molecule sequencing. Nature 2015, 517, 608–611.
27. Quail, M.A.; Smith, M.; Coupland, P.; Otto, T.D.; Harris, S.R.; Connor, T.R.; Bertoni, A.; Swerdlow, H.P.; Gu, Y. A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13, 341.
28. Rothberg, J.M.; Hinz, W.; Rearick, T.M.; Schultz, J.; Mileski, W.; Davey, M.; Leamon, J.H.; Johnson, K.; Milgrew, M.J.; Edwards, M. ; et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475, 348–352.
29. Merriman, B.; Rothberg, J.M. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 2012, 33, 3397–3417.
30. Kilianski, A.; Haas, J.L.; Corriveau, E.J.; Liem, A.T.; Willis, K.L.; Kadavy, D.R.; Rosenzweig, C.N.; Minot, S.S. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 2015, 4, 12.
31. Meller, A.; Nivon, L.; Brandin, E.; Golovchenko, J.; Branton, D. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. USA 2000, 97, 1079–1084.
32. Vercoutere, W.; Winters-Hilt, S.; Olsen, H.; Deamer, D.; Haussler, D.; Akeson, M. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat. Biotechnol. 2001, 19, 248–252.
33. Bodi, K.; Perera, A.G.; Adams, P.S.; Bintzler, D.; Dewar, K.; Grove, D.S.; Kieleczawa, J.; Lyons, R.H.; Neubert, T.A.; Noll, A.C.; et al. Comparison of commercially available target enrichment methods for next-generation sequencing. J. Biomol. Tech. 2013, 24, 73–86.
34. Mamanova, L.; Coffey, A.J.; Scott, C.E.; Kozarewa, I.; Turner, E.H.; Kumar, A.; Howard, E.; Shendure, J.; Turner, D.J. Target-enrichment strategies for next-generation sequencing. Nat. Methods 2010, 7, 111–118.
35. Mertes, F.; Elsharawy, A.; Sauer, S.; van Helvoort, J.M.; van der Zaag, P.J.; Franke, A.; Nilsson, M.; Lehrach, H.; Brookes, A.J. Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief. Funct. Genomics 2011, 10, 374–386.
36. Li, H.; Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26, 589–595.
37. Ye, K.; Schulz, M.H.; Long, Q.; Apweiler, R.; Ning, Z. Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25, 2865–2871.
38. Chen, K.; Wallis, J.W.; Kandoth, C.; Kalicki-Veizer, J.M.; Mungall, K.L.; Mungall, A.J.; Jones, S.J.; Marra, M.A.; Ley, T.J.; Mardis, E.R.; et al. BreakFusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics 2012, 28, 1923–1924.
39. McPherson, A.; Hormozdiari, F.; Zayed, A.; Giuliany, R.; Ha, G.; Sun, M.G.; Griffith, M.; Heravi Moussavi, A.; Senz, J.; Melnyk, N.; et al. deFuse: An algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol. 2011, 7, e1001138.
40. Thorvaldsdottir, H.; Robinson, J.T.; Mesirov, J.P. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief. Bioinform. 2013, 14, 178–192.
41. Kent, W.J.; Sugnet, C.W.; Furey, T.S.; Roskin, K.M.; Pringle, T.H.; Zahler, A.M.; Haussler, D. The human genome browser at UCSC. Genome Res. 2002, 12, 996–1006.
42. Wain, H.M.; Bruford, E.A.; Lovering, R.C.; Lush, M.J.; Wright, M.W.; Povey, S. Guidelines for human gene nomenclature. Genomics 2002, 79, 464–470.
43. Den Dunnen, J.T.; Antonarakis, S.E. Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum. Mutat. 2000, 15, 7–12.
44. Forbes, S.A.; Tang, G.; Bindal, N.; Bamford, S.; Dawson, E.; Cole, C.; Kok, C.Y.; Jia, M.; Ewing, R.; Menzies, A.; et al COSMIC (the Catalogue of Somatic Mutations in Cancer): A resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 2010, 38, D652–D657.
45. Stenson, P.D.; Mort, M.; Ball, E.V.; Shaw, K.; Phillips, A.; Cooper, D.N. The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum. Genet. 2014, 133, 1–9.
46. Yeh, P.; Chen, H.; Andrews, J.; Naser, R.; Pao, W.; Horn, L. DNA-Mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT): A catalog of clinically relevant cancer mutations to enable genome-directed anticancer therapy. Clin. Cancer Res. 2013, 19, 1894–1901.
47. Green, R.C.; Berg, J.S.; Grody, W.W.; Kalia, S.S.; Korf, B.R.; Martin, C.L.; McGuire, A.L.; Nussbaum, R.L. O’Daniel, J.M.; Ormond, K.E.; et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet. Med. 2013, 15, 565–574.
48. Hegde, M.; Bale, S.; Bayrak-Toydemir, P.; Gibson, J.; Jeng, L.J.; Joseph, L.; Laser, J.; Lubin, I.M.; Miller, C.E.; Ross, L.F. ; et al. Reporting incidental findings in genomic scale clinical sequencing—A clinical laboratory perspective: A report of the Association for Molecular Pathology. J. Mol. Diagn. 2015, 17, 107–117.
49. Deverka, P.A.; Dreyfus, J.C. Clinical integration of next generation sequencing: Coverage and reimbursement challenges. J. Law Med. Ethics 2014, 42, S22–S41.