Personalized sequencing and the future of medicine: Discovery, diagnosis and defeat of disease

Pharmacogenomics

Volumn 15, Issue 14, 2014, Pages 1771-1790

  Esplin, Edward D ^a   Oei, Ling ^a   Snyder, Michael P ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

cancer genomics; disease discovery; electronic medical record; genomic medicine; individualized therapy; next generation sequencing; personalized medicine; pharmacogenetics; pharmacogenomics; precision medicine; prevention; whole exome sequencing; whole genome sequencing

Indexed keywords

ABACAVIR; AMITRIPTYLINE; ARIPIPRAZOLE; ATOMOXETINE; ATORVASTATIN; AZATHIOPRINE; B RAF KINASE; B RAF KINASE INHIBITOR; BELIMUMAB; BOCEPREVIR; CARBAMAZEPINE; CLOPIDOGREL; CYTOCHROME P450 2C19; CYTOCHROME P450 2D6; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; HLA B ANTIGEN; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; IRINOTECAN; MERCAPTOPURINE; METHOTREXATE; NORTRIPTYLINE; PROTEIN TYROSINE KINASE INHIBITOR; RNA; SOLUTE CARRIER ORGANIC ANION TRANSPORTER 1B1; TAMOXIFEN; UNINDEXED DRUG; VITAMIN K EPOXIDE REDUCTASE; WARFARIN;

ACUTE LYMPHOBLASTIC LEUKEMIA; BLEEDING; BRAF GENE; BREAST CARCINOMA; CANCER GROWTH; CANCER SURVIVAL; CANCER SUSCEPTIBILITY; CARDIOVASCULAR DISEASE; CENTRAL NERVOUS SYSTEM DISEASE; COLON CANCER; COLORECTAL CANCER; CYP2D6 GENE; DEPRESSION; DIAGNOSTIC ACCURACY; DNA METHYLATION; DNA SEQUENCE; DRUG APPROVAL; DRUG HYPERSENSITIVITY; DRUG INFORMATION; EGFR GENE; ELECTRONIC MEDICAL RECORD; FAMILY HISTORY; FOOD AND DRUG ADMINISTRATION; GENE; GENE EXPRESSION; GENE MUTATION; GENETIC ANALYZER; GENETIC VARIABILITY; GENOTYPE; GERM LINE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INDIVIDUALIZATION; INFORMED CONSENT; MALIGNANT NEOPLASTIC DISEASE; MEDICAL ETHICS; MEDICAL RESEARCH; MELANOMA; MIGRAINE; MUTATIONAL ANALYSIS; MYOPATHY; NEUROLOGIC DISEASE; NEUROPATHIC PAIN; OBSESSIVE COMPULSIVE DISORDER; ONCOGENE K RAS; PATIENT CARE; PATIENT INFORMATION; PATIENT MONITORING; PERSONALIZED MEDICINE; PHARMACOGENETICS; PHARMACOGENOMICS; PROPHYLAXIS; RARE DISEASE; REVIEW; RISK ASSESSMENT; RISK BENEFIT ANALYSIS; SEQUENCE ANALYSIS; STEVENS JOHNSON SYNDROME; TPMT GENE; UNSPECIFIED SIDE EFFECT;

EID: 84917680471     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.14.117     Document Type: Review

References (105)

1. Collins FS, Green ED, Guttmacher AE, Guyer MS. A vision for the future of genomics research. Nature 422(6934), 835-847 (2003).
2. Bozic I, Antal T, Ohtsuki H et al. Accumulation of driver and passenger mutations during tumor progression. Proc. Natl Acad. Sci. USA 107(43), 18545-18550 (2010).
3. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science 339(6127), 1546-1558 (2013).
4. Ley TJ, Mardis ER, Ding L et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456(7218), 66-72 (2008).
5. Garraway LA, Lander ES. Lessons from the cancer genome. Cell 153(1), 17-37 (2013).
6. Nowell PC. The clonal evolution of tumor cell populations. Science 194(4260), 23-28 (1976).
7. Gerlinger M, Rowan AJ, Horswell S et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366(10), 883-892 (2012).
8. McLeod HL. Cancer pharmacogenomics: early promise, but concerted effort needed. Science 339(6127), 1563-1566 (2013).
9. Kreso A, O'Brien CA, Van Galen P et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science 339(6119), 543-548 (2013).
10. Sharma SV, Bell DW, Settleman J, Haber DA. Epidermal growth factor receptor mutations in lung cancer. Nat. Rev. Cancer 7(3), 169-181 (2007).
11. Chapman PB, Hauschild A, Robert C et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N. Engl. J. Med. 364(26), 2507-2516 (2011).
12. 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).
13. Irshad S, Ashworth A, Tutt A. Therapeutic potential of PARP inhibitors for metastatic breast cancer. Expert Rev. Anticancer Ther. 11(8), 1243-1251 (2011).
14. Lord CJ, Ashworth A. Mechanisms of resistance to therapies targeting BRCA-mutant cancers. Nat. Med. 19(11), 1381-1388 (2013).
15. Greaves M, Maley CC. Clonal evolution in cancer. Nature 481(7381), 306-313 (2012).
16. Ashworth A, Lord CJ, Reis-Filho JS. Genetic interactions in cancer progression and treatment. Cell 145(1), 30-38 (2011).
17. Rottenberg S, Jaspers JE, Kersbergen A et al. High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs. Proc. Natl Acad. Sci. USA 105(44), 17079-17084 (2008).
18. Gabree M, Seidel M. Genetic testing by cancer site: skin. Cancer J. 18(4), 372-380 (2012).
19. Shannon KM, Chittenden A. Genetic testing by cancer site: breast. Cancer J. 18(4), 310-319 (2012).
20. Senter L. Genetic testing by cancer site: colon (nonpolyposis syndromes). Cancer J. 18(4), 334-337 (2012).
21. Jasperson KW. Genetic testing by cancer site: colon (polyposis syndromes). Cancer J. 18(4), 328-333 (2012).
22. Chun N, Ford JM. Genetic testing by cancer site: stomach. Cancer J. 18(4), 355-363 (2012).
23. Weissman SM, Weiss SM, Newlin AC. Genetic testing by cancer site: ovary. Cancer J. 18(4), 320-327 (2012).
24. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2013. CA Cancer J. Clin. 63(1), 11-30 (2013).
25. Roberts NJ, Jiao Y, Yu J et al. ATM mutations in patients with hereditary pancreatic cancer. Cancer Discov. 2(1), 41-46 (2012).
26. Palles C, Cazier JB, Howarth KM et al. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat. Genet. 45(2), 136-144 (2013).
27. Paugh SW, Stocco G, McCorkle JR, Diouf B, Crews KR, Evans WE. Cancer pharmacogenomics. Clin. Pharmacol. Ther. 90(3), 461-466 (2011).
28. Wheeler HE, Maitland ML, Dolan ME, Cox NJ, Ratain MJ. Cancer pharmacogenomics: strategies and challenges. Nat. Rev. Genet. 14(1), 23-34 (2013).
29. Binkhorst L, Van Gelder T, Mathijssen RH. Individualization of tamoxifen treatment for breast carcinoma. Clin. Pharmacol. Ther. 92(4), 431-433 (2012).
30. Weng L, Zhang L, Peng Y, Huang RS. Pharmacogenetics and pharmacogenomics: a bridge to individualized cancer therapy. Pharmacogenomics 14(3), 315-324 (2013).
31. Wheeler DA, Wang L. From human genome to cancer genome: the first decade. Genome Res. 23(7), 1054-1062 (2013).
32. Table of Pharmacogenomic Biomarkers in Drug Labeling. www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
33. Sharaf RN, Ladabaum U. Comparative effectiveness and cost-effectiveness of screening colonoscopy vs. sigmoidoscopy and alternative strategies. Am J. Gastroenterol. 108(1), 120-132 (2013).
34. Dunn BK, Jegalian K, Greenwald P. Biomarkers for early detection and as surrogate endpoints in cancer prevention trials: issues and opportunities. Recent Results Cancer Res. 188, 21-47 (2011).
35. Kitzman JO, Snyder MW, Ventura M et al. Noninvasive whole-genome sequencing of a human fetus. Sci. Transl. Med. 4(137), 137ra176 (2012).
36. Benesova L, Belsanova B, Suchanek S et al. Mutation-based detection and monitoring of cell-free tumor DNA in peripheral blood of cancer patients. Anal. Biochem. 433(2), 227-234 (2013).
37. Bainbridge MN, Wiszniewski W, Murdock DR et al. Whole-genome sequencing for optimized patient management. Sci. Transl. Med. 3(87), 87re83 (2011).
38. Gudmundsson J, Sulem P, Gudbjartsson DF et al. A study based on whole-genome sequencing yields a rare variant at 8q24 associated with prostate cancer. Nat. Genet. 44(12), 1326-1329 (2012).
39. Jonsson T, Atwal JK, Steinberg S et al. A mutation in APP protects against Alzheimer's disease and age-related cognitive decline. Nature 488(7409), 96-99 (2012).
40. Jonsson T, Stefansson H, Steinberg S et al. Variant of TREM2 associated with the risk of Alzheimer's disease. N. Engl. J. Med. 368(2), 107-116 (2013).
41. Lupski JR, Reid JG, Gonzaga-Jauregui C et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362(13), 1181-1191 (2010).
42. Ng SB, Buckingham KJ, Lee C et al. Exome sequencing identifies the cause of a Mendelian disorder. Nat. Genet. 42(1), 30-35 (2010).
43. Peltonen L, Perola M, Naukkarinen J, Palotie A. Lessons from studying monogenic disease for common disease. Hum. Mol. Genet. 15(Spec. No. 1), R67-R74 (2006).
44. Kohane IS. (Mis)treating the pharmacogenetic incidentalome. Nat. Rev. Drug Discov. 11(2), 89-90 (2012).
45. Worthey EA, Mayer AN, Syverson GD et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 13(3), 255-262 (2011).
46. Bainbridge MN, Wiszniewski W, Murdock DR et al. Whole-genome sequencing for optimized patient management. Sci. Transl. Med. 3(87), 87re83 (2011).
47. Bamshad MJ, Ng SB, Bigham AW et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12(11), 745-755 (2011).
48. Norton N, Li D, Hershberger RE. Next-generation sequencing to identify genetic causes of cardiomyopathies. Curr. Opin. Cardiol. 27(3), 214-220 (2012).
49. Green RC, Berg JS, Grody WW et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Am. Coll. Med. Genet. Genomics 15(7), 565-574 (2013).
50. Need AC, Shashi V, Hitomi Y et al. Clinical application of exome sequencing in undiagnosed genetic conditions. J. Med. Genet. 49(6), 353-361 (2012).
51. Yang Y, Muzny DM, Reid JG et al. Clinical whole-exome sequencing for the diagnosis of Mendelian disorders. N. Engl. J. Med. 369(16), 1502-1511 (2013).
52. Atwal PS, Brennan ML, Cox R et al. Clinical whole-exome sequencing: are we there yet? Genet. Med. doi:10.1038/gim.2014.10. (2014) (Epub ahead of print).
53. Dewey FE, Grove ME, Pan C et al. Clinical interpretation and implications of whole-genome sequencing. JAMA 311(10), 1035-1045 (2014).
54. Ashley EA, Butte AJ, Wheeler MT et al. Clinical assessment incorporating a personal genome. Lancet 375(9725), 1525-1535 (2010).
55. Chen R, Mias GI, Li-Pook-Than J et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148(6), 1293-1307 (2012).
56. Gupta R, Ratan A, Rajesh C et al. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics 13, 440 (2012).
57. Peterson TA, Doughty E, Kann MG. Towards precision medicine: advances in computational approaches for the analysis of human variants. J. Mol. Biol. 425(21), 4047-4063 (2013).
58. Online Mendelian Inheritance in Man. www.omim.org
59. Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum. Genet. 133(1), 1-9 (2014).
60. The Human Gene Mutation Database. www.hgmd.org
61. ClinVar. www.ncbi.nlm.nih.gov/clinvar
62. European Genome-Phenome Archive. www.ebi.ac.uk/ega
63. Mailman MD, Feolo M, Jin Y et al. The NCBI dbGaP database of genotypes and phenotypes. Nat. Genet. 39(10), 1181-1186 (2007).
64. dbGap. www.ncbi.nlm.nih.gov/gap
65. Hindorff LA, Sethupathy P, Junkins HA et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106(23), 9362-9367 (2009).
66. Welter D, MacArthur J, Morales J et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001-D1006 (2014).
67. Yamaguchi H, Calado RT, Ly H et al. Mutations in TERT, the gene for telomerase reverse transcriptase, in aplastic anemia. N. Engl. J. Med. 352(14), 1413-1424 (2005).
68. Vaxillaire M, Cavalcanti-Proenca C, Dechaume A et al. The common P446L polymorphism in GCKR inversely modulates fasting glucose and triglyceride levels and reduces Type 2 diabetes risk in the DESIR prospective general French population. Diabetes 57(8), 2253-2257 (2008).
69. Hani EH, Boutin P, Durand E et al. Missense mutations in the pancreatic islet beta cell inwardly rectifying K+ channel gene (KIR6.2/BIR): a meta-analysis suggests a role in the polygenic basis of Type II diabetes mellitus in Caucasians. Diabetologia 41(12), 1511-1515 (1998).
70. Erlich HA, Valdes AM, Julier C, Mirel D, Noble JA. Evidence for association of the TCF7 locus with Type I diabetes. Genes Immun. 10(Suppl. 1), S54-S59 (2009).
71. PharmGKB: Pharmacogenomics. Knowledge. Implementation. www.pharmgkb.org
72. Sim SC, Altman RB, Ingelman-Sundberg M. Databases in the area of pharmacogenetics. Hum. Mutat. 32(5), 526-531 (2011).
73. PharmaADME. www.pharmaadme.org
74. The Human Cytochrome P450 (CYP) Allele Nomenclature Database. www.cypalleles.ki.se
75. University of Louisville School of Medicine: Department of Pharmacology and Toxicology. http://n-acetyltransferasenomenclature.louisville.edu
76. Pharmacogenetics of Membrane Transporters Database. http://pharmacogenetics.ucsf.edu
77. TP-Search. www.tp-search.jp
78. UGT1A and UGT2B haplotypes and SNPs tables. www.pharmacogenomics.pha.ulaval.ca/sgc/ugt-alleles
79. Gamazon ER, Duan S, Zhang W et al. PACdb: a database for cell-based pharmacogenomics. Pharmacogenet. Genomics 20(4), 269-273 (2010).
80. PACdb. www.pacdb.org
81. Group SC, Link E, Parish S et al. SLCO1B1 variants and statin-induced myopathy - a genomewide study. N. Engl. J. Med. 359(8), 789-799 (2008).
82. Feng Q, Wilke RA, Baye TM. Individualized risk for statin-induced myopathy: current knowledge, emerging challenges and potential solutions. Pharmacogenomics 13(5), 579-594 (2012).
83. Mallal S, Nolan D, Witt C et al. Association between presence of HLA-B∗5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. Lancet 359(9308), 727-732 (2002).
84. Hughes AR, Mosteller M, Bansal AT et al. Association of genetic variations in HLA-B region with hypersensitivity to abacavir in some, but not all, populations. Pharmacogenomics 5(2), 203-211 (2004).
85. Mallal S, Phillips E, Carosi G et al. HLA-B∗5701 screening for hypersensitivity to abacavir. N. Engl. J. Med. 358(6), 568-579 (2008).
86. Waters LJ, Mandalia S, Gazzard B, Nelson M. Prospective HLA-B∗5701 screening and abacavir hypersensitivity: a single centre experience. AIDS 21(18), 2533-2534 (2007).
87. UK Collaborative HIV Cohort Study Steering Committee. HLA B∗5701 status, disease progression, and response to antiretroviral therapy. AIDS 27(16), 2587-2592 (2013).
88. Hicks JK, Swen JJ, Thorn CF et al. Clinical Pharmacogenetics Implementation Consortium guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants. Clin. Pharmacol. Ther. 93(5), 402-408 (2013).
89. Macconaill LE. Existing and emerging technologies for tumor genomic profiling. J. Clin. Oncol. 31(15), 1815-1824 (2013).
90. Ulahannan D, Kovac MB, Mulholland PJ, Cazier JB, Tomlinson I. Technical and implementation issues in using next-generation sequencing of cancers in clinical practice. Br. J. Cancer 109(4), 827-835 (2013).
91. Linderman MD, Brandt T, Edelmann L et al. Analytical validation of whole exome and whole genome sequencing for clinical applications. BMC Med. Genomics 7(1), 20 (2014).
92. McCourt CM, McArt DG, Mills K et al. Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS ONE 8(7), e69604 (2013).
93. Chin EL, Da Silva C, Hegde M. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet. 14, 6 (2013).
94. Esteban-Jurado C, Garre P, Vila M et al. New genes emerging for colorectal cancer predisposition. World J. Gastroenterol. 20(8), 1961-1971 (2014).
95. Strom SP, Lee H, Das K et al. Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory. Genet. Med. 16(7), 510-515 (2014).
96. Henrikson NB, Burke W, Veenstra DL. Ancillary risk information and pharmacogenetic tests: social and policy implications. Pharmacogenomics J. 8(2), 85-89 (2008).
97. Westbrook MJ, Wright MF, Van Driest SL et al. Mapping the incidentalome: estimating incidental findings generated through clinical pharmacogenomics testing. Genet. Med. 15(5), 325-331 (2013).
98. Berg JS, Khoury MJ, Evans JP. Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time. Genet. Med. 13(6), 499-504 (2011).
99. Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y. Identifying personal genomes by surname inference. Science 339(6117), 321-324 (2013).
100. Patel CJ, Chen R, Butte AJ. Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics 28(12), i121-i126 (2012).
101. Patel CJ, Bhattacharya J, Butte AJ. An environment-wide association study (EWAS) on Type 2 diabetes mellitus. PLoS ONE 5(5), e10746 (2010).
102. Patel CJ, Cullen MR, Ioannidis JP, Butte AJ. Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels. Int. J. Epidemiol. 41(3), 828-843 (2012).
103. Snyder M, Weissman S, Gerstein M. Personal phenotypes to go with personal genomes. Mol. Syst. Biol. 5, 273 (2009).
104. Snyder M, Du J, Gerstein M. Personal genome sequencing: current approaches and challenges. Genes Dev. 24(5), 423-431 (2010).
105. Medical Genetics Test Details. www.bcm.edu/research/medical-genetics-labs/test-detail. cfm?testcode=1605