Abstract
The better understanding of variants of the genomes may improve the knowledge on the causes of the individuals’ different responses to drugs. The Affymetrix DMET (Drug Metabolizing Enzymes and Transporters) microarray platform offers the possibility to determine the gene variants of a patient and correlate them with drug-dependent adverse events. The analysis of DMET data is a growing research area. Existing approaches span from the use of simple statistical tests to more complex strategies based, for instance, on learning association rules. To support the analysis, we developed GenotypeAnalytics, a RESTFul-based software service able to automatically extract association rules from DMET datasets. GenotypeAnalytics is based on an optimised algorithm for learning rules that can outperform general purpose platforms.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Meyer, U.A.: Pharmacogenetics and adverse drug reactions. Lancet 356(9242), 1667–1671 (2000)
Li, J., Zhang, L., Zhou, H., Stoneking, M., Tang, K.: Global patterns of genetic diversity and signals of natural selection for human ADME genes. Hum. Mol. Genet. 20(3), 528–540 (2011)
Lombardi, G., Rumiato, E., Bertorelle, R., Saggioro, D., Farina, P., Della Puppa, A., Zustovich, F., Berti, F., Sacchetto, V., Marcato, R., et al.: Clinical and genetic factors associated with severe hematological toxicity in Glioblastoma patients during Radiation Plus Temozolomide treatment: a prospective study. Am. J. Clin. Oncol. 10, 1097 (2013)
Di Martino, M.T., Arbitrio, M., Guzzi, P.H., Leone, E., Baudi, F., Piro, E., Prantera, T., Cucinotto, I., Calimeri, T., Rossi, M., Veltri, P., Cannataro, M., Tagliaferri, P., Tassone, P.: A peroxisome proliferator-activated receptor gamma (PPARG) polymorphism is associated with Zoledronic acid-related Osteonecrosis of the jaw in multiple Myeloma patients: analysis by DMET microarray profiling. Br. J. Haematol. 154, 529–533 (2011)
Guzzi, P.H., Agapito, G., Milano, M., Cannataro, M.: Methodologies and experimental platforms for generating and analysing microarray and mass spectrometry-based omics data to support P4 medicine. Briefings Bioinf. 17(4), 553–561 (2015)
Arbitrio, M., Di Martino, M.T., Barbieri, V., Agapito, G., Guzzi, P.H., Botta, C., Iuliano, E., Scionti, F., Altomare, E., Codispoti, S., et al.: Identification of polymorphic variants associated with erlotinib-related skin toxicity in advanced non-small cell lung cancer patients by DMET microarray analysis. Cancer Chemother. Pharmacol. 77(1), 205–209 (2016)
Di Martino, M.T., Arbitrio, M., Leone, E., Guzzi, P.H., Saveria Rotundo, M., Ciliberto, D., Tomaino, V., Fabiani, F., Talarico, D., Sperlongano, P., Doldo, P., Cannataro, M., Caraglia, M., Tassone, P., Tagliaferri, P.: Single nucleotide polymorphisms of ABCC5 and ABCG1 transporter genes correlate to irinotecan-associated gastrointestinal toxicity in colorectal cancer patients: a DMET microarray profiling study. Cancer Biol. Ther. 12(9), 780–787 (2011)
Guzzi, P.H., Cannataro, M.: \(\mu \)-CS: an extension of the TM4 platform to manage Affymetrix binary data. BMC Bioinform. 11(1), 315 (2010)
Arbitrio, M., Di Martino, M.T., Scionti, F., Agapito, G., Guzzi, P.H., Cannataro, M., Tassone, P., Tagliaferri, P.: DMET™ (Drug Metabolism Enzymes and Transporters): a pharmacogenomic platform for precision medicine. Oncotarget 7(33), 54028 (2016)
Guzzi, P., Agapito, G., Di Martino, M., Arbitrio, M., Tassone, P., Tagliaferri, P., Cannataro, M.: DMET-analyzer: automatic analysis of Affymetrix DMET data. BMC Bioinform. 13(1), 258 (2012)
Rumiato, E., Boldrin, E., Amadori, A., Saggioro, D.: DMET (Drug-Metabolizing Enzymes and Transporters) microarray analysis of colorectal cancer patients with severe 5-fluorouraci-induced toxicity. Cancer Chemother. Pharmacol. 72(2), 483–488 (2013)
Agrawal, R., Imieliński, T., Swami, A.: Mining Association Rules Between Sets of Items in Large Databases, vol. 22, pp. 207–216. ACM, New York (1993)
Guzzi, P.H., Agapito, G., Cannataro, M.: coreSNP: parallel processing of microarray data. IEEE Trans. Comput. 63(12), 2961–2974 (2014)
Di Martino, M.T., Guzzi, P.H., Caracciolo, D., Agnelli, L., Neri, A., Walker, B.A., Morgan, G.J., Cannataro, M., Tassone, P., Tagliaferri, P.: Integrated analysis of microRNAs, transcription factors and target genes expression discloses a specific molecular architecture of hyperdiploid multiple myeloma. Oncotarget 6(22), 19132 (2015)
Di Martino, M.T., Scionti, F., Sestito, S., Nicoletti, A., Arbitrio, M., Guzzi, P.H., Talarico, V., Altomare, F., Sanseviero, M.T., Agapito, G., et al.: Genetic variants associated with gastrointestinal symptoms in fabry disease. Oncotarget 7(52), 85895 (2016)
Zaki, M.J., Hsiao, C.J.: CHARM: an efficient algorithm for closed itemset mining. In: Proceedings of the 2002 SIAM International Conference on Data Mining. SIAM, pp. 457–473 (2002)
Pei, J., Han, J., Mao, R., et al.: CLOSET: an efficient algorithm for mining frequent closed itemsets. In: ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery, vol. 4, pp. 21–30 (2000)
Agapito, G., Milano, M., Guzzi, P.H., Cannataro, M.: Extracting cross-ontology weighted association rules from gene ontology annotations. IEEE/ACM Trans. Comput. Biol. Bioinform. 13(2), 197–208 (2016)
Agapito, G., Cannataro, M., Guzzi, P.H., Milano, M.: Using go-war for mining cross-ontology weighted association rules. Comput. Methods Programs Biomed. 120(2), 113–122 (2015)
Agapito, G., Cannataro, M., Guzzi, P.H., Marozzo, F., Talia, D., Trunfio, P.: Cloud4SNP: distributed analysis of SNP microarray data on the cloud. In: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, p. 468. ACM (2013)
Agapito, G., Guzzi, P.H., Cannataro, M.: DMET-Miner: Efficient discovery of association rules from pharmacogenomic data. Journal of biomedical informatics 56, 273–283 (2015)
Agapito, G., Botta, C., Guzzi, P.H., Arbitrio, M., Di Martino, M.T., Tassone, P., Tagliaferri, P., Cannataro, M.: OSAnalyzer: a bioinformatics tool for the analysis of gene polymorphisms enriched with clinical outcomes. Microarrays 5(4), 24 (2016)
Sissung, T., English, B., Venzon, D., Figg, W., Deeken, J.: Clinical pharmacology and pharmacogenetics in a genomics era: the DMET platform. Pharmacogenomics 11, 89–103 (2010)
Marozzo, F., Talia, D., Trunfio, P.: A cloud framework for big data analytics workflows on Azure. In: Cloud Computing and Big Data. Advances in Parallel Computing, vol. 23, pp. 182–191. IOS Press (2013). https://doi.org/10.3233/978-1-61499-322-3-182
Marozzo, F., Talia, D., Trunfio, P.: Using clouds for scalable knowledge discovery applications. In: Caragiannis, I., Alexander, M., Badia, R.M., Cannataro, M., Costan, A., Danelutto, M., Desprez, F., Krammer, B., Sahuquillo, J., Scott, S.L., Weidendorfer, J. (eds.) Euro-Par 2012. LNCS, vol. 7640, pp. 220–227. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-36949-0_25
Fournier-Viger, P., Gomariz, A., Gueniche, T., Soltani, A., Wu, C.W., Tseng, V.S.: SPMF: a java open-source pattern mining library. J. Mach. Learn. Res. 15(1), 3389–3393 (2014)
Borgelt, C.: Frequent item set mining. Wiley Interdisc. Rev. Data Mining Knowl. Discovery 2(6), 437–456 (2012)
Acknowledgements
This work has been partially funded by the following research projects:
– “BA2Know-Business Analytics to Know” (PON03PE_00001_1), funded by the Italian Ministry of Education and Research (MIUR)
– INdAM - GNCS Project 2017: “Efficient Algorithms and Techniques for the Organization, Management and Analysis of Biological Big Data”.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this paper
Cite this paper
Agapito, G., Guzzi, P.H., Cannataro, M. (2018). Learning Association Rules for Pharmacogenomic Studies. In: Appice, A., Loglisci, C., Manco, G., Masciari, E., Ras, Z. (eds) New Frontiers in Mining Complex Patterns. NFMCP 2017. Lecture Notes in Computer Science(), vol 10785. Springer, Cham. https://doi.org/10.1007/978-3-319-78680-3_1
Download citation
DOI: https://doi.org/10.1007/978-3-319-78680-3_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-78679-7
Online ISBN: 978-3-319-78680-3
eBook Packages: Computer ScienceComputer Science (R0)