Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes

Semin Nephrol. 2015 May;35(3):237-44. doi: 10.1016/j.semnephrol.2015.04.003.

Abstract

In the past decade, population genetics has gained tremendous success in identifying genetic variations that are statistically relevant to renal diseases and kidney function. However, it is challenging to interpret the functional relevance of the genetic variations found by population genetics studies. In this review, we discuss studies that integrate multiple levels of data, especially transcriptome profiles and phenotype data, to assign functional roles of genetic variations involved in kidney function. Furthermore, we introduce state-of-the-art machine learning algorithms, Bayesian networks, support vector machines, and Gaussian process regression, which have been applied successfully to integrating genetic, regulatory, and clinical information to predict clinical outcomes. These methods are likely to be deployed successfully in the nephrology field in the near future.

Keywords: Gene regulation; SNP; clinical outcomes; predictions.

Publication types

  • Review

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Gene Expression Profiling / methods*
  • Gene Regulatory Networks / genetics*
  • Genotype
  • Humans
  • Kidney Diseases / genetics*
  • Kidney Diseases / metabolism
  • Phenotype
  • Prognosis