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Bioinformatics and Omics

  • Timothy Craig Allen
  • Philip T. Cagle
Part of the Molecular Pathology Library book series (MPLB, volume 1)

Abstract

The term genomics originated in 1920 to describe the complete set of chromosomes and their associated genes; however, it has been in the past decade that the use of omics—genomics, transcriptomics, and proteomics—and bioinformatics has led to dramatic advances in the understanding of the molecular and genetic bases of disease.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 This chapter briefly reviews the subject, with subsequent chapters providing more details on specific technologies.

Keywords

Philos Trans Clinical Proteomics Human Mitochondrial Genome International Human Genome Sequencing Consortium Needle Biopsy Tissue 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Biron DG, Brun C, Lefevre T, et al. The pitfalls of proteonomics experiments without the correct use of bioinformatics tools. Proteomics 2006; Sept 22; [Epub ahead of print].Google Scholar
  2. 2.
    McKusick VA. Genomics: structure and functional studies of genomes. Genomics 1997; 45:244–249.CrossRefPubMedGoogle Scholar
  3. 3.
    Palagi PM, Hernandez P, Walther D, Appel RD. Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 2006; Sept. 22; [Epub ahead of print].Google Scholar
  4. 4.
    Lisacek F, Cohen-Boulakia S, Appel RD. Proteome informatics II: bioinformatics for comparative proteomics. Proteomics 2006; Sept. 22; [Epub ahead of print].Google Scholar
  5. 5.
    Maojo V, Martin-Sanchez F. Bioinformatics: towards new directions for public health. Methods Inf Med 2004; 43:208–214.PubMedGoogle Scholar
  6. 6.
    Bilello JA. The agony and ecstasy of “OMIC” technologies in drug development. Curr Mol Med 2005; 5:39–52CrossRefPubMedGoogle Scholar
  7. 7.
    Morel NM, Holland JM, van der Greef P, et al. Primer on medial genomics part XIV: introduction to systems biology—a new approach to understanding disease and treatment. Mayo Clin Proc 2004; 79:651–658.CrossRefPubMedGoogle Scholar
  8. 8.
    Provart NJ, McCourt P. Systems approaches to understanding cell signaling and gene regulation. Curr Opin Plant Biol 2004; 7:605–609.CrossRefPubMedGoogle Scholar
  9. 9.
    Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2006; 3:129–142.CrossRefPubMedGoogle Scholar
  10. 10.
    Debouck C, Metcalf B. The impact of genomics on drug discovery. Annu Rev Pharmacol Toxicol 2000; 40:193–207.CrossRefPubMedGoogle Scholar
  11. 11.
    Ghosh D. High throughput and global approaches to gene expression. Comb Chem High Throughput Screen 2000; 3:411–420.PubMedGoogle Scholar
  12. 12.
    Hanke J. Genomics and new technologies as catalysts for change in the drug discovery paradigm. J Law Med Ethics 2000; 28(4 Suppl):15–22.PubMedGoogle Scholar
  13. 13.
    Harris T. Genetics, genomics, and drug discovery. Med Res Rev 2000; 20:203–211.CrossRefPubMedGoogle Scholar
  14. 14.
    Rudert F. Genomics and proteomics tools for the clinic. Curr Opin Mol Ther 2000; 2:633–642.PubMedGoogle Scholar
  15. 15.
    Merrick BA, Bruno ME. Genomic and proteomic profiling for biomarkers and signature profiles of toxicity. Curr Opin Mol Ther 2004; 6:600–607.PubMedGoogle Scholar
  16. 16.
    Chalkley RJ, Hansen KC, Baldwin MA. Bioinformatic methods to exploit mass spectrometric data for proteomic applications. Methods Enzymol 2005; 402:289–312.CrossRefPubMedGoogle Scholar
  17. 17.
    Dennis JL, Oien KA. Hunting the primary: novel strategies for defining the origin of tumours. J Pathol 2005; 205:236–247.CrossRefPubMedGoogle Scholar
  18. 18.
    Englbrecht CC, Facius A. Bioinformatics challenges in proteomics. Comb Chem High Throughput Screen 2005; 8:705–715.CrossRefPubMedGoogle Scholar
  19. 19.
    Fung ET, Weinberger SR, Gavin E, Zhang F. Bioinformatics approaches in clinical proteomics. Expert Rev Proteomics 2005; 2:847–862.CrossRefPubMedGoogle Scholar
  20. 20.
    Kremer A, Schneider R, Terstappen GC. A bioinformatics perspective on proteomics: data storage, analysis, and integration. Biosci Rep 2005; 25:95–106.CrossRefPubMedGoogle Scholar
  21. 21.
    Mount DW, Pandey R. Using bioinformatics and genome analysis for new therapeutic interventions. Mol Cancer Ther 2005; 4:1636–1643.CrossRefPubMedGoogle Scholar
  22. 22.
    Nishio K, Arao T, Shimoyama T, et al. Translational studies for target-based drugs. Cancer Chemother Pharmacol 2005; 56Suppl 1:90–93.CrossRefPubMedGoogle Scholar
  23. 23.
    Katoh M, Katoh M. Bioinformatics for cancer management in the post-genome era. Technol Cancer Res Treat 2006; 5:169–175.PubMedGoogle Scholar
  24. 24.
    Miles AK, Matharoo-Ball B, Li G, et al. The identification of human tumour antigens: current status and future developments. Cancer Immunol Immunother 2006; 55:996–1003.CrossRefPubMedGoogle Scholar
  25. 25.
    Quackenbush J. Microarray analysis and tumor classification. N Engl J Med 2006; 354:2463–2472.CrossRefPubMedGoogle Scholar
  26. 26.
    Redfern O, Grant A, Maibaum M, Orengo C. Survey of current protein family databases and their application in comparative, structural and functional genomics. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 815:97–107.CrossRefPubMedGoogle Scholar
  27. 27.
    Iqbal O, Fareed J. Clinical applications of bioinformatics, genomics, and pharmacogenomics. Methods Mol Biol 2006; 316:159–177.PubMedGoogle Scholar
  28. 28.
    Reeves GA, Thornton JM, BioSapiens Network of Excellence. Integrating biological data through the genome. Hum Mol Genet 2006; 15 (Spec No 1):R81–R87.CrossRefPubMedGoogle Scholar
  29. 29.
    Waggoner A. Fluorescent labels for proteomics and genomics. Curr Opin Chem Biol 2006; 10:62–66.CrossRefPubMedGoogle Scholar
  30. 30.
    Ritchie MD. Bioinformatics approaches for detecting gene-gene and gene-environment interactions in studies of human disease. Neurosurg Focus 2005; 19:E2.CrossRefPubMedGoogle Scholar
  31. 31.
    Hanai T, Hamada H, Okamoto M. Application of bioinformatics for DNA microarray data to bioscience, bioengineering and medical fields. J Biosci Bioeng 2006; 101:377–384.CrossRefPubMedGoogle Scholar
  32. 32.
    Goodman N. Biological data becomes computer literate: new advances in bioinformatics. Curr Opin Biotechnol 2002; 13:68–71.CrossRefPubMedGoogle Scholar
  33. 33.
    Ness SA. Basic microarray analysis: strategies for successful experiments. Methods Mol Biol 2006; 316:13–33.PubMedGoogle Scholar
  34. 34.
    Perco P, Rapberger R, Siehs C, et al. Transforming omics data into context: bioinformatics on genomics and proteomics raw data. Electrophoresis 2006; 27:2659–2675.CrossRefPubMedGoogle Scholar
  35. 35.
    Haoudi A, Bensmail H. Bioinformatics and data mining in proteomics. Expert Rev Proteomics 2006; 3:333–343.CrossRefPubMedGoogle Scholar
  36. 36.
    Ivanov AS, Veselovsky AV, Dubanov AV, Skvortsov VS. Bioinformatics platform development: from gene to lead compound. Methods Mol Biol 2006; 316:389–431.PubMedGoogle Scholar
  37. 37.
    Teufel A, Krupp M, Weinmann A, Galle PR. Current bioinformatics tools in genomic biomedical research [review]. Int J Mol Med 2006; 17:967–973.PubMedGoogle Scholar
  38. 38.
    Regnstrom K, Burgess DJ. Pharmacogenomics and its potential impact on drug and formulation development. Crit Rev Ther Drug Carrier Syst 2005; 22:465–492.PubMedGoogle Scholar
  39. 39.
    Willard HF, Angrist M, Ginsburg GS. Genomic medicine: genetic variation and its impact on the future of health care. Philos Trans R Soc Lond B Biol Sci 2005; 360:1543–1550.CrossRefPubMedGoogle Scholar
  40. 40.
    Garraway LA, Seller WR. From integrated genomics to tumor lineage dependency. Cancer Res 2006; 66:2506–2508.CrossRefPubMedGoogle Scholar
  41. 41.
    McDunn JE, Chung TP, Laramie JM, et al. Physiologic genomics. Surgery 2006; 139:133–139.CrossRefPubMedGoogle Scholar
  42. 42.
    Tost J, Gut IG. Genotyping single nucleotide polymorphisms by mass spectrometry. Mass Spectrom Rev 2002; 21:388–418.CrossRefPubMedGoogle Scholar
  43. 43.
    Thomas DC, Haile RW, Duggan D. Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet 2005; 77:337–345.CrossRefPubMedGoogle Scholar
  44. 44.
    Bernig T, Chanock SJ. Challenges of SNP genotyping and genetic variation: its future role in diagnosis and treatment of cancer. Expert Rev Mol Diagn 2006; 6:319–331.CrossRefPubMedGoogle Scholar
  45. 45.
    Anderson S, Bankier AT, Barrell BG, et al. Sequence and organization of the human mitochondrial genome, Nature 1981; 290:457–465.CrossRefPubMedGoogle Scholar
  46. 46.
    Mundy C. The human genome project: a historical perspective. Pharmacogenomics 2001; 2:37–49.CrossRefPubMedGoogle Scholar
  47. 47.
    International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004; 431:931–945.CrossRefGoogle Scholar
  48. 48.
    Baxevanis AD. Using genomic databases for sequencebased biological discovery. Mol Med 2003; 9:185–192.PubMedGoogle Scholar
  49. 49.
    The International HapMap Consortium. The International HapMap Project. Nature 2003; 426:789–796.CrossRefGoogle Scholar
  50. 50.
    Thorisson GA, Stein LD. The SNP Consortium website: past, present and future, Nucleic Acids Res 2003; 31:124–127.CrossRefPubMedGoogle Scholar
  51. 51.
    Liu T, Johnson JA, Casella G, Wu R. Sequencing complex diseases with HapMap. Genetics 2004; 168:503–511.CrossRefPubMedGoogle Scholar
  52. 52.
    Riva A, Kohane IS. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics 2004; 5:33.CrossRefPubMedGoogle Scholar
  53. 53.
    Kong X, Matise TC. MAP-O-MAT: internet-based linkage mapping. Bioinformatics 2005; 21:557–559.CrossRefPubMedGoogle Scholar
  54. 54.
    Brandon MC, Lott MT, Nguyen KC, et al. MITOMAP: a human mitochondrial genome database—2004 update. Nucleic Acids Res 2005; 33:D611–D613.CrossRefPubMedGoogle Scholar
  55. 55.
    Carulli JP, Artinger M, Swain PM, et al. High throughput analysis of differential gene expression. J Cell Biochem Suppl 1998; 30–31:286–396.CrossRefPubMedGoogle Scholar
  56. 56.
    Scheel J, Von Brevern MC, Horlein A, et al. Yellow pages to the transcriptome. Pharmacogenomics 2002; 3:791–807.CrossRefPubMedGoogle Scholar
  57. 57.
    Hedge PS, White IR, Debouck C. Interplay of transcriptomics and proteomics. Curr Opin Biotechnol 2003; 14:647–651.CrossRefGoogle Scholar
  58. 58.
    Suzuki M, Hayashizaki Y. Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. Bioessays 2004; 26:833–843.CrossRefPubMedGoogle Scholar
  59. 59.
    Breitling R, Herzyk P. Biological master games: using biologists’ reasoning to guide algorithm development for integrated functional genomics. OMICS2 2005; 9:225–232.CrossRefGoogle Scholar
  60. 60.
    Storck T, von Brevern MC, Behrens CK, et al. Transcriptomics in predictive toxicology. Curr Opin Drug Discov Dev 2002; 5:90–97.Google Scholar
  61. 61.
    Hu YF, Kaplow J, He Y. From traditional biomarkers to transcriptome analysis in drug development. Curr Mol Med 2005; 5:29–38.CrossRefPubMedGoogle Scholar
  62. 62.
    Kralj M, Kraljevic S, Sedic M, et al. Global approach to perinatal medicine: functional genomics and proteomics. J Perinat Med 2005; 33:5–16.CrossRefPubMedGoogle Scholar
  63. 63.
    Morgan KT, Jayyosi Z, Hower MA, et al. The hepatic transcriptome as a window on whole-body physiology and pathophysiology. Toxicol Pathol 2005; 33:136–145.CrossRefPubMedGoogle Scholar
  64. 64.
    Jansen BJ, Schalkwijk J. Transcriptomics and proteomics of human skin. Brief Funct Genomic Proteomic 2003; 1:326–341.CrossRefPubMedGoogle Scholar
  65. 65.
    Liang P, Zhu W, Zhang X, et al. Differential display using one-base anchored oligo-dT primers. Nucleic Acids Res 1994; 22:5763–5764.CrossRefPubMedGoogle Scholar
  66. 66.
    Ahmed FE. Molecular techniques for studying gene expression in carcinogenesis. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 2002; 20:77–116.PubMedGoogle Scholar
  67. 67.
    Muller-Hagen G, Beinert T, Sommer A. Aspects of lung cancer gene expression profiling. Curr Opin Drug Discov Dev 2004; 7:290–303.Google Scholar
  68. 68.
    Anderson JS, Mann M. Functional genomics by mass spectrometry. FEBS Lett 2000; 480:25–31.CrossRefGoogle Scholar
  69. 69.
    Liotta LA, Petricoin EF 3rd. The promise of proteomics. Clin Adv Hematol Oncol 2003; 1:460–462.PubMedGoogle Scholar
  70. 70.
    Jain KK. Role of oncoproteomics in the personalized management of cancer. Expert Rev Proteomics 2004; 1:49–55.CrossRefPubMedGoogle Scholar
  71. 71.
    Hanash S. Disease proteomics. Nature 2003; 422:226–32.CrossRefPubMedGoogle Scholar
  72. 72.
    Baggerman G, Vierstraete E, De Loof A, Schoofs L. Gelbased versus gel-free proteomics: a review. Comb Chem High Throughput Screen 2005; 8:669–677.CrossRefPubMedGoogle Scholar
  73. 73.
    Calvo KR, Liotta LA, Petricoin EF. Clinical proteomics: from biomarker discovery and cell signaling profiles to individualized personal therapy. Biosci Rep 2005; 25:107–125.CrossRefPubMedGoogle Scholar
  74. 74.
    Brown RE. Morphoproteomics: exposing protein circuitries in tumors to identify potential therapeutic targets in cancer patients. Expert Rev Proteomics 2005; 2:337–348.CrossRefPubMedGoogle Scholar
  75. 75.
    Kalia A, Gupta RP. Proteomics: a paradigm shift. Crit Rev Biotechnol 2005; 25:173–198.CrossRefPubMedGoogle Scholar
  76. 76.
    Scaros O, Fisler R. Biomarker technology roundup: from discovery to clinical applications, a broad set of tools is required to translate from the lab to the clinic. Biotechniques 2005 April;(Suppl):30–32.CrossRefPubMedGoogle Scholar
  77. 77.
    Clarke W, Chan DW. ProteinChips: the essential tools for proteomic biomarker discovery and future clinical diagnostics. Clin Chem Lab Med 2005; 43:1279–1280.CrossRefPubMedGoogle Scholar
  78. 78.
    Kolch W, Mischak H, Pitt AR. The molecular make-up of a tumour: proteomics in cancer research. Clin Sci (Lond) 2005; 108:369–383.CrossRefGoogle Scholar
  79. 79.
    Patel PS, Telang SD, Rawal RM, Shah MH. A review of proteomics in cancer research. Asian Pac J Cancer Prev 2005; 6:113–117.PubMedGoogle Scholar
  80. 80.
    Roboz J. Mass spectrometry in diagnostic oncoproteomics. Cancer Invest 2005; 23:465–478.PubMedGoogle Scholar
  81. 81.
    Waldburg N, Kahne T, Reisenauer A, et al. Clinical proteomics in lung diseases. Pathol Res Pract 2004; 200:147–154.CrossRefPubMedGoogle Scholar
  82. 82.
    Stroncek DF, Burns C, Martin BM, et al. Advancing cancer biotherapy with proteomics. J Immunother 2005; 28:183–192.CrossRefPubMedGoogle Scholar
  83. 83.
    Fleming K, Kelley LA, Islam SA, et al. The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci 2006; 361:441–451.CrossRefPubMedGoogle Scholar
  84. 84.
    Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 2006; 312:212–217.CrossRefPubMedGoogle Scholar
  85. 85.
    Gulmann C, Sheehan KM, Kay EW, et al. Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer. J Pathol 2006; 208:595–606.CrossRefPubMedGoogle Scholar
  86. 86.
    Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 2006; 5:310–320.CrossRefPubMedGoogle Scholar
  87. 87.
    Davis CD, Milner J. Frontiers in nutrigenomics, proteomics, metabolomics and cancer prevention. Mutat Res 2004; 551:51–64.PubMedGoogle Scholar
  88. 88.
    Griffin JL, Bollard ME. Metabonomics: its potential as a tool in toxicology for safety assessment and data integration. Curr Drug Metab 2004; 5:389–398.CrossRefPubMedGoogle Scholar
  89. 89.
    Rochfort S. Metabolomics reviewed: a new “omics” platform technology for systems biology and implications for natural products research. J Nat Prod 2005; 68:1813–1820CrossRefPubMedGoogle Scholar
  90. 90.
    Griffin JL. The Cinderella story of metabolic profiling: does metabolomics get to go to the functional genomics ball? Philos Trans R Soc Lond B Biol Sci 2006; 361:147–161.CrossRefPubMedGoogle Scholar
  91. 91.
    Ramsay G. DNA chips: State-of-the art. Nature Biotechnol 1997; 16:40–44.CrossRefGoogle Scholar
  92. 92.
    Duggan DJ, Bittner M, Chen Y, et al. Expression profiling using cDNA microarrays. Nat Genet 1999; 21(Suppl 1):10–14.CrossRefPubMedGoogle Scholar
  93. 93.
    Chen l. Ren J. High-throughput DNA analysis by microchip electrophoresis. Comb Chem High Throughput Screen 2004; 7:29–43.PubMedGoogle Scholar
  94. 94.
    Heller MJ. DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 2002; 4:129–153.CrossRefPubMedGoogle Scholar
  95. 95.
    Obeid PJ, Christopoulos TK. Microfabricated systems for nucleic acid analysis. Crit Rev Clin Lab Sci 2004; 41:429–465.CrossRefPubMedGoogle Scholar
  96. 96.
    Shi L, Tong W, Goodsaid F, et al. QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn 2004; 4:761–777.CrossRefPubMedGoogle Scholar
  97. 97.
    Zhumabayeva B, Chenchik A, Siebert PD, Herrler M. Disease profiling arrays: reverse format cDNA arrays complimentary to microarrays. Adv Biochem Eng Biotechnol 2004; 86:191–213.PubMedGoogle Scholar
  98. 98.
    Brentani RR, Carraro DM, Verjovski-Almeida S, et al. Gene expression arrays in cancer research: methods and applications. Crit Rev Oncol Hematol 2005; 54:95–105.CrossRefPubMedGoogle Scholar
  99. 99.
    Diatchenko L, Lau YF, Campbell AP, et al. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 1996; 93:6025–6030.CrossRefPubMedGoogle Scholar
  100. 100.
    Wang X, Feuerstein GZ. Suppression subtractive hybridization: application in the discovery of novel pharmacological targets. Pharmacogenomics 2000; 1:101–108.CrossRefPubMedGoogle Scholar
  101. 101.
    Velculescu VE, Vogelstein B, Kinzler KW. Analyzing uncharted transcriptomes with SAGE. Trends Genet 2000; 16:423–425.CrossRefPubMedGoogle Scholar
  102. 102.
    Polyak K, Riggins GJ. Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J Clin Oncol 2001; 19:2948–2958.PubMedGoogle Scholar
  103. 103.
    Riggins GJ. Using serial analysis of gene expression to identify tumor markers and antigens. Dis Markers 2001; 17:41–48.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC. 2008

Authors and Affiliations

  • Timothy Craig Allen
    • 1
  • Philip T. Cagle
    • 2
    • 3
  1. 1.Department of PathologyUniversity of Texas Health Center at TylerTylerUSA
  2. 2.Pathology and Laboratory MedicineWeill Medical College of Cornell UniversityNew York
  3. 3.The Methodist HospitalHoustonUSA

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