Genetic-based biomarkers and next-generation sequencing: The future of personalized care in colorectal cancer

Personalized Medicine

Volumn 8, Issue 3, 2011, Pages 331-345

  Kim, Rebecca Y ^b   Xu, Hua ^a   Myllykangas, Samuel ^a   Ji, Hanlee ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

adenocarcinoma; antineoplastic agents; biological analysis; biomarkers; cetuximab; colorectal neoplasms; EGFR inhibition; etiology; genetics; genomics; humans; panitumumab; sequencing; targeted therapies; tumor markers

Indexed keywords

5,10 METHYLENETETRAHYDROFOLATE REDUCTASE (FADH2); B RAF KINASE; CETUXIMAB; EPIDERMAL GROWTH FACTOR RECEPTOR; FLUOROURACIL; FOLINIC ACID; GENOMIC DNA; IRINOTECAN; K RAS PROTEIN; OXALIPLATIN; PANITUMUMAB; PROTEIN P53; THYMIDYLATE SYNTHASE; TUMOR MARKER;

CANCER DIAGNOSIS; CANCER GENETICS; CHROMOSOME 18Q; CHROMOSOME DELETION; COLON CARCINOGENESIS; COLORECTAL CANCER; GENE MUTATION; GENE SEQUENCE; GENOME; HUMAN; MICROSATELLITE INSTABILITY; NEXT GENERATION SEQUENCING; PERSONALIZED MEDICINE; PRIORITY JOURNAL; REVIEW;

EID: 79958116641     PISSN: 17410541     EISSN: 1744828X     Source Type: Journal    
DOI: 10.2217/pme.11.16     Document Type: Review

References (87)

1. Fry R, Mahmoud N, Maron D, Ross H, Rombeau J: Colon and rectum. In: Sabiston Textbook of Surgery (8th Edition). Townsend C, Beauchamp R, Evers B, Mattox K (Eds). Saunders, Elsevier, PA, USA (2008).
2. Engstrom P, Arnoletti J, Benson AB 3rd, et al.: NCCN guidelines: Colon Cancer. Version 1.2011 (2010).
3. Vogelstein B, Fearon ER, Hamilton SR, et al.: Genetic alterations during colorectal-tumor development. N. Engl. J. Med. 319(9), 525-532 (1988).
4. Gunderson LL, Jessup JM, Sargent DJ, Greene FL, Stewart AK: Revised TN categorization for colon cancer based on national survival outcomes data. J. Clin. Oncol. 28(2), 264-271 (2010).
5. Marshall JL: Risk assessment in stage II colorectal cancer. Oncology (Williston Park) 24(1 Suppl. 1), 9-13 (2010).
6. Gray R, Barnwell J, McConkey C, et al.: Adjuvant chemotherapy versus observation in patients with colorectal cancer: a randomised study. Lancet 370(9604), 2020-2029 (2007).
7. Becquemont L: Pharmacogenomics of adverse drug reactions: practical applications and perspectives. Pharmacogenomics 10(6), 961-969 (2009).
8. Locker GY, Hamilton S, Harris J, et al.: ASCO 2006 update of recommendations for the use of tumor markers in gastrointestinal cancer. J. Clin. Oncol. 24(33), 5313-5327 (2006). (Pubitemid 46631379)
9. Peltomaki P: Role of DNA mismatch repair defects in the pathogenesis of human cancer. J. Clin. Oncol. 21(6), 1174-1179 (2003). (Pubitemid 46594150)
10. Boland CR, Thibodeau SN, Hamilton SR, et al.: A National Cancer Institute workshop on microsatellite instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res. 58(22), 5248-5257 (1998). (Pubitemid 28521189)
11. Popat S, Hubner R, Houlston RS: Systematic review of microsatellite instability and colorectal cancer prognosis. J. Clin. Oncol. 23(3), 609-618 (2005). (Pubitemid 46224239)
12. Benatti P, Gafa R, Barana D, et al.: Microsatellite instability and colorectal cancer prognosis. Clin. Cancer Res. 11(23), 8332-8340 (2005). (Pubitemid 41746945)
13. Kim GP, Colangelo LH, Wieand HS, et al.: Prognostic and predictive roles of high-degree microsatellite instability in colon cancer: a National Cancer Institute-National Surgical Adjuvant Breast and Bowel Project Collaborative Study. J. Clin. Oncol. 25(7), 767-772 (2007). (Pubitemid 350002875)
14. Ribic CM, Sargent DJ, Moore MJ, et al.: Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. N. Engl. J. Med. 349(3), 247-257 (2003). (Pubitemid 36859476)
15. Bertagnolli MM, Niedzwiecki D, Compton CC, et al.: Microsatellite instability predicts improved response to adjuvant therapy with irinotecan, fluorouracil, and leucovorin in stage III colon cancer: Cancer and Leukemia Group B Protocol 89803. J. Clin. Oncol. 27(11), 1814-1821 (2009).
16. Des Guetz G, Schischmanoff O, Nicolas P, et al.: Does microsatellite instability predict the efficacy of adjuvant chemotherapy in colorectal cancer? A systematic review with meta-analysis. Eur. J. Cancer 45(10), 1890-1896 (2009).
17. Sargent DJ, Marsoni S, Monges G, et al.: Defective mismatch repair as a predictive marker for lack of efficacy of fluorouracil-based adjuvant therapy in colon cancer. J. Clin. Oncol. 28(20), 3219-3226 (2010).
18. Munro AJ, Lain S, Lane DP: P53 abnormalities and outcomes in colorectal cancer: a systematic review. Br. J. Cancer 92(3), 434-444 (2005). (Pubitemid 40395523)
19. Font A, Abad A, Monzo M, et al.: Prognostic value of K-ras mutations and allelic imbalance on chromosome 18q in patients with resected colorectal cancer. Dis. Colon Rectum 44(4), 549-557 (2001). (Pubitemid 32336428)
20. Jernvall P, Makinen MJ, Karttunen TJ, Makela J, Vihko P: Loss of heterozygosity at 18q21 is indicative of recurrence and therefore poor prognosis in a subset of colorectal cancers. Br. J. Cancer 79(5-6), 903-908 (1999). (Pubitemid 29082124)
21. Lanza G, Matteuzzi M, Gafa R, et al.: Chromosome 18q allelic loss and prognosis in stage II and III colon cancer. Int. J. Cancer 79(4), 390-395 (1998). (Pubitemid 28359738)
22. Watanabe T, Wu TT, Catalano PJ, et al.: Molecular predictors of survival after adjuvant chemotherapy for colon cancer. N. Engl. J. Med. 344(16), 1196-1206 (2001). (Pubitemid 32319494)
23. Fearon ER: Molecular genetics of colorectal cancer. Ann. NY Acad. Sci. 768, 101-110 (1995). (Pubitemid 26078724)
24. Kirley SD, DApuzzo M, Lauwers GY, et al.: The cables gene on chromosome 18Q regulates colon cancer progression in vivo. Cancer Biol. Ther. 4(8), 861-863 (2005).
25. Carethers JM, Hawn MT, Greenson JK, Hitchcock CL, Boland CR: Prognostic significance of allelic lost at chromosome 18q21 for stage II colorectal cancer. Gastroenterology 114(6), 1188-1195 (1998). (Pubitemid 28243904)
26. Cohn KH, Ornstein DL, Wang F, et al.: The significance of allelic deletions and aneuploidy in colorectal carcinoma. Results of a 5-year follow-up study. Cancer 79(2), 233-244 (1997). (Pubitemid 27029887)
27. Longley DB, Harkin DP, Johnston PG: 5-fluorouracil: mechanisms of action and clinical strategies. Nat. Rev. Cancer 3(5), 330-338 (2003). (Pubitemid 37328853)
28. Popat S, Matakidou A, Houlston RS: Thymidylate synthase expression and prognosis in colorectal cancer: a systematic review and meta-analysis. J. Clin. Oncol. 22(3), 529-536 (2004). (Pubitemid 41079782)
29. Boige V, Mendiboure J, Pignon JP, et al.: Pharmacogenetic assessment of toxicity and outcome in patients with metastatic colorectal cancer treated with LV5FU2 FOLFOX and FOLFIRI: FFCD 2000-2005. J. Clin. Oncol. 28: 15,2556-2564 (2010).
30. Martinez-Balibrea E, Abad A, Martinez-Cardus A, et al.: UGT1A and TYMS genetic variants predict toxicity and response of colorectal cancer patients treated with first-line irinotecan and fluorouracil combination therapy. Br. J. Cancer 103(4), 581-589 (2010).
31. Jakobsen A, Nielsen JN, Gyldenkerne N, Lindeberg J: Thymidylate synthase and methylenetetrahydrofolate reductase gene polymorphism in normal tissue as predictors of fluorouracil sensitivity. J. Clin. Oncol. 23(7), 1365-1369 (2005).
32. Etienne-Grimaldi MC, Milano G, Maindrault-Goebel F, et al.: Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms and FOLFOX response in colorectal cancer patients. Br. J. Clin. Pharmacol. 69(1), 58-66 (2010).
33. Zintzaras E, Ziogas DC, Kitsios GD, et al.: MTHFR gene polymorphisms and response to chemotherapy in colorectal cancer: a meta-analysis. Pharmacogenomics 10(8), 1285-1294 (2009).
34. Lievre A, Blons H, Laurent-Puig P: Oncogenic mutations as predictive factors in colorectal cancer. Oncogene 29(21), 3033-3043 (2010).
35. Roth AD, Tejpar S, Delorenzi M, et al.: Prognostic role of KRAS and BRAF in stage II and III resected colon cancer: results of the translational study on the PETACC-3, EORTC 40993, SAKK 60-00 trial. J. Clin. Oncol. 28(3), 466-474 (2010).
36. Andreyev HJ, Norman AR, Cunningham D, Oates JR, Clarke PA: Kirsten ras mutations in patients with colorectal cancer: the multicenter RASCAL study. J. Natl Cancer Inst. 90(9), 675-684 (1998). (Pubitemid 28222141)
37. Andreyev HJ, Norman AR, Cunningham D, et al.: Kirsten Ras mutations in patients with colorectal cancer: the RASCAL II study. Br. J. Cancer 85(5), 692-696 (2001). (Pubitemid 32929467)
38. Peeters M, Price TJ, Cervantes A, et al.: Randomized Phase III study of panitumumab with fluorouracil, leucovorin, and irinotecan (FOLFIRI) compared with FOLFIRI alone as second-line treatment in patients with metastatic colorectal cancer. J. Clin. Oncol. 28(31), 4706-4713 (2010).
39. De Roock W, Claes B, Bernasconi D, et al.: Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. Lancet Oncol. 11(8), 753-762 (2010).
40. Qiu LX, Mao C, Zhang J, et al.: Predictive and prognostic value of KRAS mutations in metastatic colorectal cancer patients treated with cetuximab: a meta-analysis of 22 studies. Eur. J. Cancer 46(15), 2781-2787 (2010).
41. Bokemeyer C, Bondarenko I, Makhson A, et al.: Fluorouracil, leucovorin, and oxaliplatin with and without cetuximab in the first-line treatment of metastatic colorectal cancer. J. Clin. Oncol. 27(5), 663-671 (2009).
42. Ocvirk J, Brodowicz T, Wrba F, et al.: Cetuximab plus FOLFOX6 or FOLFIRI in metastatic colorectal cancer: CECOG trial. World J. Gastroenterol. 16(25), 3133-3143 (2010).
43. Tol J, Koopman M, Cats A, et al.: Chemotherapy, bevacizumab, and cetuximab in metastatic colorectal cancer. N. Engl. J. Med. 360(6), 563-572 (2009).
44. Amado RG, Wolf M, Peeters M, et al.: Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J. Clin. Oncol. 26(10), 1626-1634 (2008).
45. Lievre A, Bachet JB, Boige V, et al.: KRAS mutations as an independent prognostic factor in patients with advanced colorectal cancer treated with cetuximab. J. Clin. Oncol. 26(3), 374-379 (2008). (Pubitemid 351171687)
46. Karapetis CS, Khambata-Ford S, Jonker DJ, et al.: K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N. Engl. J. Med. 359(17), 1757-1765 (2008).
47. Benvenuti S, Sartore-Bianchi A, Di Nicolantonio F, et al.: Oncogenic activation of the RAS/RAF signaling pathway impairs the response of metastatic colorectal cancers to anti-epidermal growth factor receptor antibody therapies. Cancer Res. 67(6), 2643-2648 (2007). (Pubitemid 46548951)
48. Loupakis F, Pollina L, Stasi I, et al.: PTEN expression and KRAS mutations on primary tumors and metastases in the prediction of benefit from cetuximab plus irinotecan for patients with metastatic colorectal cancer. J. Clin. Oncol. 27(16), 2622-2629 (2009).
49. Van Cutsem E, Kohne CH, Hitre E, et al.: Cetuximab and chemotherapy as initial treatment for metastatic colorectal cancer. N. Engl. J. Med. 360(14), 1408-1417 (2009).
50. Rajagopalan H, Bardelli A, Lengauer C, et al.: Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature 418(6901), 934 (2002). (Pubitemid 34976022)
51. Laurent-Puig P, Cayre A, Manceau G, et al.: Analysis of PTEN, BRAF, and EGFR status in determining benefit from cetuximab therapy in wild-type KRAS metastatic colon cancer. J. Clin. Oncol. 27(35), 5924-5930 (2009).
52. Di Nicolantonio F, Martini M, Molinari F, et al.: Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J. Clin. Oncol. 26(35), 5705-5712 (2008).
53. Sartore-Bianchi A, Di Nicolantonio F, Nichelatti M, et al.: Multi-determinants analysis of molecular alterations for predicting clinical benefit to EGFR-targeted monoclonal antibodies in colorectal cancer. PLoS ONE 4(10), e7287 (2009).
54. Rogers J: The finished genome sequence of Homo sapiens. Cold Spring Harb. Symp. Quant. Biol. 68, 1-11 (2003). (Pubitemid 38955546)
55. Ansorge WJ: Next-generation DNA sequencing techniques. Nat. Biotechnol. 25(4), 195-203 (2009).
56. Shendure J, Ji H: Next-generation DNA sequencing. Nat. Biotechnol. 26(10), 1135-1145 (2008).
57. Metzker ML: Sequencing technologies - the next generation. Nat. Rev. Genet. 11(1), 31-46 (2010).
58. Medvedev P, Stanciu M, Brudno M: Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 6(Suppl. 11), S13-S20 (2009).
59. McPherson JD: Next-generation gap. Nat. Methods 6(Suppl. 11), S2-S5 (2009).
60. Meyerson M, Gabriel S, Getz G: Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11(10), 685-696 (2010).
61. Bentley DR, Balasubramanian S, Swerdlow HP, et al.: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218), 53-59 (2008).
62. Ahn SM, Kim TH, Lee S, et al.: The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19(9), 1622-1629 (2009).
63. Wheeler DA, Srinivasan M, Egholm M, et al.: The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189), 872-876 (2008). (Pubitemid 351550870)
64. Harris M, Winship I, Spriggs M: Controversies and ethical issues in cancer - genetics clinics. Lancet Oncol. 6(5), 301-310 (2005). (Pubitemid 40590267)
65. Stanley AJ, Gaff CL, Aittomaki AK, et al.: Value of predictive genetic testing in management of hereditary non-polyposis colorectal cancer (HNPCC). Med. J. Aust. 172(7), 313-316 (2000). (Pubitemid 30202875)
66. Thomas RK, Greulich H, Yuza Y, et al.: Detection of oncogenic mutations in the EGFR gene in lung adenocarcinoma with differential sensitivity to EGFR tyrosine kinase inhibitors. Cold Spring Harb. Symp. Quant. Biol. 70, 73-81 (2005). (Pubitemid 44124858)
67. Mardis ER, Ding L, Dooling DJ, et al.: Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361(11), 1058-1066 (2009).
68. Ley TJ, Mardis ER, Ding L, et al.: DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456(7218), 66-72 (2008).
69. Berger MF, Levin JZ, Vijayendran K, et al.: Integrative analysis of the melanoma transcriptome. Genome Res. 20(4), 413-427 (2010).
70. Bueno R, De Rienzo A, Dong L, et al.: Second generation sequencing of the mesothelioma tumor genome. PLoS ONE 5(5), e10612 (2010).
71. Pleasance ED, Stephens PJ, OMeara S, et al.: A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463(7278), 184-190 (2010).
72. Yu J, Mani RS, Cao Q, et al.: An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell 17(5), 443-454 (2010).
73. Wood LD, Parsons DW, Jones S, et al.: The genomic landscapes of human breast and colorectal cancers. Science 318(5853), 1108-1113 (2007). (Pubitemid 350134889)
74. American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility. J. Clin. Oncol. 21(12), 2397-2406 (2003).
75. Health law - genetics - Congress restricts use of genetic information by insurers and employers. Genetic Information Nondiscrimination Act of 2008, Pub. L. No. 110-233, 122 Stat. 881 (to be codified in scattered sections of 26, 29, and 42 U.S.C.). Harv. Law Rev. 122(3), 1038-1045 (2009).
76. Offit K, Thom P: Ethical and legal aspects of cancer genetic testing. Semin. Oncol. 34(5), 435-443 (2007). (Pubitemid 47503275)
77. Stadler ZK, Thom P, Robson ME, et al.: Genome-wide association studies of cancer. J. Clin. Oncol. 28(27), 4255-4267 (2010).
78. Subramanian J, Simon R: Gene expression-based prognostic signatures in lung cancer: ready for clinical use? J. Natl Cancer Inst. 102(7), 464-474 (2010).
79. Garman KS, Acharya CR, Edelman E, et al.: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proc. Natl Acad. Sci. USA 105(49), 19432-19437 (2008).
80. Ali MA, Sjoblom T: Molecular pathways in tumor progression: from discovery to functional understanding. Mol. Biosyst. 5(9), 902-908 (2009).
81. Vilar E, Gruber SB: Microsatellite instability in colorectal cancer - the stable evidence. Nat. Rev. Clin. Oncol. 7(3), 153-162 (2010).
82. Gstaiger M, Aebersold R: Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet. 10(9), 617-627 (2009).
83. Kandpal R, Saviola B, Felton J: The era of omics unlimited. Biotechniques 46(5), 351-352, 4-5 (2009).
84. WHO: Cancer 2009 www.who.int/mediacentre/factsheets/fs297/en/index.html
85. SEER Cancer Statistics Review, 1975-2007. Altekruse SF, Krapcho M, Neyman N, et al. (Eds) (2010) http://seer.cancer.gov/csr/1975-2007/
86. Programs UDoEG: Human Genome Project Information http://genomics.energy. gov
87. NIH: The Cancer Genome Atlas - Mission and Goals http://cancergenome.nih. gov/about/mission. asp