Skip to main content
SpringerLink
Log in

The “Omics” Future: Genomics, Transcriptomics, and Proteomics

  • Chapter
  • First Online:
Book cover Sleep Disordered Breathing in Children

Part of the book series: Respiratory Medicine ((RM))

  • 1816 Accesses

Abstract

Rapid advancements in biotechnology and computing power have revolutionized the study of DNA, RNA, and protein at unprecedented resolution, depth, and thoroughness. These breakthroughs have led to the creation of the fields of genomics, transcriptomics, and proteomics. This chapter explains the concepts of genomics, transcriptomics, and proteomics and their potential for analyzing the genetic components of sleep disorders. Sleep and its associated disorders represent prime targets for systems-based analyses using these new approaches.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Crick F. Central dogma of molecular biology. Nature. 1970;227(5258):561–3.

    Article  PubMed  CAS  Google Scholar 

  2. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921.

    Article  PubMed  CAS  Google Scholar 

  3. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931–45.

    Article  Google Scholar 

  4. Sulem P, Gudbjartsson DF, Stacey SN, et al. Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat Genet. 2007;39(12):1443–52.

    Article  PubMed  CAS  Google Scholar 

  5. Lango Allen H, Estrada K, Lettre G, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010;467(7317):832–8.

    Article  PubMed  CAS  Google Scholar 

  6. Hancock DB, Eijgelsheim M, Wilk JB, et al. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Nat Genet. 2010;42(1):45–52.

    Article  PubMed  CAS  Google Scholar 

  7. Sotoodehnia N, Isaacs A, de Bakker PI, et al. Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet. 2010;42(12):1068–76.

    Article  PubMed  CAS  Google Scholar 

  8. Kathiresan S, Voight BF, Purcell S, et al. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet. 2009;41(3):334–41.

    Article  PubMed  CAS  Google Scholar 

  9. Voight BF, Scott LJ, Steinthorsdottir V, et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet. 2010;42(7):579–89.

    Article  PubMed  CAS  Google Scholar 

  10. Ikram MA, Seshadri S, Bis JC, et al. Genomewide association studies of stroke. N Engl J Med. 2009;360(17):1718–28.

    Article  PubMed  CAS  Google Scholar 

  11. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA. A catalog of published genome-wide association studies. www.genome.gov/gwastudies (2011). Accessed Jun 2011.

  12. Wang K, Li M, Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet. 2010;11(12):843–54.

    Article  PubMed  CAS  Google Scholar 

  13. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature. 1999;402(6761 Suppl):C47–52.

    Article  PubMed  CAS  Google Scholar 

  14. Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009;461(7261):218–23.

    Article  PubMed  CAS  Google Scholar 

  15. Winkelmann J, Schormair B, Lichtner P, et al. Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions. Nat Genet. 2007;39(8):1000–6.

    Article  PubMed  CAS  Google Scholar 

  16. Stefansson H, Rye DB, Hicks A, et al. A genetic risk factor for periodic limb movements in sleep. N Engl J Med. 2007;357(7):639–47.

    Article  PubMed  CAS  Google Scholar 

  17. Miyagawa T, Kawashima M, Nishida N, et al. Variant between CPT1B and CHKB associated with susceptibility to narcolepsy. Nat Genet. 2008;40(11): 1324–8.

    Article  PubMed  CAS  Google Scholar 

  18. Hallmayer J, Faraco J, Lin L, et al. Narcolepsy is strongly associated with the T-cell receptor alpha locus. Nat Genet. 2009;41(6):708–11.

    Article  PubMed  CAS  Google Scholar 

  19. Kornum BR, Kawashima M, Faraco J, et al. Common variants in P2RY11 are associated with narcolepsy. Nat Genet. 2011;43(1):66–71.

    Article  PubMed  CAS  Google Scholar 

  20. Larkin EK, Patel SR, Goodloe RJ, et al. A candidate gene study of obstructive sleep apnea in European Americans and African Americans. Am J Respir Crit Care Med. 2010;182(7):947–53.

    Article  PubMed  Google Scholar 

  21. Lander ES. Array of hope. Nat Genet. 1999;21(1 Suppl):3–4.

    Article  PubMed  CAS  Google Scholar 

  22. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995;270(5235):484–7.

    Article  PubMed  CAS  Google Scholar 

  23. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.

    Article  PubMed  CAS  Google Scholar 

  24. Cirelli C, Gutierrez CM, Tononi G. Extensive and divergent effects of sleep and wakefulness on brain gene expression. Neuron. 2004;41(1):35–43.

    Article  PubMed  CAS  Google Scholar 

  25. Mackiewicz M, Shockley KR, Romer MA, et al. Macromolecule biosynthesis: a key function of sleep. Physiol Genomics. 2007;31(3):441–57.

    Article  PubMed  CAS  Google Scholar 

  26. Li J, Grigoryev DN, Ye SQ, et al. Chronic intermittent hypoxia upregulates genes of lipid biosynthesis in obese mice. J Appl Physiol. 2005;99(5):1643–8.

    Article  PubMed  CAS  Google Scholar 

  27. Fan C, Iacobas DA, Zhou D, et al. Gene expression and phenotypic characterization of mouse heart after chronic constant or intermittent hypoxia. Physiol Genomics. 2005;22(3):292–307.

    Article  PubMed  CAS  Google Scholar 

  28. Gharib SA, Dayyat E, Khalyfa A, et al. Intermittent hypoxia mobilizes bone marrow-derived very small embryonic-like stem cells and activates developmental transcriptional programs in mice. Sleep. 2010;33(11):1439–46.

    PubMed  Google Scholar 

  29. Khalyfa A, Capdevila OS, Buazza MO, Serpero LD, Kheirandish-Gozal L, Gozal D. Genome-wide gene expression profiling in children with non-obese obstructive sleep apnea. Sleep Med. 2009;10(1):75–86.

    Article  PubMed  Google Scholar 

  30. Khalyfa A, Gharib SA, Kim J, et al. Peripheral blood leukocyte gene expression patterns and metabolic parameters in habitually snoring and non-snoring children with normal polysomnographic findings. Sleep. 2010;34(2):153–60.

    Google Scholar 

  31. Khalyfa A, Gharib SA, Kim J, et al. Transcriptomic analysis identifies phosphatases as novel targets for adenotonsillar hypertrophy of pediatric obstructive sleep apnea. Am J Respir Crit Care Med. 2010;181(10):1114–20.

    Article  PubMed  Google Scholar 

  32. Yates JR, Ruse CI, Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng. 2009;11:49–79.

    Article  PubMed  CAS  Google Scholar 

  33. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA. 2000;97(17):9390–5.

    Article  PubMed  CAS  Google Scholar 

  34. Washburn MP, Wolters D, Yates 3 JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001;19(3):242–7.

    Article  PubMed  CAS  Google Scholar 

  35. Kelleher NL. Top-down proteomics. Anal Chem. 2004;76(11):197A–203.

    Article  PubMed  Google Scholar 

  36. Fu X, Gharib SA, Green PS, et al. Spectral index for assessment of differential protein expression in shotgun proteomics. J Proteome Res. 2008;7(3):845–54.

    Article  PubMed  CAS  Google Scholar 

  37. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex ­protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17(10):994–9.

    Article  PubMed  CAS  Google Scholar 

  38. Gozal D, Jortani S, Snow AB, et al. Two-dimensional differential in-gel electrophoresis proteomic approaches reveal urine candidate biomarkers in pediatric obstructive sleep apnea. Am J Respir Crit Care Med. 2009;180(12):1253–61.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, 325 Ninth Avenue, 359803, Seattle, WA, 98104, USA

    Sina A. Gharib MD

  2. UW Medicine Sleep Institute and Center for Lung Biology, Department of Medicine, University of Washington, Seattle, WA, USA

    Sina A. Gharib MD

Authors
  1. Sina A. Gharib MD
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sina A. Gharib MD .

Editor information

Editors and Affiliations

  1. Section of Sleep Medicine, Pritzker School of Medicine, Department of Pediatrics, S. Maryland Ave. 5721, Chicago, 60637, Illinois, USA

    Leila Kheirandish-Gozal

  2. Pritzker School of Medicine, Comer Children's Hospital, Department of Pediatrics, S. Maryland Ave. 5721, Chicago, 60637, Illinois, USA

    David Gozal

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media New York

About this chapter

Cite this chapter

Gharib, S.A. (2012). The “Omics” Future: Genomics, Transcriptomics, and Proteomics. In: Kheirandish-Gozal, L., Gozal, D. (eds) Sleep Disordered Breathing in Children. Respiratory Medicine. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-725-9_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-725-9_17

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-724-2

  • Online ISBN: 978-1-60761-725-9

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation