Parallel-Tempered Feature Allocation for Large-Scale Tumor Heterogeneity with Deep Sequencing Data Conference Paper uri icon


  • 2019, Springer Nature Switzerland AG. We developed a parallel-tempered feature allocation algorithm to infer tumor heterogeneity from deep DNA sequencing data. The feature allocation model is based on a binomial likelihood and an Indian Buffet process prior on the latent haplotypes. A variation of parallel tempering technique is introduced to flatten peaked local modes of the posterior distribution, and yields a more efficient Markov chain Monte Carlo algorithm. Simulation studies provide empirical evidence that the proposed method is superior to competing methods at a high read depth. In our application to Glioblastoma multiforme data, we found several distinctive haplotypes that indicate the presence of multiple subclones in the tumor sample.

published proceedings

  • Springer Proceedings in Mathematics and Statistics

author list (cited authors)

  • Ni, Y., Mller, P., Shpak, M., & Ji, Y.

citation count

  • 1

complete list of authors

  • Ni, Yang||Müller, Peter||Shpak, Max||Ji, Yuan

publication date

  • January 2019