The use of genomic information to optimize cancer chemotherapy

Seminars in Oncology

Volumn 38, Issue 2, 2011, Pages 186-195

  Innocenti, Federico ^a   Cox, Nancy J ^a   Dolan, M Eileen ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; BEVACIZUMAB; BREAKPOINT CLUSTER REGION PROTEIN; CARBOPLATIN; CISPLATIN; CYCLOPHOSPHAMIDE; CYTARABINE; CYTOCHROME P450 2D6; DAUNORUBICIN; DEOXYCYTIDINE KINASE; DOCETAXEL; DOXORUBICIN; EPHRIN RECEPTOR A5; ETOPOSIDE; FLUOROURACIL; GEMCITABINE; GLUCURONOSYLTRANSFERASE 1A1; INTERLEUKIN 15; INTERLEUKIN 17F; IRINOTECAN; PACLITAXEL; SONIC HEDGEHOG PROTEIN; TAMOXIFEN;

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOBLASTIC LEUKEMIA; ADVANCED CANCER; ARTICLE; BREAST CANCER; CANCER CHEMOTHERAPY; CANCER PATIENT; CANCER SURVIVAL; CHILDHOOD LEUKEMIA; COPY NUMBER VARIATION; DISEASE FREE SURVIVAL; DNA SEQUENCE; FRAMESHIFT MUTATION; GENE EXPRESSION; GENE FREQUENCY; GENETIC VARIABILITY; GENOMICS; HUMAN; LUNG NON SMALL CELL CANCER; LUNG SMALL CELL CANCER; MISSENSE MUTATION; NEUROPATHY; NONSENSE MUTATION; OVERALL SURVIVAL; PANCREAS CANCER; PATIENT CARE; PHARMACOGENETICS; PHARMACOGENOMICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

DEOXYCYTIDINE KINASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; QUANTITATIVE TRAIT LOCI;

EID: 79952915167     PISSN: 00937754     EISSN: None     Source Type: Journal    
DOI: 10.1053/j.seminoncol.2011.01.005     Document Type: Article

References (94)

1. J.H. Barrett, N.A. Sheehan, A. Cox, J. Worthington, C. Cannings, and M.D. Teare Family based studies and genetic epidemiology: theory and practice Hum Hered 64 2007 146 148 (Pubitemid 46788224)
2. J.L. Hopper, D.T. Bishop, and D.F. Easton Population-based family studies in genetic epidemiology Lancet 366 2005 1397 1406 (Pubitemid 41443407)
3. L.S. Lindstrom, P. Hall, M. Hartman, F. Wiklund, H. Gronberg, and K. Czene Familial concordance in cancer survival: a Swedish population-based study Lancet Oncol 8 2007 1001 1006 (Pubitemid 47629885)
4. L.S. Lindstrom, P. Hall, M. Hartman, F. Wiklund, and K. Czene Is genetic background important in lung cancer survival? PLoS One 4 5 2009 e5588
5. M. Hartman, L. Lindstrom, P.W. Dickman, H.O. Adami, P. Hall, and K. Czene Is breast cancer prognosis inherited? Breast Cancer Res 9 2007 R39
6. M. Garcia-Closas, P. Hall, and H. Nevanlinna Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics PLoS Genet 4 2008 e1000054
7. K.W. Hunter Allelic diversity in the host genetic background may be an important determinant in tumor metastatic dissemination Cancer Lett 200 2003 97 105 (Pubitemid 38366089)
8. L. Coate, S. Cuffe, A. Horgan, R.J. Hung, D. Christiani, and G. Liu Germline genetic variation, cancer outcome, and pharmacogenetics J Clin Oncol 28 2010 4029 4037
9. L. Lennard, J.S. Lilleyman, J. Van Loon, and R.M. Weinshilboum Genetic variation in response to 6-mercaptopurine for childhood acute lymphoblastic leukaemia Lancet 336 1990 225 229 (Pubitemid 20229068)
10. F. Innocenti, S.D. Undevia, and L. Iyer Genetic variants in the UDP-glucuronosyltransferase 1A1 gene predict the risk of severe neutropenia of irinotecan J Clin Oncol 22 2004 1382 1388 (Pubitemid 41103619)
11. S. Borges, Z. Desta, and Y. Jin Composite functional genetic and comedication CYP2D6 activity score in predicting tamoxifen drug exposure among breast cancer patients J Clin Pharmacol 50 2010 450 458
12. M.P. Goetz, D. Toft, and J. Reid Phase I trial of 17-allylamino-17- demethoxygeldanamycin in patients with advanced cancer J Clin Oncol 23 2005 1078 1087 (Pubitemid 46202262)
13. M.J. Higgins, and V. Stearns CYP2D6 polymorphisms and tamoxifen metabolism: clinical relevance Curr Oncol Rep 12 2010 7 15
14. K. Kiyotani, T. Mushiroda, and N. Hosono Lessons for pharmacogenomics studies: association study between CYP2D6 genotype and tamoxifen response Pharmacogenet Genomics 20 2010 565 568
15. W. Schroth, U. Hamann, and P.A. Fasching CYP2D6 polymorphisms as predictors of outcome in breast cancer patients treated with tamoxifen: expanded polymorphism coverage improves risk stratification Clin Cancer Res 16 2010 4468 4477
16. C.M. Hartford, S. Duan, and S.M. Delaney Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity Blood 113 2009 2145 2153
17. R.S. Huang, S. Duan, and W.K. Bleibel A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity Proc Natl Acad Sci U S A 104 2007 9758 9763 (Pubitemid 47175340)
18. R.S. Huang, S. Duan, E.O. Kistner, C.M. Hartford, and M.E. Dolan Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans Mol Cancer Ther 7 2008 3038 3046
19. B.E. Stranger, M.S. Forrest, and M. Dunning Relative impact of nucleotide and copy number variation on gene expression phenotypes Science 315 2007 848 853
20. J.C. Cohen, R.S. Kiss, A. Pertsemlidis, Y.L. Marcel, R. McPherson, and H.H. Hobbs Multiple rare alleles contribute to low plasma levels of HDL cholesterol Science 305 2004 869 872 (Pubitemid 39038422)
21. S.P. Dickson, K. Wang, I. Krantz, H. Hakonarson, and D.B. Goldstein Rare variants create synthetic genome-wide associations PLoS Biol 8 2010 e1000294
22. K. Wang, S.P. Dickson, C.A. Stolle, I.D. Krantz, D.B. Goldstein, and H. Hakonarson Interpretation of association signals and identification of causal variants from genome-wide association studies Am J Hum Genet 86 2010 730 742
23. R.S. Spielman, L.A. Bastone, J.T. Burdick, M. Morley, W.J. Ewens, and V.G. Cheung Common genetic variants account for differences in gene expression among ethnic groups Nat Genet 39 2007 226 231 (Pubitemid 46184354)
24. J.D. Storey, J. Madeoy, J.L. Strout, M. Wurfel, J. Ronald, and J.M. Akey Gene-expression variation within and among human populations Am J Hum Genet 80 2007 502 509
25. S. Duan, R.S. Huang, and W. Zhang Genetic architecture of transcript-level variation in humans Am J Hum Genet 82 2008 1101 1113
26. W. Zhang, S. Duan, and W.K. Bleibel Identification of common genetic variants that account for transcript isoform variation between human populations Hum Genet 125 2009 81 93
27. B.E. Stranger, A.C. Nica, and M.S. Forrest Population genomics of human gene expression Nat Genet 39 2007 1217 1224 (Pubitemid 47482691)
28. M.E. Dolan, K.G. Newbold, and R. Nagasubramanian Heritability and linkage analysis of sensitivity to cisplatin-induced cytotoxicity Cancer Res 64 2004 4353 4356 (Pubitemid 38802443)
29. J.W. Watters, A. Kraja, M.A. Meucci, M.A. Province, and H.L. McLeod Genome-wide discovery of loci influencing chemotherapy cytotoxicity Proc Natl Acad Sci U S A 101 2004 11809 11814 (Pubitemid 39095376)
30. S.J. Shukla, S. Duan, J.A. Badner, X. Wu, and M.E. Dolan Susceptibility loci involved in cisplatin-induced cytotoxicity and apoptosis Pharmacogenet Genomics 18 2008 253 262 (Pubitemid 351323240)
31. S. Duan, W.K. Bleibel, and R.S. Huang Mapping genes that contribute to daunorubicin-induced cytotoxicity Cancer Res 67 2007 5425 5433 (Pubitemid 46997283)
32. W.K. Bleibel, S. Duan, and R.S. Huang Identification of genomic regions contributing to etoposide-induced cytotoxicity Hum Genet 125 2009 173 180
33. S.J. Shukla, S. Duan, X. Wu, J.A. Badner, K. Kasza, and M.E. Dolan Whole-genome approach implicates CD44 in cellular resistance to carboplatin Hum Genomics 3 2009 128 142
34. E.R. Gamazon, R.S. Huang, N.J. Cox, and M.E. Dolan Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci Proc Natl Acad Sci U S A 107 2010 9287 9292
35. R.S. Huang, S. Duan, and S.J. Shukla Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach Am J Hum Genet 81 2007 427 437 (Pubitemid 47330203)
36. R.S. Huang, S. Duan, and E.O. Kistner Genetic variants contributing to daunorubicin-induced cytotoxicity Cancer Res 68 2008 3161 3168
37. U. Scherf, D.T. Ross, and M. Waltham A gene expression database for the molecular pharmacology of cancer Nat Genet 24 2000 236 244 (Pubitemid 30132190)
38. D.T. Ross, U. Scherf, and M.B. Eisen Systematic variation in gene expression patterns in human cancer cell lines Nat Genet 24 2000 227 235 (Pubitemid 30132189)
39. L.A. Garraway, H.R. Widlund, and M.A. Rubin Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma Nature 436 2005 117 122 (Pubitemid 40966196)
40. A. Gaur, D.A. Jewell, and Y. Liang Characterization of microRNA expression levels and their biological correlates in human cancer cell lines Cancer Res 67 2007 2456 2468 (Pubitemid 46548930)
41. P.E. Blower, J.S. Verducci, and S. Lin MicroRNA expression profiles for the NCI-60 cancer cell panel Mol Cancer Ther 6 2007 1483 1491 (Pubitemid 46954015)
42. S. Nishizuka, L. Charboneau, and L. Young Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays Proc Natl Acad Sci U S A 100 2003 14229 14234 (Pubitemid 37499219)
43. R.H. Shoemaker The NCI60 human tumour cell line anticancer drug screen Nat Rev Cancer 6 2006 813 823 (Pubitemid 44450469)
44. J.E. Staunton, D.K. Slonim, and H.A. Coller Chemosensitivity prediction by transcriptional profiling Proc Natl Acad Sci U S A 98 2001 10787 10792 (Pubitemid 32878698)
45. J.N. Weinstein, T.G. Myers, and P.M. O'Connor An information-intensive approach to the molecular pharmacology of cancer Science 275 1997 343 349 (Pubitemid 27051604)
46. P.E. Blower, C. Yang, and M.A. Fligner Pharmacogenomic analysis: correlating molecular substructure classes with microarray gene expression data Pharmacogenomics J 2 2002 259 271 (Pubitemid 35023584)
47. R. Huang, A. Wallqvist, N. Thanki, and D.G. Covell Linking pathway gene expressions to the growth inhibition response from the National Cancer Institute's anticancer screen and drug mechanism of action Pharmacogenomics J 5 2005 381 399
48. Z. Dai, C. Barbacioru, Y. Huang, and W. Sadee Prediction of anticancer drug potency from expression of genes involved in growth factor signaling Pharm Res 23 2006 336 349 (Pubitemid 43237864)
49. K.H. Salter, C.R. Acharya, and K.S. Walters An integrated approach to the prediction of chemotherapeutic response in patients with breast cancer PLoS ONE 3 2008 e1908
50. Y. Ma, Z. Ding, and Y. Qian Predicting cancer drug response by proteomic profiling Clin Cancer Res 12 2006 4583 4589 (Pubitemid 44297808)
51. U.T. Shankavaram, W.C. Reinhold, and S. Nishizuka Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study Mol Cancer Ther 6 2007 820 832 (Pubitemid 46554552)
52. E.V. Stevens, S. Nishizuka, and S. Antony Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers Mol Cancer Ther 7 2008 10 18
53. P.E. Blower, J.H. Chung, and J.S. Verducci MicroRNAs modulate the chemosensitivity of tumor cells Mol Cancer Ther 7 2008 1 9
54. H. Jarjanazi, J. Kiefer, and S. Savas Discovery of genetic profiles impacting response to chemotherapy: application to gemcitabine Hum Mutat 29 2008 461 467 (Pubitemid 351536984)
55. V. Le Morvan, R. Bellott, F. Moisan, S. Mathoulin-Pelissier, J. Bonnet, and J. Robert Relationships between genetic polymorphisms and anticancer drug cytotoxicity vis-a-vis the NCI-60 panel Pharmacogenomics 7 2006 843 852 (Pubitemid 44446735)
56. S. Puyo, V. Le Morvan, and J. Robert Impact of EGFR gene polymorphisms on anticancer drug cytotoxicity in vitro Mol Diagn Ther 12 2008 225 234
57. S. Sasaki, T. Kobunai, J. Kitayama, and H. Nagawa DNA methylation and sensitivity to antimetabolites in cancer cell lines Oncol Rep 19 2008 407 412 (Pubitemid 351176101)
58. L. Shen, Y. Kondo, and S. Ahmed Drug sensitivity prediction by CpG island methylation profile in the NCI-60 cancer cell line panel Cancer Res 67 2007 11335 11343 (Pubitemid 350248560)
59. W. Liu, X. Wu, and W. Zhang Relationship of EGFR mutations, expression, amplification, and polymorphisms to epidermal growth factor receptor inhibitors in the NCI60 cell lines Clin Cancer Res 13 2007 6788 6795 (Pubitemid 350206817)
60. A. Raza, S. Gezer, and J. Anderson Relationship of [3H]Ara-C incorporation and response to therapy with high-dose Ara-C in AML patients: a Leukemia Intergroup study Exp Hematol 20 1992 1194 1200
61. E. Estey, W. Plunkett, D. Dixon, M. Keating, K. McCredie, and E.J. Freireich Variables predicting response to high dose cytosine arabinoside therapy in patients with refractory acute leukemia Leukemia 1 1987 580 583 (Pubitemid 18005688)
62. C.M. Galmarini, X. Thomas, and K. Graham Deoxycytidine kinase and cN-II nucleotidase expression in blast cells predict survival in acute myeloid leukaemia patients treated with cytarabine Br J Haematol 122 2003 53 60 (Pubitemid 36819338)
63. J.K. Lamba, K. Crews, and S. Pounds Pharmacogenetics of deoxycytidine kinase: identification and characterization of novel genetic variants J Pharmacol Exp Ther 323 2007 935 945 (Pubitemid 350146062)
64. A. Galvan, J.P. Ioannidis, and T.A. Dragani Beyond genome-wide association studies: genetic heterogeneity and individual predisposition to cancer Trends Genet 26 2010 132 141
65. Z.K. Stadler, P. Thom, and M.E. Robson Genome-wide association studies of cancer J Clin Oncol 28 2010 4255 4267
66. L.A. Hindorff, H.A. Junkins, P.N. Hall, J.P. Mehta, and T.A. Manolio A catalog of published genome-wide association studies www.genome.gov/gwastudies Accessed August 2010
67. J.J. Yang, C. Cheng, and W. Yang Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia JAMA 301 2009 393 403
68. J.J. van Dongen, T. Seriu, and E.R. Panzer-Grumayer Prognostic value of minimal residual disease in acute lymphoblastic leukaemia in childhood Lancet 352 1998 1731 1738 (Pubitemid 28534955)
69. G. Cario, S. Izraeli, and A. Teichert High interleukin-15 expression characterizes childhood acute lymphoblastic leukemia with involvement of the CNS J Clin Oncol 25 2007 4813 4820 (Pubitemid 350086486)
70. I. Tinhofer, I. Marschitz, T. Henn, A. Egle, and R. Greil Expression of functional interleukin-15 receptor and autocrine production of interleukin-15 as mechanisms of tumor propagation in multiple myeloma Blood 95 2000 610 618 (Pubitemid 30041677)
71. X.J. Zhang, K.L. Yan, and Z.M. Wang Polymorphisms in interleukin-15 gene on chromosome 4q31.2 are associated with psoriasis vulgaris in Chinese population J Invest Dermatol 127 2007 2544 2551
72. C. Wu, B. Xu, P. Yuan, J. Ott, Y. Guan, and Y. Liu Genome-wide examination of genetic variants associated with response to platinum-based chemotherapy in patients with small-cell lung cancer Pharmacogenet Genomics 20 2010 389 395
73. O. Gautschi, P.C. Mack, A.M. Davies, D.M. Jablons, R. Rosell, and D.R. Gandara Pharmacogenomic approaches to individualizing chemotherapy for non-small-cell lung cancer: current status and new directions Clin Lung Cancer 9 Suppl 3 2008 S129 S138
74. H.L. Kindler, D. Niedzwiecki, and D. Hollis Gemcitabine plus bevacizumab compared with gemcitabine plus placebo in patients with advanced pancreatic cancer: phase III trial of the Cancer and Leukemia Group B (CALGB 80303) J Clin Oncol 28 2010 3617 3622
75. F. Innocenti, W. Owzar, and N. Cox Heritable interleukin-17F (IL17F) gene variation and overall survival (OS) in pancreatic cancer patients (pts): Results from a genome-wide association study (GWAS) in CALGB 80303 [abstract] J Clin Oncol 27 2009 15s
76. M. Kawaguchi, D. Takahashi, and N. Hizawa IL-17F sequence variant (His161Arg) is associated with protection against asthma and antagonizes wild-type IL-17F activity J Allergy Clin Immunol 117 2006 795 801
77. T. Starnes, M.J. Robertson, and G. Sledge Cutting edge: IL-17F, a novel cytokine selectively expressed in activated T cells and monocytes, regulates angiogenesis and endothelial cell cytokine production J Immunol 167 2001 4137 4140 (Pubitemid 32954284)
78. Y. Sato, N. Yamamoto, and H. Kunitoh Genome-wide association scan detected candidate polymorphisms associated with overall survival (OS) in advanced non-small cell lung cancer (NSCLC) treated with carboplatin (CBDCA) and paclitaxel (PTX) [abstract] J Clin Oncol 27 2009 15s
79. D. Kroetz, R.M. Baldwin, and K. Owzar Inherited genetic variation in EPHA5, FGD4, and NRDG1 and paclitaxel (P)-induced peripheral neuropathy (PN): Results from a genome-wide association study (GWAS) in CALGB 40101 [abstract] J Clin Oncol 28 2010 15s
80. Y. Tanaka, N. Nishida, M. Sugiyama, M. Kurosaki, K. Matsuura, and N. Sakamoto Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C Nat Genet 41 2009 1105 1109
81. M.R. Spitz, X. Wu, and G. Mills Integrative epidemiology: from risk assessment to outcome prediction J Clin Oncol 23 2005 267 275 (Pubitemid 46206878)
82. Y. Liu, S. Shete, and C.J. Etzel Polymorphisms of LIG4, BTBD2, HMGA2, and RTEL1 genes involved in the double-strand break repair pathway predict glioblastoma survival J Clin Oncol 28 2010 2467 2474
83. C.A. Salinas, J.S. Koopmeiners, and E.M. Kwon Clinical utility of five genetic variants for predicting prostate cancer risk and mortality Prostate 69 2009 363 372
84. S.L. Zheng, J. Sun, and F. Wiklund Cumulative association of five genetic variants with prostate cancer N Engl J Med 358 2008 910 919 (Pubitemid 351397090)
85. R.J. Klein, C. Hallden, and A.M. Cronin Blood biomarker levels to aid discovery of cancer-related single-nucleotide polymorphisms: kallikreins and prostate cancer Cancer Prev Res (Phila) 3 2010 611 619
86. McWilliams R, Bamlet WR, Fernandez-Zapico M, et al. Association of sonic hedgehog variant with survival in pancreatic cancer [abstract]. Gastrointestinal Cancers Symposium; Orlando, FL; January 22-24, 2010.
87. K. Garber Stromal depletion goes on trial in pancreatic cancer J Natl Cancer Inst 102 2010 448 450
88. M.R. Nelson, S.A. Bacanu, and M. Mosteller Genome-wide approaches to identify pharmacogenetic contributions to adverse drug reactions Pharmacogenomics J 9 2009 23 33
89. E. Link, S. Parish, and J. Armitage SLCO1B1 variants and statin-induced myopathya genomewide study N Engl J Med 359 2008 789 799
90. A.K. Daly, and C.P. Day Genetic association studies in drug-induced liver injury Semin Liver Dis 29 2009 400 411
91. N. Siva 1000 Genomes project Nat Biotechnol 26 2008 256
92. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
93. F. Innocenti, and R.L. Schilsky Translating the cancer genome into clinically useful tools and strategies Dis Model Mech 2 2009 426 429
94. M.E. Robson, C.D. Storm, J. Weitzel, D.S. Wollins, and K. Offit American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility J Clin Oncol 28 2010 893 901