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Omics of Cancer

  • Bhati, Aniruddha (Division Medical Biotechnology, School of BioSciences and Technology, VIT) ;
  • Garg, H. (Division Medical Biotechnology, School of BioSciences and Technology, VIT) ;
  • Gupta, A. (Division Medical Biotechnology, School of BioSciences and Technology, VIT) ;
  • Chhabra, H. (Division Medical Biotechnology, School of BioSciences and Technology, VIT) ;
  • Kumari, A. (Division Medical Biotechnology, School of BioSciences and Technology, VIT) ;
  • Patel, T. (Division Medical Biotechnology, School of BioSciences and Technology, VIT)
  • Published : 2012.09.30

Abstract

With the advances in modern diagnostic expertise for cancer, certain approaches allowing scanning of the complete genome and the proteome are becoming very useful for researchers. These high throughput techniques have already proven power, over traditional detection methods, in differentiating disease sub-types and identifying specific genetic events during progression of cancer. This paper introduces major branches of omics-technology and their applications in the field of cancer. It also addresses current road blocks that need to be overcome and future possibilities of these methods in oncogenic detection.

Keywords

References

  1. Barddli A, Parsons DW. Silliman N, et al (2003). Mutational analysis of the tyrosine kinome in colorectal cancers. Science, 300, 949. https://doi.org/10.1126/science.1082596
  2. Bentley OR (2006). Whole-genome re-sequencing. Curr Opin Genel Dev, 16,545-52. https://doi.org/10.1016/j.gde.2006.10.009
  3. Benvenuti S, Arena S, BardelliA (2005). Identification of cancer genes by mutational profiling of turnor genomes. FEBS Lea, 579, 1884-90. https://doi.org/10.1016/j.febslet.2005.02.015
  4. Bemstein BE, Meissner A, Lander ES (2007). The manunalian epigenome. Cell, 2, 669-81.
  5. Bird A (2007). Perceptions of epigenetics. Nalure, 447,396-8.
  6. Ding L, Getz G, Wheeler DA, et al (2008). Somatic mUlations affect key pathways in lung adenocarcinoma. Nature, 455,1069-75. https://doi.org/10.1038/nature07423
  7. Estecio MR, issa JP (2011 ). Dissecting DNA hypermethyiation in cancer. FEBS Letters, 585, 2078-86. https://doi.org/10.1016/j.febslet.2010.12.001
  8. Feber A (2010). Global profiling of methylation in the cancer genome. Cancer Genet Cytagenet, 203, 44-65.
  9. Fiers W, Contreras R, Duerinck F (1976). Complete nucleotidesequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene. Nature , 260, 500-7. https://doi.org/10.1038/260500a0
  10. Hanash SM, Pitteri SJ, Faca VM (2008). Mining the piasma proteome for cancer biomarkers. Nature, 452, 571 -9. https://doi.org/10.1038/nature06916
  11. Holliday R (1990). Mechanisms for the control of gene activity druingdevelopment. BiolRevCambr PhilosSoc, 65,431-71.
  12. Hoque MO, Kim MS, Ostrow KL, et al (2008). Genomewide promoter analysis uncovers portions of the cancer methylome. Cancer Res, 68, 2661-70. https://doi.org/10.1158/0008-5472.CAN-07-5913
  13. http://www.ncbi.nlm.nih.gov/genome.
  14. Hudson TJ, Anderson W, Artez A, et al (2010). International Cancer Genome Consortium International network of cancer genome projects. Nature, 464,993-8. https://doi.org/10.1038/nature08987
  15. Jones S, Hruban RH, Kamiyama M, et al (2009). Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science, 324, 217. https://doi.org/10.1126/science.1171202
  16. La Deana WH, Valerie R, Philip G, et al (2009). Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res, 19, 657-66. https://doi.org/10.1101/gr.088112.108
  17. Lander ES, Linton LM, Birren B, et al (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860-921. https://doi.org/10.1038/35057062
  18. Lay JO, Borgmann S, Liyanage R Wilkins CL(2006). Problems with the "omics". Trends in Analytical Chemistry, 25, 11 . https://doi.org/10.1016/j.trac.2005.04.019
  19. Laderberg J, McCray AT (2001). 'Ome Sweet 'Ontics -- A genealogical treasury of words. The Scientist, 15, 8.
  20. Li X, Shen S, Wu M, et at (2011 ). Transcriptomic regulation and molecular mechanism of polygenic tumor at different stages. Zhong Nan Da Xue Xue Bao Yi Xue Ban, 36, 585-91.
  21. Moore LE, Pfeiffer RM, Zhang Z, et al (2012). Proteomic biomarkers in combination with CA 125 for detection of epithelial ovarian cancer using pre-diagnostic senun samples from the prostate lung colon and ovary (PLCO) cancer screening trial. Cancer, 118, 91-100. https://doi.org/10.1002/cncr.26241
  22. Morel NM, Holland lM, van der Greef J, et al (2004). Primer on medical genomics part XIV: Introduction to systems biology-A new approach to understanding disease and treatment. Maya Clin Proc, 79, 651-8. https://doi.org/10.4065/79.5.651
  23. MUlTay S, Linardou H (2004). Proteomics and Cancer. STEP K$\Lambda$INIKHZ$\Sigma$ O$\Gamma$KO$\Lambda$O$\Gamma$I$\Sigma$, 3, 49-56.
  24. Ng PC, Levy S, Huang J, et al (2008). Genetic variation in an individual human exome. PLoS Genetics, 4, 1000160. https://doi.org/10.1371/journal.pgen.1000160
  25. Olsvik O , Wahlberg J, Peuerson B, et al (1993).- Use of automated sequencing of polymerase chain reactiongenerated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains. J Clin Microbiol, 31,22-5.
  26. Pettersson E, Lundeberg J, Ahmadian A (2009). Generations of sequencing technologies. Genomics, 93, 105- 11. https://doi.org/10.1016/j.ygeno.2008.10.003
  27. Raphael BJ, Volik S, Collins C, Pevzner PA (2003). Reconstructing tumor genome architectures. Bioinformatics, 19, 162-71.
  28. Sanger F, Air GM, Barrell BG, et al (1977). Nucleotide sequence of bacteriophage phi X174 DNA. Nature, 265, 687-95. https://doi.org/10.1038/265687a0
  29. Sarah BN, Entily HT, Peggy DR, et al (2009), Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272-76. https://doi.org/10.1038/nature08250
  30. Schuster SC (2008). Next-generation sequencing transforms today's biology. Nat Methods, 5, 16-8. https://doi.org/10.1038/nmeth1156
  31. Shah Sp, MorinRD, Khattra J, et al (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809-13. https://doi.org/10.1038/nature08489
  32. Sjoblom T, Jones S, Wood LD, et al (2006). The consensus coding sequences of human breast and colorectal cancers. Science, 314,268-74. https://doi.org/10.1126/science.1133427
  33. Stadler ZK, Vijai J , Thorn P, el al (2010). Genome-wide association studies of cancer predisposition. Hematol Oncol Clin North Am, 24, 973-96. https://doi.org/10.1016/j.hoc.2010.06.009
  34. Stephens PJ, McBride DJ, Lin ML, et al (2009). Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 462, 1005-10. https://doi.org/10.1038/nature08645
  35. Taguchi A, Politi K, Pitteri, et al (2011 ). Lung cancer signatures in plasma based on proteome profiling of mouse tumor models. Cancer Cell, 20, 289-99. https://doi.org/10.1016/j.ccr.2011.08.007
  36. Tripathi AK, Koringa PG , Jakhesara SJ, et al (2012). A preliminary sketch of horn cancer transcriplome in Indian zebu cattle. Gene, 1, 124-31.
  37. Varela I, Tarpey P, Rame K, et al (2011). Exome sequencing identifies frequentmutation of the SWUSNF complex gene PBRMI in renal carcinoma. Nature, 469, 539-42 https://doi.org/10.1038/nature09639
  38. Venter Cl, Adams DM, Myers WE, et at (2001). The sequence of the human genome. Science, 291, 1304-51. https://doi.org/10.1126/science.1058040
  39. Volik S, Zhao S, Chin K, et al (2003), End-sequence profiling: Sequence-based analysis of aberrant genomes. Proc Natl Acad Sci, 100, 7696-701. https://doi.org/10.1073/pnas.1232418100
  40. Wei X, Walia V, LinJC, et al (2011). Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nature Genetics, 43, 442-6. https://doi.org/10.1038/ng.810
  41. Weir BA, Michele S. Woo MS, Getz G, et al (2007). Characterizing the cancer genome in Iung adenocarcinoma. Nature, 450, 893-8. https://doi.org/10.1038/nature06358
  42. Wilkins MR, Appel R, Jennifer EVE, et al (1994), Guidelines for next 10 years of proteins. Proteomics, 6, 4-8.

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