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@ARTICLE{Geisenberger:299467,
      author       = {C. Geisenberger$^*$ and E. Chimal and P. Jurmeister$^*$ and
                      F. Klauschen$^*$},
      title        = {{A} cost-effective and scalable approach for {DNA}
                      extraction from {FFPE} tissues.},
      journal      = {Biology methods $\&$ protocols},
      volume       = {10},
      number       = {1},
      issn         = {2396-8923},
      address      = {Oxford},
      publisher    = {Oxford University Press},
      reportid     = {DKFZ-2025-00427},
      pages        = {bpaf003},
      year         = {2025},
      abstract     = {Genomic profiling of cancer plays an increasingly vital
                      role for diagnosis and therapy planning. In addition,
                      research of novel diagnostic applications such as DNA
                      methylation profiling requires large training and validation
                      cohorts. Currently, most diagnostic cases processed in
                      pathology departments are stored as formalin-fixed and
                      paraffin embedded tissue blocks (FFPE). Consequently, there
                      is a growing demand for high-throughput extraction of
                      nucleic acids from FFPE tissue samples. While proprietary
                      kits are available, they are expensive and offer little
                      flexibility. Here, we present ht-HiTE, a high-throughput
                      implementation of a recently published and highly efficient
                      DNA extraction protocol. This approach enables manual and
                      automated processing of 96-well plates with a liquid
                      handler, offers two options for purification and utilizes
                      off-the-shelf reagents. Finally, we show that NGS and DNA
                      methylation microarray data obtained from DNA processed with
                      ht-HiTE are of equivalent quality as compared to a manual,
                      kit-based approach.},
      keywords     = {DNA extraction (Other) / DNA methylation (Other) / FFPE
                      (Other) / NGS (Other) / exome sequencing (Other) / molecular
                      pathology (Other)},
      cin          = {MU01},
      ddc          = {570},
      cid          = {I:(DE-He78)MU01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39995602},
      pmc          = {pmc:PMC11849955},
      doi          = {10.1093/biomethods/bpaf003},
      url          = {https://inrepo02.dkfz.de/record/299467},
}