Abstract
The Human genome project transformed biology and pharmacology into a computational, mathematical, and big-data science. In this paper we dissect the science and technology of big-data translational genomics and precision medicine - we present various components of this complex Genomics 3.0 science. We also identify diverse idiosyncrasies of big-data with respect to application of computer algorithms and mathematics in genomics. We discuss the 7Vs of big-data in biology; we discuss genomic data and its relevance with respect to formal database systems. Genomics big-data analysis is a combination of top-down, bottom-up, and middle-out approaches with all the constituent parts integrated into a single system through complex meta-analysis. Finally, we present two big-data platforms iOMICS and DiscoverX. iOMICS platform is deployed at Google cloud for translational genomics; whereas, DiscoverX is deployed at Amazon Web Services for precision medicine.
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References
Sackett, D.L., Rosenberg, W.M., Gray, J., Haynes, R.B., Richardson, W.S.: Evidence based medicine: what it is and what it isn’t. Br. Med. J. (BMJ) 312(7023), 71 (1996)
Di Ventura, B., Lemerle, C., Michalodimitrakis, K., Serrano, L.: From in vivo to in silico biology and back. Nature 443(7111), 527–533 (2006)
Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al.: The sequence of the human genome. Science 291(5507), 1304–1351 (2001)
Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., Covert, M.W.: A whole-cell computational model predicts phenotype from genotype. Cell 150(2), 389–401 (2012)
Kohl, P., Noble, D.: Systems biology and the virtual physiological human. Mol. Syst. Biol. 5(1), 292 (2009)
Precision medicine initiatives. http://www.nih.gov/precisionmedicine/
Collins, F.S., Hamburg, M.A.: First FDA authorization for next-generation sequencer. N. Engl. J. Med. 369(25), 2369–2371 (2013)
Liu, X., Jian, X., Boerwinkle, E.: dbNSFP v2. 0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat. 34(9), E2393–E2402 (2013)
Steinhauser, M.O.: Computational Multiscale Modeling of Fluids and Solids. Springer, New York (2008)
List of biological databases. https://en.wikipedia.org/wiki/List_of_biological_databases
Galperin, M.Y., Rigden, D.J., Fernández-Suárez, X.M.: The 2015 nucleic acids research database issue and molecular biology database collection. Nucleic Acids Res. 43(D1), D1–D5 (2015)
Engineering statistics handbook: Exploratory data analysis. http://www.itl.nist.gov/div898/handbook/eda/eda.htm
Biogrid. http://thebiogrid.org/
Intact molecular interaction database. https://www.ebi.ac.uk/intact/
Reconx. http://humanmetabolism.org/
Geneontology. http://geneontology.org/
Kyoto encyclopedia of genes and genomes. http://www.genome.jp/kegg/
Panther. http://www.pantherdb.org/pathway/
Surveillance, epidemiology, and end results program. http://seer.cancer.gov/data/
The sam/bam format specification working group, sequence alignment/map format specification (2015). https://samtools.github.io/hts-specs/SAMv1.pdf
Integrated rule-oriented data system irods. http://irods.org/
Hana. http://hana.sap.com/
Li, H.: Tabix: fast retrieval of sequence features from generic tab-delimited files. Bioinformatics 27(5), 718–719 (2011)
Cellml. https://www.cellml.org/about
iomics. http://iomics.in
Talukder, A.K., Ravishankar, S., Sasmal, K., Gandham, S., Prabhukumar, J., Achutharao, P.H., Barh, D., Blasi, F.: Xomannotate: analysis of heterogeneous and complex exome-a step towards translational medicine. PLoS ONE 10, e0123569 (2015)
Gracia-Aznarez, F.J., Fernandez, V., Pita, G., Peterlongo, P., Dominguez, O., de la Hoya, M., Duran, M., Osorio, A., Moreno, L., Gonzalez-Neira, A., et al.: Whole exome sequencing suggests much of non-BRCA1/BRCA2 familial breast cancer is due to moderate and low penetrance susceptibility alleles. PloS one 8(2), e55681 (2013)
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Talukder, A.K. (2015). Genomics 3.0: Big-data in Precision Medicine. In: Kumar, N., Bhatnagar, V. (eds) Big Data Analytics. BDA 2015. Lecture Notes in Computer Science(), vol 9498. Springer, Cham. https://doi.org/10.1007/978-3-319-27057-9_14
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DOI: https://doi.org/10.1007/978-3-319-27057-9_14
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