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Genomics

  • Desh Deepak Singh
  • Manali DattaEmail author
Chapter

Abstract

Genomics refers to the study of function, structure, and interactions of the genome, and it is one of the most rapidly developing scientific areas. An organism’s complete set of DNA, including both protein-coding and noncoding genes, constitutes the genome. The completion of the Human Genome Project in 2003 laid a foundation for in-depth study of genomics and led to the beginning of the “genomics era.” Next-generation sequencing including exome and DNA sequencing has provided a plethora of means by which we can dissect the genome at structural and functional levels. During the last decade, developments and advances in the field of genomics have led to a better understanding of human genome architecture, discovery of disease-associated genetic variants, and development of newer diagnostic methods in the field of clinical genomics. The Encyclopedia of DNA Elements (ENCODE) Project in 2010 established yet another landmark for the genomics era. The ENCODE Project characterized and annotated the functional elements hidden within the human genome’s 3.2 billion bases with the aid of next-generation sequencing technologies, chromosomal conformation capture techniques, and epigenomic methods. It resolved the widespread myth about junk DNA being nonfunctional and provided evidence that the DNA between protein-coding genes consists of myriad elements (such as enhancers, silencers, and insulators) that regulate gene expression by switching transcription on or off, or by regulating messenger RNA turnover and consequently affecting translational efficiency.

This chapter provides readers with an up-to-date and coherent view of human genome architecture and also provides information about different milestones in the genomics era and new technological advances in the field.

Keywords

Human Genome Project ENCODE Sequencing Comparative genomics Functional genomics Clinical genomics 

References

  1. Baylin, S. B., & Ohm, J. E. (2006). Epigenetic gene silencing in cancer—a mechanism for early oncogenic pathway addiction? Nature Reviews Cancer, 6(2), 107–116.CrossRefGoogle Scholar
  2. Cavalli-Sforza, L. L. (2005). The human genome diversity project: Past, present and future. Nature Reviews Genetics, 6(4), 333.CrossRefGoogle Scholar
  3. Chial, H. (2008). DNA sequencing technologies key to the Human Genome Project. Nature Education, 1(1), 219.Google Scholar
  4. ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57.CrossRefGoogle Scholar
  5. Haubold, B., & Wiehe, T. (2004). Comparative genomics: Methods and applications. Naturwissenschaften, 91(9), 405–421.CrossRefGoogle Scholar
  6. Ho, J. W., Bishop, E., Karchenko, P. V., Nègre, N., White, K. P., & Park, P. J. (2011). ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis. BMC Genomics, 12(1), 134.CrossRefGoogle Scholar
  7. Jia, M., Guan, J., Zhai, Z., Geng, S., Zhang, X., Mao, L., & Li, A. (2017). Wheat functional genomics in the era of next generation sequencing: An update. The Crop Journal, 6(1), 7–14.CrossRefGoogle Scholar
  8. Kanwal, R., & Gupta, S. (2012). Epigenetic modifications in cancer. Clinical Genetics, 81(4), 303–311.CrossRefGoogle Scholar
  9. Kchouk, M., Gibrat, J. F., & Elloumi, M. (2017). Generations of sequencing technologies: From first to next generation. Biology and Medicine, 9(3), 3–8.CrossRefGoogle Scholar
  10. Koonin, E. V., & Galperin, M. Y. (2003). Genome annotation and analysis. In Sequence—evolution—function (pp. 193–226). Boston: Springer.CrossRefGoogle Scholar
  11. Peschansky, V. J., & Wahlestedt, C. (2014). Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics, 9(1), 3–12.CrossRefGoogle Scholar
  12. Snyder, M. W., Adey, A., Kitzman, J. O., & Shendure, J. (2015). Haplotype-resolved genome sequencing: Experimental methods and applications. Nature Reviews Genetics, 16(6), 344.CrossRefGoogle Scholar
  13. Tessarz, P., & Kouzarides, T. (2014). Histone core modifications regulating nucleosome structure and dynamics. Nature Reviews Molecular Cell Biology, 15(11), 703.CrossRefGoogle Scholar
  14. Vijay, P., McIntyre, A. B., Mason, C. E., Greenfield, J. P., & Li, S. (2016). Clinical genomics: Challenges and opportunities. Critical Reviews™ in Eukaryotic Gene Expression, 26(2), 97.CrossRefGoogle Scholar
  15. Villota-Salazar, N. A., Mendoza-Mendoza, A., & González-Prieto, J. M. (2016). Epigenetics: From the past to the present. Frontiers in Life Science, 9(4), 347–370.CrossRefGoogle Scholar
  16. Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017). 10 years of GWAS discovery: Biology, function, and translation. The American Journal of Human Genetics, 101(1), 5–22.CrossRefGoogle Scholar
  17. Waterson, R. H., Lander, E. S., & Wilson, R. K. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437(7055), 69.CrossRefGoogle Scholar
  18. Wei, L., Liu, Y., Dubchak, I., Shon, J., & Park, J. (2002). Comparative genomics approaches to study organism similarities and differences. Journal of Biomedical Informatics, 35(2), 142–150.CrossRefGoogle Scholar
  19. Yan, H., Tian, S., Slager, S. L., Sun, Z., & Ordog, T. (2015). Genome-wide epigenetic studies in human disease: A primer on -omic technologies. American Journal of Epidemiology, 183(2), 96–109.PubMedPubMedCentralGoogle Scholar
  20. Yan, H., Tian, S., Slager, S. L., & Sun, Z. (2016). ChIP-seq in studying epigenetic mechanisms of disease and promoting precision medicine: Progresses and future directions. Epigenomics, 8(9), 1239–1258.CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Amity Institute of BiotechnologyAmity University RajasthanJaipurIndia

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