GWAS in cancer: progress and challenges

Abstract

The genome-wide association study (GWAS) is an effective method to detect single-nucleotide polymorphisms (SNPs) of multiple individual genes based on linkage disequilibrium (LD). GWAS examines genotypes and distinguishing gene characteristics that are exhibited in diseases. In the past few decades, more and more literature has reported the results of applying GWAS to study tumors. Although many pleiotropic loci associated with complex phenotypes have been identified by GWAS, the biological functions of many genetic variation loci remain unclear, and the genetic mechanisms of most complex phenotypes cannot be systematically explained. In this article, we will review the new findings of several tumor types, and categorize the new sites and mechanisms that have recently been discovered. We linked the mechanisms of action of various tumors and searched for links to related gene expression pathways. We found that susceptible sites can be divided into hub genes and peripheral genes; the two interact to link gene expression in a variety of diseases.

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Acknowledgements

We would like to thank Alan Larson (a7larson@health.ucsd.edu), Department of Family Medicine and Public Health, School of Medicine, University of California San Diego, and Biaoru Li (bli@augusta.edu), Cancer Center, Medical College of Georgia in Augusta University for English language revision.

Funding

This work was supported partly by the Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang (ZJW-2019-07); National Natural Science Foundation of China (81541153); Guangdong Provincial Science and Technology Department (2016A050503046, 2015A050502048 and 2016B030309002); The Public Service Platform of South China Sea for R&D Marine Biomedicine Resources (GDMUK201808), Zhanjiang Science and Technology Plan (2017A06012); Guangdong Province Natural Science Foundation (2018A030310155); and “Group-type” Special Supporting Project for Educational Talents in Universities (4SG19057G). The funding sources had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Correspondence to Haiqing Luo or Xiao Zhu.

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Liang, B., Ding, H., Huang, L. et al. GWAS in cancer: progress and challenges. Mol Genet Genomics 295, 537–561 (2020). https://doi.org/10.1007/s00438-020-01647-z

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Keywords

  • GWAS
  • SNPs
  • Cancer
  • Susceptible gene
  • Review
  • Genotype