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Classification and Survival Prediction in Diffuse Large B-Cell Lymphoma by Gene Expression Profiling

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Book cover Machine Learning, Optimization, and Data Science (LOD 2018)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11331))

Abstract

We present a novel framework for developing a risk model for class prediction from high-dimensional gene expression data; we define a new model that relies on several already known classification methods. We make use of the model for a survival analysis of tumor and immune subtype from Diffuse Large B-cell Lymphoma patients. Experimental analyses show good level of accuracy in the detection of Cell-of-Origin of diseases.

The work is partially funded by Dottorato innovativo a caratterizzazione industriale PON R&I FSE FESR 2014–2020.

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Notes

  1. 1.

    https://www.ncbi.nlm.nih.gov/geo/.

References

  1. National Institutes of Health: Understanding emerging and re-emerging infectious diseases. Biological Sciences Curriculum Study, Bethesda, MD, US (2007)

    Google Scholar 

  2. Sandlund, J.T., Martin, M.G.: Non-Hodgkin lymphoma across the pediatric and adolescent and young adult age spectrum. ASH Educ. Program Book 2016(1), 589–597 (2016)

    Google Scholar 

  3. Zhao, Y., Simon, R.: Gene expression deconvolution in clinical samples. Genome Med. 2(12), 93 (2010)

    Article  Google Scholar 

  4. Van’t Veer, L.J., et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415(6871), 530 (2002)

    Article  Google Scholar 

  5. Ando, T., Suguro, M., Hanai, T., Kobayashi, T., Honda, H., Seto, M.: Fuzzy neural network applied to gene expression profiling for predicting the prognosis of diffuse large B-cell lymphoma. Jpn. J. Cancer Res. 93, 1207–1212 (2002)

    Article  Google Scholar 

  6. Dabney, A.R.: Classification of microarrays to nearest centroids. Bioinformatics 21, 4148–4154 (2005)

    Article  Google Scholar 

  7. Hedström, G., Hagberg, O., Jerkeman, M., Enblad, G.: The impact of age on survival of diffuse large B-cell lymphoma - a population-based study. Acta Oncol. 54(6), 916–23 (2015)

    Article  Google Scholar 

  8. Khoshhali, M., Mahjub, H., Saidijam, M., Poorolajal, J., Soltanian, A.R.: Predicting the survival time for diffuse large B-cell lymphoma using microarray data. J. Mol. Genet. Med. 6, 287–292 (2012)

    Article  Google Scholar 

  9. Lenz, G.: Novel therapeutic targets in diffuse large B-cell lymphoma. EJC Suppl. 11, 262–263 (2013)

    Article  Google Scholar 

  10. Scott, D.W., Wright, G.W., Williams, P.M., et al.: Determining cell-of-origin subtypes of diffuse large B-cell lymphoma using gene expression in formalin-fixed paraffin-embedded tissue. Blood 123, 1214–1217 (2014)

    Article  Google Scholar 

  11. Wang, S., Wang, J., Chen, H., Zhang, B.: SVM-based tumor classification with gene expression data. In: Li, X., Zaïane, O.R., Li, Z. (eds.) ADMA 2006. LNCS (LNAI), vol. 4093, pp. 864–870. Springer, Heidelberg (2006). https://doi.org/10.1007/11811305_94

    Chapter  Google Scholar 

  12. Sharma, A., Paliwal, K.K.: Cancer classification by gradient LDA technique using microarray gene expression data. Data Knowl. Eng. 66(2), 338–347 (2008)

    Article  Google Scholar 

  13. Li, B., Zheng, C.H., Huang, D.S., Zhang, L., Han, K.: Gene expression data classification using locally linear discriminant embedding. Comput. Biol. Med. 40(10), 802–810 (2010)

    Article  Google Scholar 

  14. Orsborne, C., Byers, R.: Impact of gene expression profiling in lymphoma diagnosis and prognosis. Histopathology 58(1), 106–127 (2011)

    Article  Google Scholar 

  15. Wang, S.L., Fang, Y., Fang, J.: Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template. In: BMC Bioinformatics, vol. 14, pp. 11 (2013)

    Google Scholar 

  16. Newman, A.M., et al.: Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12(5), 453–457 (2015)

    Article  Google Scholar 

  17. Altman, D.G.: Analysis of Survival times. In: Practical Statistics for Medical Research, pp. 365–93. CRC Press, Boca Raton (1990)

    Google Scholar 

  18. Goel, M.K., Khanna, P., Kishore, J.: Understanding survival analysis: Kaplan-Meier estimate. Int. J. Ayurveda Res. 1(4), 274 (2010)

    Article  Google Scholar 

  19. Mahmoud, O., et al.: A feature selection method for classification within functional genomics experiments based on the proportional overlapping score. BMC Bioinf. 15(1), 274 (2014)

    Article  Google Scholar 

  20. Klassen, M., Kim, N.: Nearest shrunken centroid as feature selection of microarray data. In: CATA, pp. 227–232 (2009)

    Google Scholar 

  21. Choi, B.Y., Bair, E., Lee, J.W.: Nearest shrunken centroids via alternative genewise shrinkages. PloS one 12(2), e0171068 (2017)

    Article  Google Scholar 

  22. Shaffer, A.L., Rosenwald, A., Staudt, L.M.: Decision making in the immune system: Lymphoid Malignancies: the dark side of B-cell differentiation. Nat. Rev. Immunol. 2(12), 920 (2002)

    Article  Google Scholar 

  23. Povey, S., Lovering, R., Bruford, E., Wright, M., Lush, M., Wain, H.: The HUGO gene nomenclature committee (HGNC). Hum. Genet. 109(6), 678–680 (2001)

    Article  Google Scholar 

  24. Bland, J.M., Altman, D.G.: The logrank test. BMJ 328(7447), 1073 (2004)

    Article  Google Scholar 

  25. Kao, L.S., Green, C.E.: Analysis of variance: is there a difference in means and What does it mean? J. Surg. Res. 144(1), 158–170 (2008)

    Article  Google Scholar 

  26. Indrayan, A., Surmukaddam, S.B.: Measurement of community health and survival analysis. Med. Biostat. 7, 232–42 (2001)

    Google Scholar 

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Authors and Affiliations

  1. Department of Mathematics and Computer Science, University of Calabria, Rende, Italy

    Pierangela Bruno, Francesco Calimeri & Aldo Marzullo

Authors
  1. Pierangela Bruno
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  2. Francesco Calimeri
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  3. Aldo Marzullo
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Corresponding author

Correspondence to Pierangela Bruno .

Editor information

Editors and Affiliations

  1. University of Catania, Catania, Italy and University of Reading, Reading, UK

    Giuseppe Nicosia

  2. University of Florida, Gainesville, FL, USA

    Panos Pardalos

  3. University of Catania, Catania, Italy

    Giovanni Giuffrida

  4. Harvard University, Cambridge, MA, USA

    Renato Umeton

  5. IBM, Tivoli Research Lab, Rome, Italy

    Vincenzo Sciacca

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Bruno, P., Calimeri, F., Marzullo, A. (2019). Classification and Survival Prediction in Diffuse Large B-Cell Lymphoma by Gene Expression Profiling. In: Nicosia, G., Pardalos, P., Giuffrida, G., Umeton, R., Sciacca, V. (eds) Machine Learning, Optimization, and Data Science. LOD 2018. Lecture Notes in Computer Science(), vol 11331. Springer, Cham. https://doi.org/10.1007/978-3-030-13709-0_14

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  • DOI: https://doi.org/10.1007/978-3-030-13709-0_14

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-13708-3

  • Online ISBN: 978-3-030-13709-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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