Information de reference pour ce titreAccession Number: | 00005042-201604000-00001.
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Author: | Raymond, Victoria M.; Gray, Stacy W.; Roychowdhury, Sameek; Joffe, Steve; Chinnaiyan, Arul M.; Parsons, D. Williams; Plon, Sharon E.
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Institution: | Affiliations of authors: Departments of Internal Medicine (VMR) and Pathology (AMC), University of Michigan, Ann Arbor, MI; Dana-Farber Cancer Institute, Boston, MA (SWG); Harvard Medical School, Boston, MA (SWG); The Ohio State University, Columbus, OH (SR); University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (SJ); Texas Children's Cancer Center, Houston, TX (DWP, SEP); Baylor College of Medicine, Houston, TX (DWP, SEP).
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Title: | |
Source: | Journal of the National Cancer Institute. 108(4), April 2016.
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Abstract: | Precision oncology holds great potential to improve patient therapies and outcomes. Tumor sequencing is rapidly moving into clinical care as our understanding of the cancer genome and the availability of targeted therapies increase. Analysis of the cancer genome is most informative when paired with germline genomic DNA to delineate inherited and somatic variants. Although tumor-only analysis remains the most common methodology for numerous reasons, it holds the potential to identify clinically significant germline variants. Here, we provide anticipatory guidance and points to consider for laboratories and clinicians regarding the potential for germline findings in tumor sequencing.
(C) Copyright Oxford University Press 2016.
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References: | 1. Roychowdhury S, Iyer MK, Robinson DR, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med. 2011;3(111):111ra121.
2. Garraway LA. Genomics-driven oncology: framework for an emerging paradigm. J Clin Oncol. 2013;31 (15):1806-1814.
3. Mody RJ, Wu Y-M, Lonigro RJ, et al. Use of Integrative Clinical Sequencing in the Management of Pediatric Cancer Patients. J Am Med Assoc. 2015;314 (9):1-13.
4. Hammond MEH, Hayes DF, Dowsett M, et al. American Society of Clinical Oncology/College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. J Clin Oncol. 2010;28 (16):2784-2795.
5. Wolff AC, Hammond MEH, Hicks DG, et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. J Clin Oncol. 2013;31 (31):3997-4013.
6. Seeger RC, Brodeur GM, Sather H, et al. Association of multiple copies of the N-myc oncogene with rapid progression of neuroblastomas. N Engl J Med. 1985;313 (18):1111-1116.
7. De Gramont A, Watson S, Ellis LM, et al. Pragmatic issues in biomarker evaluation for targeted therapies in cancer. Nat Rev Clin Oncol. 2014;12 (4):197-212.
8. Van Allen EM, Wagle N, Levy MA. Clinical analysis and interpretation of cancer genome data. J Clin Oncol. 2013;31 (15):1825-1833.
9. Catenacci DVT, Amico AL, Nielsen SM, et al. Tumor genome analysis includes germline genome: are we ready for surprises? Int J Cancer. 2015;136 (7):1559-1567.
10. Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15 (7):565-574.
11. Jones S, Anagnostou V, Lytle K, et al. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Transl Med. 2015;7(283):283ra53-ra283ra53.
12. Bombard Y, Robson M, Offit K. Revealing the incidentalome when targeting the tumor genome. JAMA. 2013;310 (8):795-796.
13. King M-C, Marks JH, Mandell JB. Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science. 2003;302(5645):643-646.
14. Briggs S, Tomlinson I. Germline and somatic polymerase [epsilon] and [delta] mutations define a new class of hypermutated colorectal and endometrial cancers. J Pathol. 2013;230 (2):148-153.
15. Rausch T, Jones DTW, Zapatka M, et al. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 2012;148(1-2):59-71.
16. Meric-Bernstam F, Brusco L, Daniels MS, et al. Prevalence of incidental actionable germline mutations in 1,000 advanced cancer patients on a prospective somatic genomic profiling program. In: American Society of Clinical Oncology Annual Meeting; 2015.
17. Schrader KA, Cheng DT, Vijai J, et al. Tumor relevant germline findings in targeted tumor sequencing using matched normal DNA of 1,570 unselected cases. In: American Society of Clinical Oncology Annual Meeting; 2015.
18. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20 (9):1297-1303.
19. Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22 (3):568-576.
20. Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31 (3):213-219.
21. Saunders CT, Wong WSW, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012;28 (14):1811-1817.
22. Gargis AS, Kalman L, Berry MW, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol. 2012;30 (11):1033-1036.
23. Gargis AS, Kalman L, Bick DP, et al. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nat Biotechnol. 2015;33 (7):689-693.
24. Sun J, Frampton G, Wang K, et al. A computational method for somatic vs. germline variant status determination from targeted next generation sequencing of clinical cancer specimens without a matched normal control. In: Presented at the American Academy of Cancer Research Annual Meeting; 2013.
25. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17 (5):405-424.
26. Robson ME, Bradbury AR, Arun B, et al. American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. J Clin Oncol. 2015.
27. Yang Y, Muzny DM, Xia F, et al. Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing. JAMA. 2014;312 (18):1870-1879.
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Language: | English.
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Document Type: | Commentary.
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Journal Subset: | Clinical Medicine.
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ISSN: | 0027-8874
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NLM Journal Code: | j9j, 7503089
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DOI Number: | https://dx.doi.org/10.1093/jnci/...- ouverture dans une nouvelle fenêtre
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