% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Truong:301368,
      author       = {T. T. Truong and K. Mikloska and J. Sum and M. Oberländer
                      and N. von Bubnoff and L. Christiansen and S. Tornow and S.
                      Derer and F. Janke$^*$ and H. Sültmann$^*$ and S. Zeissig
                      and M. Linnebacher and C. Schafmayer and M. Lehnert and T.
                      Hutzenlaub and N. Paust and P. Juelg},
      title        = {{C}oupling {I}mmunoprecipitation with {M}ultiplexed
                      {D}igital {PCR} for {C}ell-{F}ree {DNA} {M}ethylation
                      {D}etection in {S}mall {P}lasma {V}olumes of {E}arly-{O}nset
                      {C}olorectal {C}ancer.},
      journal      = {Analytical chemistry},
      volume       = {97},
      number       = {21},
      issn         = {0003-2700},
      address      = {Columbus, Ohio},
      publisher    = {American Chemical Society},
      reportid     = {DKFZ-2025-01006},
      pages        = {11259-11268},
      year         = {2025},
      note         = {2025 Jun 3;97(21):11259-11268},
      abstract     = {Colorectal cancer (CRC) remains a major global health
                      challenge, with an increasing incidence of early-onset cases
                      among young adults. Targeted analysis of cell-free DNA
                      (cfDNA) methylation in blood has emerged as a promising
                      minimally invasive diagnostic approach. While digital PCR
                      (dPCR) offers high sensitivity and low turnaround times,
                      conventional bisulfite-based dPCR assays require large
                      plasma volumes due to cfDNA degradation, limiting clinical
                      feasibility. To overcome this limitation, we developed a
                      bisulfite-free, low-plasma-volume assay by coupling
                      cell-free methylated DNA immunoprecipitation (cfMeDIP) with
                      multiplexed dPCR for methylation detection. Assays were
                      designed for CRC targets based on publicly available
                      bisulfite-based plasma data and optimized for native,
                      bisulfite-untreated cfDNA. The cfMeDIP-dPCR assays were
                      first developed and optimized on circulating tumor DNA
                      surrogates derived from HCT116 cells and subsequently
                      validated in a pilot study, including 32 early-onset CRC
                      (EO-CRC) patients and 29 non-CRC individuals. Methylation
                      ratios, defined as the proportion of methylated to total
                      cfDNA copies per marker, served as a diagnostic indicator.
                      Three out of four selected markers (SEPT9, KCNQ5, and
                      C9orf50) were successfully adapted, with significantly
                      higher methylation ratios (p ≤ 0.001) in the EO-CRC
                      cohort. KCNQ5 demonstrated the highest diagnostic
                      performance, achieving an $85\%$ sensitivity at a $90\%$
                      specificity, with methylation ratios correlating with the
                      tumor stage. This study presents the first cfMeDIP-dPCR
                      approach, demonstrating its potential as a sensitive liquid
                      biopsy assay. Requiring only 0.5 mL of plasma, i.e., more
                      than 20 times less than a sensitivity-matched
                      bisulfite-based assay, cfMeDIP-dPCR facilitates clinical
                      implementation for CRC and other diseases with epigenetic
                      signatures.},
      cin          = {B063},
      ddc          = {540},
      cid          = {I:(DE-He78)B063-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40380352},
      doi          = {10.1021/acs.analchem.5c01361},
      url          = {https://inrepo02.dkfz.de/record/301368},
}