Detecting repeated cancer evolution from multi-region tumor sequencing data

Research output: Contribution to journalArticlepeer-review

Authors

  • Giulio Caravagna
  • Ylenia Giarratano
  • Daniele Ramazzotti
  • Trevor A. Graham
  • Guido Sanguinetti
  • Andrea Sottoriva

Colleges, School and Institutes

Abstract

Recurrent successions of genomic changes, both within and between patients, reflect repeated evolutionary processes that are valuable for the anticipation of cancer progression. Multi-region sequencing allows the temporal order of some genomic changes in a tumor to be inferred, but the robust identification of repeated evolution across patients remains a challenge. We developed a machine-learning method based on transfer learning that allowed us to overcome the stochastic effects of cancer evolution and noise in data and identified hidden evolutionary patterns in cancer cohorts. When applied to multi-region sequencing datasets from lung, breast, renal, and colorectal cancer (768 samples from 178 patients), our method detected repeated evolutionary trajectories in subgroups of patients, which were reproduced in single-sample cohorts (n = 2,935). Our method provides a means of classifying patients on the basis of how their tumor evolved, with implications for the anticipation of disease progression.

Details

Original languageEnglish
Pages (from-to)707-714
Number of pages8
JournalNature Methods
Volume15
Issue number9
Publication statusPublished - 31 Aug 2018