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@ARTICLE{Jeong:182764,
      author       = {H. Jeong and K. Grimes and K. K. Rauwolf and P.-M. Bruch
                      and T. Rausch and P. Hasenfeld and E. Benito and T. Roider
                      and R. Sabarinathan and D. Porubsky and S. A. Herbst and B.
                      Erarslan-Uysal and J.-C. Jann and T. Marschall and D. Nowak
                      and J.-P. Bourquin and A. E. Kulozik and S. Dietrich$^*$ and
                      B. Bornhauser and A. D. Sanders and J. Korbel$^*$},
      title        = {{F}unctional analysis of structural variants in single
                      cells using {S}trand-seq.},
      journal      = {Nature biotechnology},
      volume       = {41},
      number       = {6},
      issn         = {0733-222X},
      address      = {New York, NY},
      publisher    = {Springer Nature},
      reportid     = {DKFZ-2022-02904},
      pages        = {832-844},
      year         = {2023},
      note         = {#LA:B480# / 2023 Jun;41(6):832-844},
      abstract     = {Somatic structural variants (SVs) are widespread in cancer,
                      but their impact on disease evolution is understudied due to
                      a lack of methods to directly characterize their functional
                      consequences. We present a computational method, scNOVA,
                      which uses Strand-seq to perform haplotype-aware integration
                      of SV discovery and molecular phenotyping in single cells by
                      using nucleosome occupancy to infer gene expression as a
                      readout. Application to leukemias and cell lines identifies
                      local effects of copy-balanced rearrangements on gene
                      deregulation, and consequences of SVs on aberrant signaling
                      pathways in subclones. We discovered distinct SV subclones
                      with dysregulated Wnt signaling in a chronic lymphocytic
                      leukemia patient. We further uncovered the consequences of
                      subclonal chromothripsis in T cell acute lymphoblastic
                      leukemia, which revealed c-Myb activation, enrichment of a
                      primitive cell state and informed successful targeting of
                      the subclone in cell culture, using a Notch inhibitor. By
                      directly linking SVs to their functional effects, scNOVA
                      enables systematic single-cell multiomic studies of
                      structural variation in heterogeneous cell populations.},
      cin          = {B480 / B340},
      ddc          = {660},
      cid          = {I:(DE-He78)B480-20160331 / I:(DE-He78)B340-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36424487},
      doi          = {10.1038/s41587-022-01551-4},
      url          = {https://inrepo02.dkfz.de/record/182764},
}