Next-generation sequencing in clinical oncology: Next steps towards clinical validation

Cancers

Volumn 6, Issue 4, 2014, Pages 2296-2312

  Bennett, Nigel C ^a   Farah, Camile S ^a,b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b Australian Centre for Oral Oncology Research and Education   (Australia)

Author keywords

Clinical oncology; Massively parallel sequencing; Next generation sequencing; Validation

Indexed keywords

GENOMIC DNA;

BIOINFORMATICS; CANCER DIAGNOSIS; CLONAL VARIATION; DNA STRUCTURE; FALSE POSITIVE RESULT; GENE IDENTIFICATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOTYPE; HEAD AND NECK CANCER; HEALTH CARE UTILIZATION; HUMAN; INCIDENTAL FINDING; MEDICAL INFORMATION; MEDICAL SOCIETY; NEXT GENERATION SEQUENCING; ONCOGENE; ORGANIZATIONAL DOWNSIZING; ORGANIZATIONAL EFFICIENCY; OUTCOME ASSESSMENT; PHENOTYPE; PRACTICE GUIDELINE; QUALITY CONTROL; REVIEW; SEQUENCE ANALYSIS; VALIDATION PROCESS;

EID: 84925447968     PISSN: None     EISSN: 20726694     Source Type: Journal    
DOI: 10.3390/cancers6042296     Document Type: Review

References (51)

1. Sheridan, C. Milestone approval lifts Illumina’s NGS from research into clinic. Nat. Biotechnol. 2014, 32, 111-112.
2. New York State Department of Health. “Next Generation” Sequencing (NGS) guidelines for somatic genetic variant detection. Available online: http://www.wadsworth.org/labcert/TestApproval??forms/NextGenSeq_ONCO_Guidelines.pdf (accessed on 19 May 2014).
3. New York State Department of Health. Test Approval Policy. Available online: http://www.wadsworth.org/labcert/TestApproval??(accessed on 19 May 2014).
4. Royal College of Pathologists of Australasia (RCPA). Implementation of Massively Parallel Sequencing in Diagnostic Medical Genetic Testing. Available online: http://pathwiki.rcpaqap.com.au?pathwiki/index.php/Introduction (accessed 20 May 2014).
5. 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.
6. U.S. Food and Drug Administration. Ultra High Throughput Sequencing for Clinical Diagnostic Applications—Approaches to Assess Analytical Validity, Silver Spring, MD, USA, 23 June 2011.
7. Weiss, M.M.; van der Zwaag, B.; Jongbloed, J.D.; Vogel, M.J.; Bruggenwirth, H.T.; Lekanne Deprez, R.H.; Mook, O.; Ruivenkamp, C.A.; van Slegtenhorst, M.A.; van den Wijngaard, A., et al. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: A national collaborative study of Dutch genome diagnostic laboratories. Hum. Mutat. 2013, 34, 1313-1321.
8. 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.
9. Ellard, S.; Lindsay, H.; Camm, N.; Watson, C.; Abbs, S.; Mattocks, C.; Taylor, G.R.; Charlton, R. Practice guidelines for targeted Next Generation Sequencing analysis and interpretation. Association for Clinical Genetic Science (ACGS). Available online: http://www.acgs.uk.com/media?815227/bpg_for_targeted_next_generation_sequencing_201113__4_.pdf (accessed on 2 June 2014).
10. Clinical and Laboratory Standards Institute. Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline—Second Edition. Available online: http://shopping.netsuite.com/s.nl/c.1253739/it.A/id.1787/.f (accessed on 3 June 2014).
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. ACMG clinical laboratory standards for next-generation sequencing. Genet. Med. 2013, 15, 733-747.
12. The Provision of Direct to Consumer Genetic Tests, Guiding Principles for Providers: National Pathology Accreditation Advisory Council, Australia. Available online: http://www.health.gov.au?internet/main/publishing.nsf/Content/health-npaac-path-bestpractice (accessed on 23 July 2014).
13. Human Genome Variation Society: Guidelines for Sequence Variation (“mutation”) Nomenclature. Available online: http://www.hgvs.org/content/guidelines (accessed 19 May 2014).
14. Park, J.Y.; Kricka, L.J.; Fortina, P. Next-generation sequencing in the clinic. Nat. Biotechnol. 2013, 31, 990-992.
15. Ding, L.; Wendl, M.C.; McMichael, J.F.; Raphael, B.J. Expanding the computational toolbox for mining cancer genomes. Nat. Rev. Genet. 2014, 15, 556-570.
16. European Society for Medical Oncology. Clinical Practice Guidelines by Tumour Type. Available online: http://www.esmo.org/Guidelines-Practice/Clinical-Practice-Guidelines (accessed 28 May 2014).
17. National Comprehensive Cancer Network. Clinical Practice Guidelines in Oncology. Available online: http://www.nccn.org/professionals/physician_gls/f_guidelines.asp (accessed 28 May 2014).
18. Cancer Council, Australia. Clinical Practice Guidelines. Available online: http://www.cancer.org.au?health-professionals/clinical-guidelines?(accessed 28 May 2014).
19. American Society of Clinical Oncology. Clinical Practice Guidelines. Available online: http://www.asco.org/quality-guidelines/guidelines (accessed 28 May 2014).
20. Parkinson, D.R.; Johnson, B.E.; Sledge, G.W. Making personalized cancer medicine a reality: Challenges and opportunities in the development of biomarkers and companion diagnostics. Clin. Cancer Res. 2012, 18, 619-624.
21. Hudson, T.J.; Anderson, W.; Artez, A.; Barker, A.D.; Bell, C.; Bernabe, R.R.; Bhan, M.K.; Calvo, F.; Eerola, I.; Gerhard, D.S., et al. International network of cancer genome projects. Nature 2010, 464, 993-998.
22. Yachida, S.; Jones, S.; Bozic, I.; Antal, T.; Leary, R.; Fu, B.; Kamiyama, M.; Hruban, R.H.; Eshleman, J.R.; Nowak, M.A., et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010, 467, 1114-1117.
23. Gerlinger, M.; Rowan, A.J.; Horswell, S.; Larkin, J.; Endesfelder, D.; Gronroos, E.; Martinez, P.; Matthews, N.; Stewart, A.; Tarpey, P., et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 2012, 366, 883-892.
24. Sottoriva, A.; Spiteri, I.; Shibata, D.; Curtis, C.; Tavare, S. Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer Res. 2013, 73, 41-49.
25. Vogelstein, B.; Papadopoulos, N.; Velculescu, V.E.; Zhou, S.; Diaz, L.A., Jr.; Kinzler, K.W. Cancer genome landscapes. Science 2013, 339, 1546-1558.
26. Braakhuis, B.J.; Bloemena, E.; Leemans, C.R.; Brakenhoff, R.H. Molecular analysis of surgical margins in head and neck cancer: more than a marginal issue. Oral Oncol. 2010, 46, 485-491.
27. Gerlinger, M.; Catto, J.W.; Orntoft, T.F.; Real, F.X.; Zwarthoff, E.C.; Swanton, C. Intratumour Heterogeneity in Urologic Cancers: From Molecular Evidence to Clinical Implications. Eur. Urol. 2014, doi:10.1016/j.eururo.2014.04.014.
28. McWhinney, S.R.; McLeod, H.L. Using germline genotype in cancer pharmacogenetic studies. Pharmacogenomics 2009, 10, 489-493.
29. Slaughter, D.P.; Southwick, H.W.; Smejkal, W. Field cancerization in oral stratified squamous epithelium; clinical implications of multicentric origin. Cancer 1953, 6, 963-968.
30. Brownstein, C.A.; Beggs, A.H.; Homer, N.; Merriman, B.; Yu, T.W.; Flannery, K.C.; Dechene, E.T.; Towne, M.C.; Savage, S.K.; Price, E.N., et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 2014, 15, R53.
31. Salto-Tellez, M.; Gonzalez de Castro, D. Next generation sequencing: A change of paradigm in molecular diagnostic validation. J. Pathol. 2013, doi:10.1002/path.4365.
32. Clark, M.J.; Chen, R.; Lam, H.Y.; Karczewski, K.J.; Chen, R.; Euskirchen, G.; Butte, A.J.; Snyder, M. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 2011, 29, 908-914.
33. Kim, S.Y.; Speed, T.P. Comparing somatic mutation-callers: Beyond Venn diagrams. BMC Bioinformatics 2013, 14, 189.
34. Goode, D.L.; Hunter, S.M.; Doyle, M.A.; Ma, T.; Rowley, S.M.; Choong, D.; Ryland, G.L.; Campbell, I.G. A simple consensus approach improves somatic mutation prediction accuracy. Genome Med. 2013, 5, 90.
35. Simon, R.; Roychowdhury, S. Implementing personalized cancer genomics in clinical trials. Nat. Rev. Drug Discov. 2013, 12, 358-369.
36. Jessri, M.; Farah, C.S. Next generation sequencing and its application in deciphering head and neck cancer. Oral Oncol. 2014, 50, 247-253.
37. Jessri, M.; Farah, C.S. Harnessing massively parallel sequencing in personalized head and neck oncology. J. Dent. Res. 2014, 93, 437-444.
38. Gray, K.A.; Yates, B.; Seal, R.L.; Wright, M.W.; Bruford, E.A. Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2014, doi:10.1093/nar/gku1071.
39. Chang, F.; Li, M.M. Clinical application of amplicon-based next-generation sequencing in cancer. Cancer Genet. 2013, 206, 413-419.
40. Richards, C.S.; Bale, S.; Bellissimo, D.B.; Das, S.; Grody, W.W.; Hegde, M.R.; Lyon, E.; Ward, B.E. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet. Med. 2008, 10, 294-300.
41. Dienstmann, R.; Dong, F.; Borger, D.; Dias-Santagata, D.; Ellisen, L.W.; Le, L.P.; Iafrate, A.J. Standardized decision support in next generation sequencing reports of somatic cancer variants. Mol. Oncol. 2014, 8, 859-873.
42. Kassahn, K.S.; Scott, H.S.; Caramins, M.C. Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge. Hum. Mutat. 2014, 35, 413-423.
43. Tarczy-Hornoch, P.; Amendola, L.; Aronson, S.J.; Garraway, L.; Gray, S.; Grundmeier, R.W.; Hindorff, L.A.; Jarvik, G.; Karavite, D.; Lebo, M., et al. A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record. Genet. Med. 2013, 15, 824-832.
44. 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.
45. Lawrence, L.; Sincan, M.; Markello, T.; Adams, D.R.; Gill, F.; Godfrey, R.; Golas, G.; Groden, C.; Landis, D.; Nehrebecky, M., et al. The implications of familial incidental findings from exome sequencing: the NIH Undiagnosed Diseases Program experience. Genet. Med. 2014, 16, 741-750.
46. Johnston, J.J.; Rubinstein, W.S.; Facio, F.M.; Ng, D.; Singh, L.N.; Teer, J.K.; Mullikin, J.C.; Biesecker, L.G. Secondary variants in individuals undergoing exome sequencing: Screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am. J. Hum. Genet. 2012, 91, 97-108.
47. Dorschner, M.O.; Amendola, L.M.; Turner, E.H.; Robertson, P.D.; Shirts, B.H.; Gallego, C.J.; Bennett, R.L.; Jones, K.L.; Tokita, M.J.; Bennett, J.T., et al. Actionable, pathogenic incidental findings in 1,000 participants’ exomes. Am. J. Hum. Genet. 2013, 93, 631-640.
48. O’Rawe, J.; Jiang, T.; Sun, G.; Wu, Y.; Wang, W.; Hu, J.; Bodily, P.; Tian, L.; Hakonarson, H.; Johnson, W.E., et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013, 5, 28.
49. Liu, Q.; Guo, Y.; Li, J.; Long, J.; Zhang, B.; Shyr, Y. Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics 2012, 13, S8.
50. Tarabeux, J.; Zeitouni, B.; Moncoutier, V.; Tenreiro, H.; Abidallah, K.; Lair, S.; Legoix-Ne, P.; Leroy, Q.; Rouleau, E.; Golmard, L., et al. Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model. Eur. J. Hum. Genet. 2014, 22, 535-541.
51. American Society of Clinical Oncology. The state of cancer care in america, 2014: A report by the American Society of Clinical Oncology. J. Oncol. Pract. 2014, 10, 119-142.