Genomics, Other “OMIC” Technologies, Precision Medicine, and Additional Biotechnology-Related Techniques

  • Robert D. SindelarEmail author


The products resulting from the techniques and processes of biotechnology continue to grow at an exponential rate, and the expectations are that an even greater percentage of drug development and clinically-utilized pharmaceuticals worldwide will be classified as biologics. A recent Pharmaceutical Research and Manufacturers of America report (PhRMA, 2017 industry profile: medicines are transforming the trajectory of disease. Available at, 2017) notes that there are currently about 7000 medicines in clinical development globally and 80% in the pipeline have the potential to be first-in-class treatments. Most pertinent to this textbook, the majority of these medicines in development were impacted directly or indirectly by biotechnologies at one or more points during their lifetime via: target identification, and/or lead identification, and/or lead optimization, and/or clinical development and evaluation and/or product production. Pharmaceutical biotechnology techniques are at the core of most methodologies used today for drug discovery and development of both biologics and small molecules. While recombinant DNA technology and hybridoma techniques were the major methods utilized in pharmaceutical biotechnology through most of its historical timeline, our ever-widening understanding of human cellular function and disease processes and a wealth of additional and innovative biotechnologies have been, and will continue to be, developed in order to harvest the information found in the human genome. These technological advances will provide a better understanding of the relationship between genetics and biological function, unravel the underlying causes of disease, explore the association of genomic variation and drug response, enable personalized and precision medicine, enhance pharmaceutical research, and fuel the discovery and development of new and novel biopharmaceuticals. These revolutionary technologies and additional biotechnology-related techniques are improving the very competitive and costly process of drug development of new medicinal agents, diagnostics, and medical devices. Some of the technologies and techniques described in this chapter are both well established and commonly used applications of biotechnology producing clinically-utilized medicines as well as potential therapeutic products now in the developmental pipeline. New techniques are emerging at a rapid and unprecedented pace and their full impact on the future of molecular medicine will turn dreams into realities.


Human Genome Project (HGP) Genomics Single-nucleotide polymorphisms (SNPs) Next-generation genome sequencing (NGS) Whole-genome seuencing (WGS) Whole-exome sequencing (WES) Phenotype Biobanks Bioinformatics Big data Electronic health records (EHRs) Transcriptomics Proteomics Druggable genome Microarrays Lab-on-a-chip High-throughput screening Biomarker Metabolomics Glycomics Lipidomics Nutragenomics Microbiome Genome-wide association studies (GWAS) Epigenetics Toxicogenomics CRISPR Chemical genomics 



I wish to acknowledge the tremendous contribution of Dr. Arlene Marie Sindelar, my wife, to some of the graphics found in figures in all five editions of this textbook.


  1. Adams R, Steckel M, Nicke B (2016) Functional genomics in pharmaceutical drug discovery. Handb Exp Pharmacol 232:25–41PubMedCrossRefGoogle Scholar
  2. Ahles A, Engelhardt S (2014) Polymorphic variants of adrenoceptors: pharmacology, physiology, and role in disease. Pharmacol Rev 66:598–637PubMedCrossRefGoogle Scholar
  3. Ahmad P, Ashraf M, Younis M, Hu X, Kumar A, Akram NA, Al-Qurainy F (2012) Role of transgenic plants in agriculture and biopharming. Biotechnol Adv 30:524–540PubMedCrossRefGoogle Scholar
  4. Ahmed S, Zhou Z, Zhou J, Chen S (2016) Pharmacogenomics of drug metabolizing enzymes and transporters: relevance to precision medicine. Genomics Proteomics Bioinformatics 14:298–313PubMedPubMedCentralCrossRefGoogle Scholar
  5. Altelaar AF, Munoz J, Heck AJ (2013) Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet 14:35–48PubMedCrossRefGoogle Scholar
  6. Alyass A, Turcotte M, Meyre D (2015) From big data analysis to personalized medicine for all: challenges and opportunities. BMC Med Genet 8:33–44Google Scholar
  7. Anderson DC, Kodukula K (2014) Biomarkers in pharmacology and drug discovery. Biochem Pharmacol 87:172–188PubMedCrossRefGoogle Scholar
  8. Aronson SJ, Rehm HL (2015) Building the foundation for genomics in precision medicine. Nature 526:336–342PubMedPubMedCentralCrossRefGoogle Scholar
  9. Ayadi A, Birling MC, Bottomley J, Bussell J, Fuchs H, Fray M, Gailus-Durner V, Greenaway S, Houghton R, Karp N, Leblanc S, Lengger C, Maier H, Mallon AM, Marschall S, Melvin D, Morgan H, Pavlovic G, Ryder E, Skarnes WC, Selloum M, Ramirez-Solis R, Sorg T, Teboul L, Vasseur L, Walling A, Weaver T, Wells S, White JK, Bradley A, Adams DJ, Steel KP, Hrabě de Angelis M, Brown SD, Herault Y (2012) Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project. Mamm Genome 23:600–610PubMedPubMedCentralCrossRefGoogle Scholar
  10. Beckmann JS, Lew D (2016) Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities. Genome Med 8:134PubMedPubMedCentralCrossRefGoogle Scholar
  11. Beitelshees AL, Voora D, Lewis JP (2015) Personalized antiplatelet and anticoagulation therapy: applications and significance of pharmacogenomics. Pharmgenomics Pers Med 8:43–61PubMedPubMedCentralGoogle Scholar
  12. Benjak A, Sala C, Hartkoorn RC (2015) Whole-genome sequencing for comparative genomics and de novo genome assembly. Methods Mol Biol 1285:1–16PubMedCrossRefGoogle Scholar
  13. Berná G, Oliveras-López MJ, Jurado-Ruíz E, Tejedo J, Bedoya F, Soria B, Martín F (2014) Nutrigenetics and nutrigenomics insights into diabetes etiopathogenesis. Nutrients 6:5338–5369PubMedPubMedCentralCrossRefGoogle Scholar
  14. Bertolini LR, Meade H, Lazzarotto CR, Martins LT, Tavares KC, Bertolini M, Murray JD (2016) The transgenic animal platform for biopharmaceutical production. Transgenic Res 25:329–343PubMedCrossRefGoogle Scholar
  15. Bheda P, Schneider R (2014) Epigenetics reloaded: the single-cell revolution. Trends Cell Biol 24:712–723PubMedCrossRefGoogle Scholar
  16. Biesecker LG, Spinner NB (2013) A genomic view of mosaicism and human disease. Nat Rev Genet 14:307–320PubMedCrossRefGoogle Scholar
  17. Bingol K, Bruschweller-Li L, Li D, Zhang B, Xie M, Bruschweiler R (2016) Emerging new strategies for successful metabolite identification in metabolomics. Bioanalysis 8:557–573PubMedPubMedCentralCrossRefGoogle Scholar
  18. Birling MC, Schaefer L, André P, Lindner L, Maréchal D, Ayadi A, Sorg T, Pavlovic G, Hérault Y (2017) Efficient and rapid generation of large genomic variants in rats and mice using CRISMERE. Sci Rep 7:43331PubMedPubMedCentralCrossRefGoogle Scholar
  19. Bisson WH (2012) Drug repurposing in chemical genomics: can we learn from the past to improve the future? Curr Top Med Chem 12:1883–1888PubMedCrossRefGoogle Scholar
  20. Bitto A, Pallio G, Messina S, Arcoraci V, Pizzino G, Russo GT, Pallio S, Squadrito F, Altavilla D (2016) Genomic variations affecting biological effects of statins. Curr Drug Metab 17:566–572PubMedCrossRefGoogle Scholar
  21. Blumenthal GM, Mansfield E, Pazdur R (2016) Next-generation sequencing in oncology in the era of precision medicine. JAMA Oncol 2:13–14PubMedCrossRefGoogle Scholar
  22. Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W (2012) The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 23:580–586PubMedPubMedCentralCrossRefGoogle Scholar
  23. Brazeau DA, Brazeau GA (2011a) Principles of the human genome and pharmacogenomics. American Pharmacists Association, Washington, DC, pp 1–10CrossRefGoogle Scholar
  24. Brazeau DA, Brazeau GA (2011b) Principles of the human genome and pharmacogenomics. American Pharmacists Association, Washington, DC, pp 11–34CrossRefGoogle Scholar
  25. Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Ban Eld JF (2017) New CRISPR-Cas systems from uncultivated microbes. Nature 542:237–241PubMedCrossRefGoogle Scholar
  26. Cameron DE, Bashor CJ, Collins JJ (2014) A brief history of synthetic biology. Nat Rev Microbiol 12:381–390PubMedCrossRefGoogle Scholar
  27. Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773–782PubMedPubMedCentralCrossRefGoogle Scholar
  28. Caspar SM, Dubacher N, Kopps AM, Maienberg J, Henggeler C, Matyas C (2017) Clinical sequencing: from raw data to diagnosis with lifetime value. Clin Genet 93(3):508–519CrossRefGoogle Scholar
  29. Cénit MC, Matzaraki V, Tigchelaar EF, Zhernakova A (2014) Rapidly expanding knowledge on the role of the gut microbiome in health and disease. Biochim Biophys Acta 1842:1981–1992PubMedCrossRefGoogle Scholar
  30. Cesario A, Auffray C, Russo P, Hood L (2014) P4 medicine needs P4 education. Curr Pharm Des 20:6071–6072PubMedCrossRefPubMedCentralGoogle Scholar
  31. Chambliss AB, Chan DW (2016) Precision medicine: from pharmacogenomics to pharmacoproteomics. Clin Proteomics 13:25–33PubMedPubMedCentralCrossRefGoogle Scholar
  32. Chang SY, Weber EJ, Ness KV, Eaton DL, Kelly EJ (2016) Liver and kidney on chips: microphysiological models to understand transporter function. Clin Pharmacol Ther 100:464–478PubMedPubMedCentralCrossRefGoogle Scholar
  33. Chau SB, Thomas RE (2015) The amplichip: a review of itas analytic and clinical validity and clinical utility. Curr Drug Saf 10:113–124PubMedCrossRefGoogle Scholar
  34. Chaudhry SR, Muhammad S, Eidens M, Klemm M, Khan D, Efferth T, Weisshaar MP (2014) Pharmacogenetic prediction of individual variability in drug response based on CYP2D6, CYP2C9 and CYP2C19 genetic polymorphisms. Curr Drug Metab 15:711–718PubMedCrossRefGoogle Scholar
  35. Chen M, Zhang L (2011) Epigenetic mechanisms in developmental programming of adult disease. Drug Discov Today 16:1007–1018PubMedPubMedCentralCrossRefGoogle Scholar
  36. Chen M, Zhang M, Borlak J, Tong W (2012) A decade of toxicogenomic research and its contribution to toxicological science. Toxicol Sci 130:217–228PubMedCrossRefGoogle Scholar
  37. Chen M, Bisgin H, Tong L, Hong H, Fang H, Borlak J, Tong W (2014) Toward predictive models for drug-induced liver injury in humans: are we there yet? Biomark Med 8:201–213PubMedCrossRefPubMedCentralGoogle Scholar
  38. Chouchana L, Narjoz C, Roche D, Golmard JL, Pineau B, Chatellier G, Beaune P, Loriot MA (2014) Interindividual variability in TPMT enzyme activity: 10 years of experience with thiopurine pharmacogenetics and therapeutic drug monitoring. Pharmacogenomics 15:745–757PubMedCrossRefGoogle Scholar
  39. Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R (2014) Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 15(4):289–294PubMedCrossRefPubMedCentralGoogle Scholar
  40. Collins LJ, Schonfeld B (2011) The epigenetics of non-coding RNA. In: Tollefsbol T (ed) Handbook of epigenetics: the new molecular and medical genetics. Elsevier, London, pp 49–61CrossRefGoogle Scholar
  41. Cong F, Cheung AK, Huang SM (2012) Chemical genetics-based target identification in drug discovery. Annu Rev Pharmacol Toxicol 52:57–78PubMedCrossRefPubMedCentralGoogle Scholar
  42. Costa AR, Rodrigues ME, Henriques M, Oliveira R, Azeredo J (2014) Glycosylation: impact, control and improvement during therapeutic protein production. Crit Rev Biotechnol 34:281–299PubMedCrossRefPubMedCentralGoogle Scholar
  43. Cummings RD, Pierce JM (2014) The challenge and promise of glycomics. Chem Biol 21:1–15PubMedPubMedCentralCrossRefGoogle Scholar
  44. Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Ulugbek KJ, Baymuradov K, Narayanan AK (2018) The encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res 41:D36–D42Google Scholar
  45. Dawson MA, Kouzarides T (2012) Cancer epigenetics: from mechanism to therapy. Cell 150:12–27CrossRefGoogle Scholar
  46. Daxinger L, Whitelaw E (2012) Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet 13:153–162PubMedCrossRefPubMedCentralGoogle Scholar
  47. De R, Bush WS, Moore JH (2014) Bioinformatics challenges in genome-wide association studies (GWAS). Methods Mol Biol 1168:63–81PubMedCrossRefPubMedCentralGoogle Scholar
  48. Denner J (2017) Advances in organ transplant from pigs. Science 357:1238–1239PubMedCrossRefPubMedCentralGoogle Scholar
  49. Dopazo J (2014) Genomics and transcriptomics in drug discovery. Drug Discov Today 19:126–132PubMedCrossRefPubMedCentralGoogle Scholar
  50. Drabovich AP, Martinez-Morillo E, Diamandis EP (2015) Toward an integrated pipeline for protein biomarker development. Biochim Biophys Acta 1854:677–686PubMedCrossRefPubMedCentralGoogle Scholar
  51. Drew L (2016) Pharmacogenetics: the right drug for you. Nature 537:S60–S62PubMedCrossRefPubMedCentralGoogle Scholar
  52. Dugger SA, Platt A, Goldstein DB (2017) Drug development in the era of precision medicine. Nat Rev Drug Discov 17(3):183–196PubMedPubMedCentralCrossRefGoogle Scholar
  53. Ebhardt HA, Root A, Sander C, Aebersold R (2015) Applications of targeted proteomics in systems biology and translational medicine. Proteomics 15:3193–3208PubMedPubMedCentralCrossRefGoogle Scholar
  54. Eddy JA, Funk CC, Price ND (2013) Fostering synergy between cell biology and systems biology. Methods Mol Biol 1021:1–11CrossRefGoogle Scholar
  55. Eder J, Herrling PL (2016) Trends in modern drug discovery. Handb Exp Pharmacol 232:3–20PubMedCrossRefPubMedCentralGoogle Scholar
  56. Everett JR (2015) Academic drug discovery: current status and prospects. Expert Opin Drug Discov 10:937–944PubMedCrossRefPubMedCentralGoogle Scholar
  57. Fatehullah A, Tan SH, Barker N (2016) Organoids as an in vitro model of human development and disease. Nat Cell Biol 18:246–254PubMedCrossRefPubMedCentralGoogle Scholar
  58. Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T, Eirksdottir G, Harris TB, Launer L, Gudnason V, Fallin MD (2010) Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med 2:45–51CrossRefGoogle Scholar
  59. Ferguson LR, De Caterina R, Görman U, Allayee H, Kohlmeier M, Prasad C, Choi MS, Curi R, de Luis DA, Gil Á, Kang JX, Martin RL, Milagro FI, Nicoletti CF, Nonino CB, Ordovas JM, Parslow VR, Portillo MP, Santos JL, Serhan CN, Simopoulos AP, Velázquez-Arellano A, Zulet MA, Martinez JA (2016) Guide and position of the International Society of Nutrigenetics/Nutrigenomics on personalised nutrition: part 1 - fields of precision nutrition. J Nutrigenet Nutrigenomics 9:12–27PubMedCrossRefGoogle Scholar
  60. Filipski KK, Murphy JD, Helzlsouer KJ (2017) Updating the landscape of direct-to-consumer pharmacogenomic testing. Pharmgenomics Pers Med 10:229–232PubMedPubMedCentralGoogle Scholar
  61. Fluck J, Hofmann-Apitius M (2014) Text mining for systems biology. Mol Gen Genomics 289:727–734CrossRefGoogle Scholar
  62. Foley KE (2017) Organoids: a better in vitro model. Nat Methods 14:559–562PubMedCrossRefPubMedCentralGoogle Scholar
  63. Frick A, Benton CS, Scolaro KL, McLaughlin JE, Bradley CL, Suzuki OT, Wang N, Wiltshire T (2016) Transitioning pharmacogenomics into the clinical setting: training future pharmacists. Pharmacogenomics 17:535–539CrossRefGoogle Scholar
  64. Friedman AA, Letai A, Fisher DE, Flaherty KT (2015) Precision medicine for cancer with next-generation functional diagnostics. Nat Rev Cancer 15:747–756PubMedPubMedCentralCrossRefGoogle Scholar
  65. Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405PubMedPubMedCentralCrossRefGoogle Scholar
  66. Garate Z, Quintana-Bustamante O, Crane AM, Olivier E, Poirot L, Galetto R, Kosinski P, Hill C, Kung C, Agirre X, Orman I, Cer- rato L, Alberquilla O, Rodriguez-Fornes F, Fusaki N, Garcia- Sanchez F, Maia TM, Ribeiro ML, Sevilla J, Prosper F, Jin S, Mountford J, Guenechea G, Gouble A, Bueren JA, Davis BR, Segovia JC (2015) Generation of a high number of healthy erythroid cells from gene-edited pyruvate kinase deficiency patient-specifc induced pluripotent stem cells. Stem Cell Rep 5:1053–1066CrossRefGoogle Scholar
  67. Glass JI, Smith HO, Hutchison III CA, Alperovich NY, Assad-Garcia N (2007) Minimal bacterial genome. United States Patent Application 20070122826, May 31, 2007Google Scholar
  68. Global Market Insights (2017) Precision medicine market worth over $96 Bn by 2024. Accessed 24 Jan 2018
  69. Goundrey-Smith S (2013) Information technology in pharmacy. Springer, LondonCrossRefGoogle Scholar
  70. Greene CS, Tan J, Ung M, Moore JH, Cheng C (2014) Big data bioinformatics. J Cell Physiol 229:1896–1900PubMedPubMedCentralCrossRefGoogle Scholar
  71. Harms DW, Quadros RM, Seruggia D, Ohtsuka M, Takahashi G, Montoliu L, Gurumurthy CB (2014) Mouse genome editing using the CRISPR/Cas system. Curr Protoc Hum Genet 83:1–27Google Scholar
  72. Hasin Y, Seldin M, Lusis A (2017) Multi-omics approaches to disease. Genome Biol 18:1–15CrossRefGoogle Scholar
  73. Hatz MH, Schremser K, Rogowski WH (2014) Is individualized medicine more cost-effective? A systematic review. PharmacoEconomics 32:443–455PubMedCrossRefGoogle Scholar
  74. Hayes DF, Markus HS, Leslie RD, Topol EJ (2014) Personalized medicine: risk prediction, targeted therapies and mobile health technology. BMC Med 12:37–44PubMedPubMedCentralCrossRefGoogle Scholar
  75. Hehir-Kwa JY, Pfundt R, Veltman JA (2015) Exome sequencing and whole genome sequencing for the detection of copy number variation. Expert Rev Mol Diagn 15:1023–1032PubMedCrossRefGoogle Scholar
  76. Hertz DL, Rae JM (2016) Pharmacogenetic predictors of response. Adv Exp Med Biol 882:191–215PubMedCrossRefGoogle Scholar
  77. Höglund M (1998) Glycosylated and non-glycosylated recombinant human granulocyte colony-stimulating factor (rhG-CSF)--what is the difference? Med Oncol 15:229–233PubMedCrossRefGoogle Scholar
  78. Höhne M, Kabisch J (2016) Brewing painkillers: a yeast cell factory for the production of opioids from sugar. Angew Chem Int Ed Engl 55:1248–1125PubMedCrossRefGoogle Scholar
  79. Hollebecque A, Massard C, Soria JC (2014) Implementing precision medicine initiatives in the clinic: a new paradigm in drug development. Curr Opin Oncol 26:340–346PubMedCrossRefGoogle Scholar
  80. Hyman DM, Solit DB, Arcila ME, Cheng DT, Sabbatini P, Baselga J, Berger MF, Ladanyi M (2015) Precision medicine at Memorial Sloan Kettering Cancer Center: clinical next-generation sequencing enabling next-generation targeted therapy trials. Drug Discov Today 20:1422–1428PubMedPubMedCentralCrossRefGoogle Scholar
  81. Inbar-Feigenberg M, Choufani S, Butcher DT, Roifman M, Weksberg R (2013) Basic concepts of epigenetics. Fertil Steril 99:607–615PubMedCrossRefGoogle Scholar
  82. IOM (Institute of Medicine) (2013) Best care at lower cost: the path to continuously learning health care in America. The National Academies Press, Washington DCGoogle Scholar
  83. Jacob HJ et al (2013) Genomics in clinical practice: lessons from the front lines. Sci Transl Med 5:1–5CrossRefGoogle Scholar
  84. Ji B, Nielsen J (2015) From next-generation sequencing to systematic modeling of the gut microbiome. Front Genet 6:219PubMedPubMedCentralCrossRefGoogle Scholar
  85. Jiang J, Tian F, Cai Y, Qian X, Coatello CE, Ying W (2014) Site-specific qualitative and quantitative analysis of the N- and O-glycoforms in recombinant human erythropoietin. Anal Bioanal Chem 406:6265–6274PubMedPubMedCentralCrossRefGoogle Scholar
  86. Jiang Z, Zhou X, Li R, Michal JJ, Zhang S, Dodson MV, Zhang Z, Harland RM (2015) Whole transcriptome analysis with sequencing: methods, challenges and potential solutions. Cell Mol Life Sci 72:3425–3439PubMedPubMedCentralCrossRefGoogle Scholar
  87. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821PubMedPubMedCentralCrossRefGoogle Scholar
  88. Joly Y, Saulnier KM, Osien G, Knoppers BM (2014) The ethical framing of personalized medicine. Curr Opin Allergy Clin Immunol 14:404–408PubMedCrossRefGoogle Scholar
  89. Joung JK, Sander JD (2013) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14:49–55PubMedCrossRefGoogle Scholar
  90. Jung HJ, Kwon HJ (2015) Target deconvolution of bioactive small molecules: the heart of chemical biology and drug discovery. Arch Pharm Res 38:1627–1641PubMedCrossRefGoogle Scholar
  91. Karahalil B (2016) Overview of systems biology and omics technologies. Curr Med Chem 23:4221–4230PubMedCrossRefGoogle Scholar
  92. Kell DB (2013) Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. FEBS J 280:5957–5980PubMedCrossRefGoogle Scholar
  93. Kelsey G, Stegle O, Reik W (2017) Single-cell epigenomics: recording the past and predicting the future. Science 358:69–75PubMedCrossRefGoogle Scholar
  94. Khan SR, Baghdasarian A, Fahlman RP, Michail K, Siraki AG (2014) Current status and future prospects of toxicogenomics in drug discovery. Drug Discov Today 19:562–578PubMedCrossRefGoogle Scholar
  95. Kim H, Kim JS (2014) A guide to genome engineering with programmable nucleases. Nat Rev Genet 15:321–334PubMedCrossRefGoogle Scholar
  96. Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620PubMedCrossRefGoogle Scholar
  97. Koo BC, Kwon MS, Kim T (2014) Retrovirus-mediated gene transfer. In: Pinkert CA (ed) Transgenic animal technology, 3rd edn. Elsevier, London, pp 167–194CrossRefGoogle Scholar
  98. Kwapisz D (2017) The first liquid biopsy test approved. Is it a new era of mutation testing for non-small cell lung cancer? Ann Transl Med 5:46PubMedPubMedCentralCrossRefGoogle Scholar
  99. Lamas-Toranzo I, Guerrero-Sánchez J, Miralles-Bover H, Alegre-Cid G, Pericuesta E, Bermejo-Álvarez P (2017) CRISPR is knocking on barn door. Reprod Domest Anim 52(Suppl 4):39–47PubMedCrossRefGoogle Scholar
  100. Lawrie DS, Petrov DA (2014) Comparative population genomics: power and principles for the inference of functionality. Trends Genet Apr 30:133–139CrossRefGoogle Scholar
  101. Lee JW, Aminkeng F, Bhavsar AP, Shaw K, Carleton BC, Hayden MR, Ross CJ (2014) The emerging era of pharmacogenomics: current successes, future potential, and challenges. Clin Genet 86:21–28PubMedPubMedCentralCrossRefGoogle Scholar
  102. Levy SE, Myers RM (2016) Advancements in next-generation Sequencing. Annu Rev Genomics Hum Genet 17:95–115PubMedCrossRefGoogle Scholar
  103. Li W, Li M, Pu X, Guo Y (2017) Distinguishing the disease-associated SNPs based on composition frequency analysis. Interdiscip Sci 9:459–467PubMedCrossRefGoogle Scholar
  104. Lindon JC, Nicholson JK (2014) The emergent role of metabolic phenotyping in dynamic patient stratification. Expert Opin Drug Metab Toxicol 10:915–919PubMedCrossRefGoogle Scholar
  105. Madhusoodanan J (2014) Human gene set shrinks again. The Scientist 28:17Google Scholar
  106. Mandrycky C, Wang Z, Kim K, Kim DH (2016) 3D bioprinting for engineering complex tissues. Biotechnol Adv 34:422–434PubMedCrossRefGoogle Scholar
  107. Mastrangelo A, Armitage EG, Garcia A, Barbas C (2014) Metabolomics as a tool for drug discovery and personalized medicine. A review. Curr Top Med Chem 14:2627–2636PubMedCrossRefGoogle Scholar
  108. Medina MÁ (2013) Systems biology for molecular life sciences and its impact in biomedicine. Cell Mol Life Sci 70:1035–1053PubMedCrossRefGoogle Scholar
  109. Miao X (2013) Recent advances in the development of new transgenic animal technology. Cell Mol Life Sci 70:815–828PubMedCrossRefGoogle Scholar
  110. Mojica FJ, Montoliu L (2016) On the origin of CRISPR-Cas technology: from prokaryotes to mammals. Trends Microbiol 24:811–820PubMedCrossRefGoogle Scholar
  111. Moody SE, Boehm JS, Barbie DA, Hahn WC (2010) Functional genomics and cancer drug target discovery. Curr Opin Mol Ther 12:284–293PubMedGoogle Scholar
  112. Morgan H, Simon M, Mallon AM (2012) Accessing and mining data from large-scale mouse phenotyping projects. Int Rev Neurobiol 104:47–70PubMedCrossRefGoogle Scholar
  113. Murdoch TB, Detsky AS (2013) The inevitable application of big data to health care. JAMA 3019:1351CrossRefGoogle Scholar
  114. Nature Editors (2018) Monkeys cloned in China. Nature 553:387–388CrossRefGoogle Scholar
  115. Niu D, Wei HJ, Lin L, George H, Wang T, Lee IH, Zhao HY, Wang Y, Kan Y, Shrock E, Lesha E, Wang G, Luo Y, Qing Y, Jiao D, Zhao H, Zhou X, Wang S, Wei H, Güell M, Church GM, Yang L (2017) Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357:1303–1307PubMedPubMedCentralCrossRefGoogle Scholar
  116. Omenn GS, Lane L, Lundberg EK, Beavis RC, Obverall CM, Deutsch EW (2016) Metrics for the human proteome project 2016: progress on identifying and characterizing the human proteome, including post-translational modifications. J Proteome Res 15:3951–3960PubMedPubMedCentralCrossRefGoogle Scholar
  117. Papastergiou J, Tolios P, Li W, Li J (2017) The innovative canadian pharmacogenomic screening initiative in community pharmacy (ICANPIC) study. J Am Pharm Assoc 57:624–629CrossRefGoogle Scholar
  118. Patel JN (2015) Cancer pharmacogenomics: implications on ethnic diversity and drug response. Pharmacogenet Genomics 25:223–230PubMedCrossRefGoogle Scholar
  119. Patti GJ, Yanes O, Siuzdak G (2012) Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 13:263–269PubMedPubMedCentralCrossRefGoogle Scholar
  120. Paul A, Paul S (2014) The breast cancer susceptibility genes (BRCA) in breast and ovarian cancers. Front Biosci 19:605–618CrossRefGoogle Scholar
  121. PhRMA (2017) 2017 Industry profile: Medicines are Transforming the Trajectory of Disease. Available at Accessed 11 Jan 2018
  122. Pinkert CA (2014) Introduction to transgenic animal technology. In: Pinkert CA (ed) Transgenic animal technology, 3rd edn. Elsevier, London, pp 1–14Google Scholar
  123. Polites HG, Johnson LW, Pinkert CA (2014) DNA microinjection, embryo handling, and germplasm preservation. In: Pinkert CA (ed) Transgenic animal technology, 3rd edn. Elsevier, London, pp 17–70CrossRefGoogle Scholar
  124. Prasad V, Fojo T, Brada M (2016) Precision oncology: origins, optimism, and potential. Lancet Oncol 17:e81–e86PubMedCrossRefGoogle Scholar
  125. Premsrirut P (2017) Drug discovery in the age of big data. Drug Discov World 17:8–15CrossRefGoogle Scholar
  126. Prokopuk L, Western PS, Stringer JM (2015) Transgenerational epigenetic inheritance: adaptation through the germline epigenome? Epigenomics 7(5):829–846PubMedCrossRefGoogle Scholar
  127. Raciti GA, Nigro C, Longo M, Parrillo L, Miele C, Formisano P, Béguinot F (2014) Personalized medicine and type 2 diabetes: lesson from epigenetics. Epigenomics 6:229–238PubMedCrossRefGoogle Scholar
  128. Raghavachari N (2012) Overview of omics. In: Barh D, Blum K, Madigan MA (eds) OMICS-biomedical perspectives and applications. CRC Press, Boca Raton, pp 1–19Google Scholar
  129. Ravi M, Paramesh V, Kaviya SR, Anuradha E, Solomon FD (2015) 3D cell culture systems: advantages and applications. J Cell Physiol 230:16–26CrossRefGoogle Scholar
  130. Relling MV, Evans WE (2015) Pharmacogenomics in the clinic. Nature 526:343–350PubMedPubMedCentralCrossRefGoogle Scholar
  131. Roden DM (2016) Cardiovascular pharmacogenomics: current status and future directions. J Hum Genet 61:79–85PubMedCrossRefPubMedCentralGoogle Scholar
  132. Rozek LS, Dolinoy DC, Sartor MA, Omenn GS (2014) Epigenetics: relevance and implications for public health. Annu Rev Public Health 35:105–122PubMedPubMedCentralCrossRefGoogle Scholar
  133. Rudd P, Karlsson NG, Khoo K-H, Packer NH (2017) Glycomics and glycoproteomics. In: Varki A, Cummings RD, Esko JD, Stanley P, Hart GW, Aebi M, Darvill AG, Kinoshita T, Packer NH, Prestegard JH, Schnaar RL, Seeberger PH (eds) Essentials of glycobiology, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  134. Rudolph NS (1995) Advances continue in production of proteins in transgenic animal milk. Genet Eng News 15:8–9Google Scholar
  135. Russell C, Rahman A, Mohammed AR (2013) Application of genomics, proteomics and metabolomics in drug discovery, development and clinic. Ther Deliv 4:395–413PubMedCrossRefPubMedCentralGoogle Scholar
  136. Rybicki EP (2014) Plant-based vaccines against viruses. Virol J 11:205. CrossRefPubMedPubMedCentralGoogle Scholar
  137. Sabatier R, Gonçalves A, Bertucci F (2014) Personalized medicine: present and future of breast cancer management. Crit Rev Oncol Hematol 91:223–233PubMedCrossRefPubMedCentralGoogle Scholar
  138. Sagner M, McNeil A, Puska P, Auffray C, Price ND, Hood L, Lavie CJ, Han Z, Chen Z, Brahmachari SK, McEwen BS, Soares MB, Balling R, Epel E, Arena R (2017) The P4 health spectrum – a predictive, preventive, personalized and participatory continuum for promoting healthspan. Prog Cardiovasc Dis 59:506–521PubMedCrossRefPubMedCentralGoogle Scholar
  139. Sanford LP, Doetschman T (2014) Gene targeting in embryonic stem cells, I: history and methodology. In: Pinkert CA (ed) Transgenic animal technology, 3rd edn. Elsevier, London, pp 109–140CrossRefGoogle Scholar
  140. Schneider MV (2014) Defining systems biology: a brief overview of the term and field. Drug Discov Today 19:140–144CrossRefGoogle Scholar
  141. Schneider HC, Klabunde T (2013) Understanding drugs and diseases by systems biology. Bioorg Med Chem Lett 23:1168–1176PubMedCrossRefGoogle Scholar
  142. Schneider D, Riegman PH, Cronin M, Negrouk A, Moch H, Balling R, Penault-Llorca F, Zatloukal K, Horgan D (2016) Accelerating the development and validation of new value-based diagnostics by leveraging biobanks. Public Health Genomics 19:160–169PubMedCrossRefPubMedCentralGoogle Scholar
  143. Schumacher S, Muekusch S, Seitz H (2015) Up-to-date applications of microarrays and their way to commercialization. Microarrays 4:196–213PubMedPubMedCentralCrossRefGoogle Scholar
  144. Schweiger MR, Barmeyer C, Timmermann B (2013) Genomics and epigenomics: new promises of personalized medicine for cancer patients. Brief Funct Genomics 12:411–421PubMedCrossRefPubMedCentralGoogle Scholar
  145. Selimović S, Dokmeci MR, Khademhosseini A (2013) Organs-on-a-chip for drug discovery. Curr Opin Pharmacol 13:829–833PubMedCrossRefPubMedCentralGoogle Scholar
  146. Servick K (2017) Embryo editing takes another step to clinic. Science 357:436–437PubMedCrossRefPubMedCentralGoogle Scholar
  147. Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH (2017) DNA sequencing at 40: past, present and future. Nature 550:345–353PubMedCrossRefPubMedCentralGoogle Scholar
  148. Sheridan C (2017) CRISPR therapeutics push into human testing. Nat Biotechnol 35:3–5PubMedCrossRefPubMedCentralGoogle Scholar
  149. Sinha G (2017) The organoid architect. Science 357:746–749PubMedCrossRefPubMedCentralGoogle Scholar
  150. Skardal A, Shupe T, Atala A (2016) Organoid-on-a-chip and body-on-a-chip systems for drug screening and disease modeling. Drug Discov Today 21:1399–1411PubMedCrossRefPubMedCentralGoogle Scholar
  151. Smaglik P (2017) The genetic microscope. Nature 545:S25–S27PubMedCrossRefPubMedCentralGoogle Scholar
  152. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ (2016) The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Microbiol 14:273–287CrossRefGoogle Scholar
  153. Tang H, Mayampurath A, Yu CY, Mechref Y (2014) Bioinformatics protocols in glycomics and glycoproteomics. Curr Protoc Protein Sci 76:1–7Google Scholar
  154. The Cancer Genome Atlas Research Network (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507:315–322PubMedCentralCrossRefPubMedGoogle Scholar
  155. The International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921CrossRefGoogle Scholar
  156. Thompson MD, Cole DE, Capra V, Siminovitch KA, Rovati GE, Burnham WM, Rana BK (2014) Pharmacogenetics of the G protein-coupled receptors. Methods Mol Biol 1175:189–242PubMedCrossRefGoogle Scholar
  157. Tuddenham S, Sears CL (2015) The intestinal microbiome and health. Curr Opin Infect Dis 28:464–470PubMedPubMedCentralCrossRefGoogle Scholar
  158. U.S. DOE (2018) Human genome project information. Available at: Accessed 11 Jan 2018
  159. U.S. National Academies (2011) Toward precision medicine: building a knowledge network for biomedical research and a new taxonomy of disease. The National Academies Press, Washington, DC, pp 1–4Google Scholar
  160. van Duinen V, Trietsch SJ, Joore J, Vulto P, Hankemeier T (2015) Microfluidic 3D cell culture: from tools to tissue models. Curr Opin Biotechnol 35:118–126PubMedCrossRefPubMedCentralGoogle Scholar
  161. van Rooij T, Wilson DM, Marsh S (2012) Personalized medicine policy challenges: measuring clinical utility at point of care. Expert Rev Pharmacoecon Outcomes Res 12:289–295PubMedCrossRefGoogle Scholar
  162. Venter JC et al (2001) The sequence of the human genome. Science 291:1304–1351PubMedPubMedCentralCrossRefGoogle Scholar
  163. Vijaya Bhaskar Reddy A, Yusop Z, Jaafar J, Madhavi V, Madhavi G (2016) Advances in drug discovery: impact of genomics and role of analytical instrumentation. Curr Drug Discov Technol 13:211–224PubMedCrossRefPubMedCentralGoogle Scholar
  164. Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, Yang J (2017) 10 years of GWAS discovery: biology, function, and translation. Am J Hum Genet 101:5–22PubMedPubMedCentralCrossRefGoogle Scholar
  165. Waltz E (2017) When pig organs will fly. Nat Biotechnol 35:1133–1138PubMedCrossRefPubMedCentralGoogle Scholar
  166. Wetterstrand KA (2017) DNA sequencing costs: data from the NHGRI genome sequencing program (GSP) Available at: Accessed 23 Dec 2017
  167. Wiktorowicz JE, Brasier AR (2016) Introduction to clinical proteomics. Adv Exp Med Biol 919:435–441PubMedCrossRefPubMedCentralGoogle Scholar
  168. Wildt S, Gerngross TU (2005) The humanization of N-glycosylation pathways in yeast. Nat Rev Microbiol 3:119–126PubMedCrossRefPubMedCentralGoogle Scholar
  169. Wishart DS, Mandal R, Stanislaus AS, Ramirez-Gaona M (2016) Cancer metabolomics and the human metabolome database. Metabolites 6:1–17CrossRefGoogle Scholar
  170. Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vazquez-Fresno R, Sajed T, Johnson D, Li C, Karu N, Sayeeda Z, Lo E, Assempour N, Berjanski M, Singhai S, Arndt D, Liang Y, Badran H, Grant J, Serra-Cayuela A, Liu Y, Mandal R, Neveu V, Pon A, Knox C, Wilson M, Manach C, Scalbert A (2018) HMDB: the human metabolome database for 2018. Nucleic Acids Res 46:D608–D617PubMedCrossRefPubMedCentralGoogle Scholar
  171. Wright FA et al (2001) A draft annotation and overview of the human genome. Genome Biol 2:1–18Google Scholar
  172. Yadav M, Verma MK, Chauhan NS (2017) A review of metabolic potential of human gut microbiome in human nutrition. Arch Microbiol 200(2):203–217PubMedCrossRefGoogle Scholar
  173. Zanders ED (2012) Overview of chemical genomics and proteomics. Methods Mol Biol 800:3–10PubMedCrossRefGoogle Scholar
  174. Zdanowicz MM (2017) Pharmacogenomics: past, present, and future. In: Zdanowicz MM (ed) Concepts in pharmacogenomics. American Society of Health-systems Pharmacists, Bethesda, pp 3–18Google Scholar
  175. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (2015) Cpf1 is a single RNA-guided endo- nuclease of a class 2 CRISPR-Cas system. Cell 163:759–771PubMedPubMedCentralCrossRefGoogle Scholar
  176. Zhang B, Radisic M (2017) Organ-on-a-chip devices advance to market. Lab Chip 17:2395–2420PubMedCrossRefGoogle Scholar
  177. Zhang HM, Nan ZR, Hui GQ, Liu XH, Sun Y (2014) Application of genomics and proteomics in drug target discovery. Genet Mol Res 13:198–204PubMedCrossRefGoogle Scholar
  178. Zhao Y, Brasier AR (2015) Qualification and verification of protein biomarker candidates. Adv Exp Med Biol 919:493–514CrossRefGoogle Scholar
  179. Zhao X, Modur V, Carayannopoulos LN, Laterza OF (2015) Biomarkers in pharmaceutical research. Clin Chem 61:1342–1353Google Scholar
  180. Zhao YY, Cheng XL, Lin RC, Wei F (2015a) Lipidomics applications for disease biomarker discovery in mammal models. Biomark Med 9:153–168PubMedCrossRefGoogle Scholar
  181. Zhao YY, Miao H, Cheng XL, Wei F (2015b) Lipidomics: novel insight into the biochemical mechanism of lipid metabolism and dysregulation-associated disease. Chem Biol Interact 240:220–238PubMedCrossRefGoogle Scholar
  182. Zhu Y, Xiao T, Lei S, Zhou F, Wang MW (2015) Application of chemical biology in target identification and drug discovery. Arch Pharm Res 38:1642–1650PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Faculty of Pharmaceutical Sciences and The Centre for Health Evaluation & Outcomes Sciences (CHEOS)The University of British Columbia (UBC)VancouverCanada
  2. 2.Global Drug Commercialization Centre (GDCC)-China and GDCC-worldwideChengduChina

Personalised recommendations