The future of clinical cancer genomics

Seminars in Oncology

Volumn 43, Issue 5, 2016, Pages 615-622

  Offit, Kenneth ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

Cancer; Genomics; Inherited

Indexed keywords

DNA;

ARTICLE; CANCER PREVENTION; CLINICAL GENETICS; DNA SEQUENCE; GENETIC SCREENING; GENETIC VARIABILITY; GENOMICS; HUMAN; NEOPLASM; PHARMACOGENOMICS; PRIORITY JOURNAL; GENETICS;

GENETIC TESTING; GENOMICS; HUMANS; NEOPLASMS; SEQUENCE ANALYSIS, DNA;

EID: 84999176905     PISSN: 00937754     EISSN: 15328708     Source Type: Journal    
DOI: 10.1053/j.seminoncol.2016.10.002     Document Type: Article

References (89)

1. [1] Stadler, Z.K., Schrader, K.A., Vijai, J., Robson, M.E., Offit, K., Cancer genomics and inherited risk. J Clin Oncol 32:7 (2014), 687–698.
2. [2] Weitzel, J.N., Blazer, K.R., MacDonald, D.J., Culver, J.O., Offit, K., Genetics, genomics, and cancer risk assessment: state of the art and future directions in the era of personalized medicine. CA Cancer J Clin 61:5 (2011), 327–359.
3. [3] Offit, K., Bradbury, A., Storm, C., Merz, J.F., Noonan, K.E., Spence, R., Gene patents and personalized cancer care: impact of the Myriad case on clinical oncology. J Clin Oncol 31:21 (2013), 2743–2748.
4. [4] Offit, K., Personalized medicine: new genomics, old lessons. Hum Genet 130:1 (2011), 3–14.
5. [5] Kuhn TS. Thestructure of scientific revolutions. 3rd ed. Chicago, IL: University of Chicago Press;1996.
6. [6] Shah, S., Schrader, K.A., Waanders, E., et al. A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia. Nat Genet 45:10 (2013), 1226–1231.
7. [7] Topka, S., Vijai, J., Walsh, M.F., et al. Germline ETV6 mutations confer susceptibility to acute lymphoblastic leukemia and thrombocytopenia. PLoS Genet, 11(6), 2015, e1005262.
8. [8] Vijai, J., Topka, S., Villano, D., et al. A recurrent ERCC3 truncating mutation confers moderate risk for breast cancer. Cancer Disc, 2016 [Epub ahead of print].
9. [9] Domchek, S.M., Bradbury, A., Garber, J.E., Offit, K., Robson, M.E., Multiplex genetic testing for cancer susceptibility: out on the high wire without a net?. J Clin Oncol 31:10 (2013), 1267–1270.
10. [10] Pollack, A., After patent ruling, availability of gene tests could broaden. The New York Times, Jun 13, 2013.
11. [11] Kurian, A.W., Hare, E.E., Mills, M.A., et al. Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment. J Clin Oncol 32:19 (2014), 2001–2009.
12. [12] Offit, K., Garber, J.E., Time to check CHEK2 in families with breast cancer?. J Clin Oncol 26:4 (2008), 519–520.
13. [13] Easton, D.F., Pharoah, P.D., Antoniou, A.C., Tischkowitz, M., Tavtigian, S.V., Nathanson, K.L., et al. Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med 372:23 (2015), 2243–2257.
14. [14] Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. The EGAPP initiative: lessons learned. Genet Med 16:3 (2014), 217–224.
15. [15] Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. Recommendations from the EGAPP Working Group: does the use of Oncotype DX tumor gene expression profiling to guide treatment decisions improve outcomes in patients with breast cancer?. Genet Med 18:8 (2016), 770–779.
16. [16] Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. Recommendations from the EGAPP Working Group: can UGT1A1 genotyping reduce morbidity and mortality in patients with metastatic colorectal cancer treated with irinotecan?. Genet Med 11:1 (2009), 15–20.
17. [17] Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. Recommendations from the EGAPP Working Group: genetic testing strategies in newly diagnosed individuals with colorectal cancer aimed at reducing morbidity and mortality from Lynch syndrome in relatives. Genet Med 11:1 (2009), 35–41.
18. [18] Global Alliance for Genomics and Health [Internet]. 2016. Available from: https://genomicsandhealth.org/work-products-demonstration-projects/brca-challenge-0.
19. [19] Rehm, H.L., Berg, J.S., Brooks, L.D., et al. ClinGen—the clinical genome resource. N Engl J Med 372:23 (2015), 2235–2242.
20. [20] ClinGen - Clinical Genome Resource [Internet]. 2016. Available from: https://clinicalgenome.org/about/working-groups/clinical-domain/cancer/.
21. [21] PROMPT PatientCrossroads [cited 2016 02/24/2016]. Available from: https://connect.patientcrossroads.org/?org=prompt.
22. [22] Balmana, J., Digiovanni, L., Gaddam, P., et al. Conflicting interpretation of genetic variants and cancer risk by commercial laboratories as assessed by the prospective registry of multiplex testing. J Clin Oncol, 2016 [Epub ahead of print].
23. [23] Gail Jarvik, H.R., Dan, Roden, Panel 2: Consistency of interpretation of variants across expert labs / groups, clinvar submissions?. Genomic Medicine VIII, 2015 Available from https://www.genome.gov/Multimedia/Slides/GM8/Panel2.pdf.
24. [24] Genetic Testing and Couseling Program: Cigna; [cited 2016]. Available from: http://www.cigna.com/healthcare-professionals/resources-for-health-care-professionals/genetic-testing-and-counseling-program.
25. [25] Lee, J., Cigna to require counseling prior to some genetic tests. Modern Healthcare, 2013 Available from http://www.modernhealthcare.com/article/20130725/NEWS/307259958.
26. [26] New Cigna policy on cancer genetic testing poses risks to high quality cancer care: ASCO; 2013. Available from: http://www.asco.org/advocacy/new-cigna-policy-cancer-genetic-testing-poses-risks-high-quality-cancer-care.
27. [27] Zweig, D., Aetna, Anthem and Cigna don't cover genetic tests made popular by ‘Angelina effect’. FierceHealthPayer, 2015 Available from http://www.fiercehealthpayer.com/story/aetna-anthem-and-cigna-dont-cover-genetic-tests-made-popular-angelina-effec/2015-04-13.
28. [28] Bombard, Y., Robson, M., Offit, K., Revealing the incidentalome when targeting the tumor genome. JAMA 310:8 (2013), 795–796.
29. [29] Bombard, Y., Bach, P.B., Offit, K., Translating genomics in cancer care. J Natl Compr. Cancer Netw 11:11 (2013), 1343–1353.
30. [30] Jones, S., Anagnostou, V., Lytle, K., et al. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Translat Med, 7(283), 2015 283ra53.
31. [31] Zhang, J., Walsh, M.F., Wu, G., et al. Germline Mutations in Predisposition Genes in Pediatric Cancer. N Engl J Med 373:24 (2015), 2336–2346.
32. [32] Schrader, K.A., Cheng, D.T., Joseph, V., et al. Germline variants in targeted tumor sequencing using matched normal DNA. JAMA Oncol 2:1 (2016), 104–111.
33. [33] Parsons, D.W., Roy, A., Yang, Y., Wang, T., Scollon, S., Bergstrom, K., et al. Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA Oncol 2:5 (2016), 616–624.
34. [34] Mody, R.J., Wu, Y.M., Lonigro, R.J., et al. Integrative clinical sequencing in the management of refractory or relapsed cancer in youth. JAMA 314:9 (2015), 913–925.
35. [35] Pritchard, C.C., Mateo, J., Walsh, M.F., et al. Inherited DNA-repair gene mutations in men with metastatic prostate cancer. N Engl J Med 375:5 (2016), 443–453.
36. [36] Offit, K., Clinical cancer genetics: risk counseling and management. 1998, Wiley, New York.
37. [37] Couch, F.J., Nathanson, K.L., Offit, K., Two decades after BRCA: setting paradigms in personalized cancer care and prevention. Science (New York, NY) 343:6178 (2014), 1466–1470.
38. [38] Daly, M.B., Pilarski, R., Axilbund, J.E., et al. Genetic/familial high-risk assessment: breast and ovarian, version 1.2014. J Natl Compr Cancer Netw 12:9 (2014), 1326–1338.
39. [39] Nelson, H.D., Fu, R., Goddard, K., et al. Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer: systematic review to update the US Preventive Services Task Force Recommendation. U.S. Preventive Services Task Force Evidence Syntheses, formerly Systematic Evidence Reviews. Rockville (MD), 2013.
40. [40] Force U.S.P.S.T. Genetic risk assessment and BRCA mutation testing for breast and ovarian cancer susceptibility: recommendation statement. Ann Intern Med 143:5 (2005), 355–361.
41. [41] King, M.C., Levy-Lahad, E., Lahad, A., Population-based screening for BRCA1 and BRCA2: 2014 Lasker Award. JAMA 312:11 (2014), 1091–1092.
42. [42] Levy-Lahad, E., Lahad, A., King, M.C., Precision medicine meets public health: population screening for BRCA1 and BRCA2. J Natl Cancer Inst, 107(1), 2015, 420.
43. [43] Yurgelun, M.B., Hiller, E., Garber, J.E., Population-wide screening for germline BRCA1 and BRCA2 mutations: too much of a good thing?. J Clin Oncol 33:28 (2015), 3092–3095.
44. [44] Neuhausen, S., Gilewski, T., Norton, L., et al. Recurrent BRCA2 6174delT mutations in Ashkenazi Jewish women affected by breast cancer. Nat Genet 13:1 (1996), 126–128.
45. [45] Roa, B.B., Boyd, A.A., Volcik, K., Richards, C.S., Ashkenazi Jewish population frequencies for common mutations in BRCA1 and BRCA2. Nat Genet 14:2 (1996), 185–187.
46. [46] Struewing, J.P., Abeliovich, D., Peretz, T., et al. The carrier frequency of the BRCA1 185delAG mutation is approximately 1 percent in Ashkenazi Jewish individuals. Nat Genet 11:2 (1995), 198–200.
47. [47] Oddoux, C., Struewing, J.P., Clayton, C.M., et al. The carrier frequency of the BRCA2 6174delT mutation among Ashkenazi Jewish individuals is approximately 1%. Nat Genet 14:2 (1996), 188–190.
48. [48] Struewing, J.P., Hartge, P., Wacholder, S., et al. The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among Ashkenazi Jews. N Engl J Med 336:20 (1997), 1401–1408.
49. [49] Moslehi, R., Chu, W., Karlan, B., et al. BRCA1 and BRCA2 mutation analysis of 208 Ashkenazi Jewish women with ovarian cancer. Am J Hum Genet 66:4 (2000), 1259–1272.
50. [50] King, M.C., Marks, J.H., Mandell, J.B., New York Breast Cancer Study Group. Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science (New York, NY) 302:5645 (2003), 643–646.
51. [51] Risch, H.A., McLaughlin, J.R., Cole, D.E., et al. Prevalence and penetrance of germline BRCA1 and BRCA2 mutations in a population series of 649 women with ovarian cancer. Am J Hum Genet 68:3 (2001), 700–710.
52. [52] Hartman, A.R., Kaldate, R.R., Sailer, L.M., et al. Prevalence of BRCA mutations in an unselected population of triple-negative breast cancer. Cancer 118:11 (2012), 2787–2795.
53. [53] Metcalfe, K.A., Poll, A., Royer, R., et al. A comparison of the detection of BRCA mutation carriers through the provision of Jewish population-based genetic testing compared with clinic-based genetic testing. Br J Cancer 109:3 (2013), 777–779.
54. [54] Manchanda, R., Loggenberg, K., Sanderson, S., et al. Population testing for cancer predisposing BRCA1/BRCA2 mutations in the Ashkenazi-Jewish community: a randomized controlled trial. J Natl Cancer Inst, 107(1), 2015, 379.
55. [55] Finch, A.P., Lubinski, J., Moller, P., et al. Impact of oophorectomy on cancer incidence and mortality in women with a BRCA1 or BRCA2 mutation. J Clin Oncol 32:15 (2014), 1547–1553.
56. [56] Gabai-Kapara, E., Lahad, A., Kaufman, B., et al. Population-based screening for breast and ovarian cancer risk due to BRCA1 and BRCA2. Proc Natl Acad Sci U S A 111:39 (2014), 14205–14210.
57. [57] Warner, E., Foulkes, W., Goodwin, P., et al. Prevalence and penetrance of BRCA1 and BRCA2 gene mutations in unselected Ashkenazi Jewish women with breast cancer. J Natl Cancer Inst 91:14 (1999), 1241–1247.
58. [58] Manchanda, R., Legood, R., Burnell, M., et al. Cost-effectiveness of population screening for BRCA mutations in Ashkenazi jewish women compared with family history-based testing. J Natl Cancer Inst, 107(1), 2015, 380.
59. [59] Offit, K., The BRCA gene and breast cancer. The New York Times. The Opinion Pages, Letters., Oct 5, 2015.
60. [60] Regeneron launches 100k-patient genomics study with Geisinger, forms new genetics center: GenomeWeb; 2014. Available from: https://www.genomeweb.com/sequencing/regeneron-launches-100k-patient-genomics-study-geisinger-forms-new-genetics-cent.
61. [61] Wheeler, H.E., Maitland, M.L., Dolan, M.E., Cox, N.J., Ratain, M.J., Cancer pharmacogenomics: strategies and challenges. Nat Rev Genet 14:1 (2013), 23–34.
62. [62] Offit, K., Robson, M.E., New pharmacogenomic paradigm in breast cancer treatment. J Clin Oncol 28:31 (2010), 4665–4666.
63. [63] Aminkeng, F., Bhavsar, A.P., A coding variant in RARG confers susceptibility to anthracycline-induced cardiotoxicity in childhood cancer. Nat Genet., 47(9), 2015, 1079–1084.
64. [64] Richards, T., Montori, V.M., Godlee, F., Lapsley, P., Paul, D., Let the patient revolution begin. BMJ, 346, 2013, f2614.
65. [65] Shirts, B.H., Salama, J.S., Aronson, S.J., et al. CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc 22:6 (2015), 1231–1242.
66. [66] Prasad, V., Fojo, T., Brada, M., Precision oncology: origins, optimism, and potential. Lancet Oncol 17:2 (2016), e81–e86.
67. [67] Williams, M.S., Is the genomic translational pipeline being disrupted?. Hum Genom, 9, 2015, 9.
68. [68] Offit, K., Genomic profiles for disease risk: predictive or premature?. JAMA 299:11 (2008), 1353–1355.
69. [69] Offit, K., Decade in review—genomics: a decade of discovery in cancer genomics. Nat Rev Clin. Clin Oncol 11:11 (2014), 632–634.
70. [70] Jones, S., Hruban, R.H., Kamiyama, M., et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science (New York, NY), 324(5924), 2009, 217.
71. [71] Roberts, N.J., Jiao, Y., Yu, J., et al. ATM mutations in patients with hereditary pancreatic cancer. Cancer Disc 2:1 (2012), 41–46.
72. [72] Comino-Mendez, I., Gracia-Aznarez, F.J., Schiavi, F., et al. Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma. Nat Genet 43:7 (2011), 663–667.
73. [73] Mahamdallie, S.S., Hanks, S., Karlin, K.L., et al. Mutations in the transcriptional repressor REST predispose to Wilms tumor. Nat Genet 47:12 (2015), 1471–1474.
74. [74] Ostergaard, P., Simpson, M.A., Connell, F.C., et al. Mutations in GATA2 cause primary lymphedema associated with a predisposition to acute myeloid leukemia (Emberger syndrome). Nat Genet 43:10 (2011), 929–931.
75. [75] Saliba, J., Saint-Martin, C., Di Stefano, A., et al. Germline duplication of ATG2B and GSKIP predisposes to familial myeloid malignancies. Nat Genet 47:10 (2015), 1131–1140.
76. [76] Yokoyama, S., Woods, S.L., Boyle, G.M., et al. A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma. Nature 480:7375 (2011), 99–103.
77. [77] Horn, S., Figl, A., Rachakonda, P.S., et al. TERT promoter mutations in familial and sporadic melanoma. Science 339:6122 (2013), 959–961.
78. [78] Testa, J.R., Cheung, M., Pei, J., et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet 43:10 (2011), 1022–1025.
79. [79] Farley, M.N., Schmidt, L.S., Mester, J.L., et al. A novel germline mutation in BAP1 predisposes to familial clear-cell renal cell carcinoma. Mol Cancer Res 11:9 (2013), 1061–1071.
80. [80] Palles, C., Cazier, J.B., Howarth, K.M., et al. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet 45:2 (2013), 136–144.
81. [81] Weren, R.D., Ligtenberg, M.J., Kets, C.M., et al. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer. Nat Genet 47:6 (2015), 668–671.
82. [82] Gara, S.K., Jia, L., Merino, M.J., et al. Germline HABP2 mutation causing familial nonmedullary thyroid cancer. N Engl J Med 373:5 (2015), 448–455.
83. [83] Park, D.J., Lesueur, F., Nguyen-Dumont, T., et al. Rare mutations in XRCC2 increase the risk of breast cancer. Am J Hum Genet 90:4 (2012), 734–739.
84. [84] Park, D.J., Odefrey, F.A., Hammet, F., et al. FAN1 variants identified in multiple-case early-onset breast cancer families via exome sequencing: no evidence for association with risk for breast cancer. Breast Cancer Res Treat 130:3 (2011), 1043–1049.
85. [85] Ruark, E., Snape, K., Humburg, P., et al. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature 493:7432 (2013), 406–410.
86. [86] Cybulski, C., Carrot-Zhang, J., Kluzniak, W., et al. Germline RECQL mutations are associated with breast cancer susceptibility. Nat Genet 47:6 (2015), 643–646.
87. [87] Rafnar, T., Gudbjartsson, D.F., Sulem, P., et al. Mutations in BRIP1 confer high risk of ovarian cancer. Nat Genet 43:11 (2011), 1104–1107.
88. [88] Noetzli, L., Lo, R.W., Lee-Sherick, A.B., et al. Germline mutations in ETV6 are associated with thrombocytopenia, red cell macrocytosis and predisposition to lymphoblastic leukemia. Nat Genet 47:5 (2015), 535–538.
89. [89] Zhang, M.Y., Churpek, J.E., Keel, S.B., et al. Germline ETV6 mutations in familial thrombocytopenia and hematologic malignancy. Nat Genet 47:2 (2015), 180–185.