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@ARTICLE{Lindenhofer:304284,
      author       = {D. Lindenhofer and J. R. Bauman and J. A. Hawkins$^*$ and
                      D. Fitzgerald and U. Yildiz and H. Jung and A. Korosteleva
                      and M. Marttinen and M. Kueblbeck and J. B. Zaugg and K.-M.
                      Noh and S. Dietrich and W. Huber and O. Stegle$^*$ and L. M.
                      Steinmetz},
      title        = {{F}unctional phenotyping of genomic variants using joint
                      multiomic single-cell {DNA}-{RNA} sequencing.},
      journal      = {Nature methods},
      volume       = {nn},
      issn         = {1548-7091},
      address      = {London [u.a.]},
      publisher    = {Nature Publishing Group},
      reportid     = {DKFZ-2025-01824},
      pages        = {nn},
      year         = {2025},
      note         = {epub},
      abstract     = {Genetic variants (both coding and noncoding) can impact
                      gene function and expression, driving disease mechanisms
                      such as cancer progression. The systematic study of
                      endogenous genetic variants is hindered by inefficient
                      precision editing tools, combined with technical limitations
                      in confidently linking genotypes to gene expression at
                      single-cell resolution. We developed single-cell DNA-RNA
                      sequencing (SDR-seq) to simultaneously profile up to 480
                      genomic DNA loci and genes in thousands of single cells,
                      enabling accurate determination of coding and noncoding
                      variant zygosity alongside associated gene expression
                      changes. Using SDR-seq, we associate coding and noncoding
                      variants with distinct gene expression in human induced
                      pluripotent stem cells. Furthermore, we demonstrate that in
                      primary B cell lymphoma samples, cells with a higher
                      mutational burden exhibit elevated B cell receptor signaling
                      and tumorigenic gene expression. SDR-seq provides a powerful
                      platform to dissect regulatory mechanisms encoded by genetic
                      variants, advancing our understanding of gene expression
                      regulation and its implications for disease.},
      cin          = {B260},
      ddc          = {610},
      cid          = {I:(DE-He78)B260-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40890552},
      doi          = {10.1038/s41592-025-02805-0},
      url          = {https://inrepo02.dkfz.de/record/304284},
}