Evolution-informed modeling improves outcome prediction for cancers

Li Liu, Yung Chang, Tao Yang, David P. Noren, Byron Long, Steven Kornblau, Amina Qutub, Jieping Ye

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

Despite wide applications of high-throughput biotechnologies in cancer research, many biomarkers discovered by exploring large-scale omics data do not provide satisfactory performance when used to predict cancer treatment outcomes. This problem is partly due to the overlooking of functional implications of molecular markers. Here, we present a novel computational method that uses evolutionary conservation as prior knowledge to discover bona fide biomarkers. Evolutionary selection at the molecular level is nature's test on functional consequences of genetic elements. By prioritizing genes that show significant statistical association and high functional impact, our new method reduces the chances of including spurious markers in the predictive model. When applied to predicting therapeutic responses for patients with acute myeloid leukemia and to predicting metastasis for patients with prostate cancers, the new method gave rise to evolution-informed models that enjoyed low complexity and high accuracy. The identified genetic markers also have significant implications in tumor progression and embrace potential drug targets. Because evolutionary conservation can be estimated as a gene-specific, position-specific, or allele-specific parameter on the nucleotide level and on the protein level, this new method can be extended to apply to miscellaneous “omics” data to accelerate biomarker discoveries.

Original languageEnglish (US)
Pages (from-to)68-76
Number of pages9
JournalEvolutionary Applications
Volume10
Issue number1
DOIs
StatePublished - Jan 1 2017

Keywords

  • evolutionary medicine
  • genomics/proteomics
  • molecular evolution
  • transcriptomics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Agricultural and Biological Sciences(all)

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