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@ARTICLE{Watkins:284953,
      author       = {T. B. K. Watkins and E. C. Colliver and M. R. Huska and T.
                      L. Kaufmann and E. L. Lim and C. B. Duncan and K. Haase$^*$
                      and P. Van Loo and C. Swanton and N. McGranahan and R. F.
                      Schwarz},
      title        = {{R}efphase: {M}ulti-sample phasing reveals
                      haplotype-specific copy number heterogeneity.},
      journal      = {PLoS Computational Biology},
      volume       = {19},
      number       = {10},
      issn         = {1553-734X},
      address      = {San Francisco, Calif.},
      publisher    = {Public Library of Science},
      reportid     = {DKFZ-2023-02151},
      pages        = {e1011379},
      year         = {2023},
      abstract     = {Most computational methods that infer somatic copy number
                      alterations (SCNAs) from bulk sequencing of DNA analyse
                      tumour samples individually. However, the sequencing of
                      multiple tumour samples from a patient's disease is an
                      increasingly common practice. We introduce Refphase, an
                      algorithm that leverages this multi-sampling approach to
                      infer haplotype-specific copy numbers through multi-sample
                      phasing. We demonstrate Refphase's ability to infer
                      haplotype-specific SCNAs and characterise their intra-tumour
                      heterogeneity, to uncover previously undetected allelic
                      imbalance in low purity samples, and to identify parallel
                      evolution in the context of whole genome doubling in a
                      pan-cancer cohort of 336 samples from 99 tumours.},
      cin          = {BE01},
      ddc          = {610},
      cid          = {I:(DE-He78)BE01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37871126},
      doi          = {10.1371/journal.pcbi.1011379},
      url          = {https://inrepo02.dkfz.de/record/284953},
}