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Bulletin of Mathematical Biology

, Volume 80, Issue 8, pp 2124–2136 | Cite as

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

  • Bin Huang
  • Ning Zhong
  • Lili Xia
  • Guiping Yu
  • Hongbao Cao
Original Article

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.

Keywords

Esophageal squamous cell carcinoma Sparse representation Gene selection 

Notes

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.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

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Copyright information

© Society for Mathematical Biology 2018

Authors and Affiliations

  1. 1.Department of Cardiothoracic SurgeryThe Affiliated Jiangyin Hospital of Southeast University Medical CollegeJiangyinChina
  2. 2.Department of Cardiothoracic SurgeryThe First People’s Hospital of KunshanKunshanChina
  3. 3.Department of UltrasoundThe People’s Hospital of TonglingTonglingChina
  4. 4.Department of Genomics Research, R&D SolutionsElsevier Inc.RockvilleUSA
  5. 5.Unit on Statistical GenomicsNational Institute of Health (NIH)BethesdaUSA

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