Learning smoothing models of copy number profiles using breakpoint annotations

Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis Bach, Jean Philippe Vert

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


Background: Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using various heuristics.Results: We present three contributions for copy number profile smoothing model selection. First, we propose to select the model and degree of smoothness that maximizes agreement with visual breakpoint region annotations. Second, we develop cross-validation procedures to estimate the error of the trained models. Third, we apply these methods to compare 17 smoothing models on a new database of 575 annotated neuroblastoma copy number profiles, which we make available as a public benchmark for testing new algorithms.Conclusions: Whereas previous studies have been qualitative or limited to simulated data, our annotation-guided approach is quantitative and suggests which algorithms are fastest and most accurate in practice on real data. In the neuroblastoma data, the equivalent pelt.n and cghseg.k methods were the best breakpoint detectors, and exhibited reasonable computation times.

Original languageEnglish (US)
Article number164
JournalBMC Bioinformatics
Issue number1
StatePublished - May 22 2013
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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