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Sparse Representation-Based Patient-Specific Diagnosis and Treatment for Esophageal Squamous Cell Carcinoma

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Abstract

Precision medicine and personalized treatment have attracted attention in recent years. However, most genetic medicines mainly target one genetic site, while complex diseases like esophageal squamous cell carcinoma (ESCC) usually present heterogeneity that involves variations of many genetic markers. Here, we seek an approach to leverage genetic data and ESCC knowledge data to forward personalized diagnosis and treatment for ESCC. First, 851 ESCC-related gene markers and their druggability were studied through a comprehensive literature analysis. Then, a sparse representation-based variable selection (SRVS) was employed for patient-specific genetic marker selection using gene expression datasets. Results showed that the SRVS method could identify a unique gene vector for each patient group, leading to significantly higher classification accuracies compared to randomly selected genes (100, 97.17, 100, 100%; permutation p values: 0.0032, 0.0008, 0.0004, and 0.0008). The SRVS also outperformed an ANOVA-based gene selection method in terms of the classification ratio. The patient-specific gene markers are targets of ESCC effective drugs, providing specific guidance for medicine selection. Our results suggest the effectiveness of integrating previous database utilizing SRVS in assisting personalized medicine selection and treatment for ESCC.

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Acknowledgements

We would like to thank Rachel Amey from University of Delaware for her contribution to the English writing of the manuscript. This study is partly supported by non-small cell lung cancer research funding, Jiangsu Provincial Planning Commission; by clinical diagnosis and treatment of small lung lesions and normative research, Wuxi City Health Planning Commission, MS201625; and by 2017 Fifth Provincial ‘333 Project’ Research Project.

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Author notes

  1. Bin Huang and Ning Zhong have contributed equally to this work.

Authors and Affiliations

  1. Department of Cardiothoracic Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, No. 163 Shoushan Rd, Jiangyin, 214400, Jiangsu, China

    Bin Huang & Guiping Yu

  2. Department of Cardiothoracic Surgery, The First People’s Hospital of Kunshan, Kunshan, 215300, Jiangsu, China

    Ning Zhong

  3. Department of Ultrasound, The People’s Hospital of Tongling, Tongling, 215300, Anhui, China

    Lili Xia

  4. Department of Genomics Research, R&D Solutions, Elsevier Inc., Rockville, MD, 20852, USA

    Hongbao Cao

  5. Unit on Statistical Genomics, National Institute of Health (NIH), Bethesda, MD, 20892, USA

    Hongbao Cao

Authors
  1. Bin Huang
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  2. Ning Zhong
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  3. Lili Xia
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  4. Guiping Yu
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Correspondence to Guiping Yu or Hongbao Cao.

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Huang, B., Zhong, N., Xia, L. et al. Sparse Representation-Based Patient-Specific Diagnosis and Treatment for Esophageal Squamous Cell Carcinoma. Bull Math Biol 80, 2124–2136 (2018). https://doi.org/10.1007/s11538-018-0449-8

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  • DOI: https://doi.org/10.1007/s11538-018-0449-8

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