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Parallel-Tempered Feature Allocation for Large-Scale Tumor Heterogeneity with Deep Sequencing Data

  • Yang Ni
  • Peter Müller
  • Max Shpak
  • Yuan JiEmail author
Conference paper
Part of the Springer Proceedings in Mathematics & Statistics book series (PROMS, volume 218)

Abstract

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.

Keywords

Haplotype deconvolution Single nucleotide variants Next-generation sequencing data Indian buffet process Glioblastoma multiforme 

Notes

Acknowledgements

YN, YJ and PM were partially funded by grant NIH R01 CA132891-06A1. MS was supported by the St. David’s Foundation impact fund. Specimen collection, processing and analysis were supported by funds from the St. David’s Impact Fund and the NeuroTexas Research Foundation.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Statistics and Data SciencesThe University of Texas at AustinAustinUSA
  2. 2.Department of MathematicsThe University of Texas at AustinAustinUSA
  3. 3.Sarah Cannon Research InstituteNashvilleUSA
  4. 4.Center for Systems and Synthetic BiologyThe University of Texas at AustinAustinUSA
  5. 5.Fresh Pond Research InstituteCambridgeUSA
  6. 6.Program of Computational Genomics & MedicineNorthShore University HealthSystemEvanstonUSA
  7. 7.Department of Public Health SciencesThe University of ChicagoChicagoUSA

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