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@ARTICLE{Lee:125288,
      author       = {J. S. Lee and R. S. Mackie and T. Harrison and B. Shariat
                      and T. Kind and T. Kehl$^*$ and M. Löchelt$^*$ and C.
                      Boucher and S. VandeWoude},
      title        = {{T}argeted {E}nrichment for {P}athogen {D}etection and
                      {C}haracterization in {T}hree {F}elid {S}pecie},
      journal      = {Journal of clinical microbiology},
      volume       = {55},
      number       = {6},
      issn         = {1098-660X},
      address      = {Washington, DC},
      publisher    = {Soc.},
      reportid     = {DKFZ-2017-01426},
      pages        = {1658 - 1670},
      year         = {2017},
      abstract     = {Traditional diagnostic assays often lack sensitivity and
                      can be difficult to multiplex across many pathogens.
                      Next-generation sequencing (NGS) can overcome some of these
                      problems but has limited application in the detection of
                      low-copy-number pathogens in complex samples. Targeted
                      genome capture (TGC) utilizes oligonucleotide probes to
                      enrich specific nucleic acids in heterogeneous extracts and
                      can therefore increase the proportion of NGS reads for
                      low-abundance targets. While earlier studies have
                      demonstrated the utility of this technology for detection of
                      novel pathogens in human clinical samples, the capacity and
                      practicality of TGC-NGS in a veterinary diagnostic setting
                      have not yet been evaluated. Here we report the use of
                      TGC-NGS assays for the detection and characterization of
                      diverse feline pathogen taxa. We detected 31 pathogens
                      comprising nine pathogen taxa in 28 felid samples analyzed.
                      This included 20 pathogens detected via traditional PCR and
                      11 additional pathogens that had not been previously
                      detected in the same samples. Most of the pathogens detected
                      were sequenced at sufficient breadth and depth to
                      confidently classify them at the species or subspecies
                      level. Target nucleic acids were enriched from a low of
                      58-fold to 56 million-fold relative to host nucleic acids.
                      Despite the promising performance of these assays, a number
                      of pathogens detected by conventional PCR or serology were
                      not isolated by TGC-NGS, suggesting that further validation
                      is required before this technology can be used in lieu of
                      quality-controlled standard assays. We conclude that TGC-NGS
                      offers great potential as a broad multiplex pathogen
                      characterization assay in veterinary diagnostic and research
                      settings.},
      cin          = {F020 / V155},
      ddc          = {570},
      cid          = {I:(DE-He78)F020-20160331 / I:(DE-He78)V155-20160331},
      pnm          = {316 - Infections and cancer (POF3-316)},
      pid          = {G:(DE-HGF)POF3-316},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:28330894},
      pmc          = {pmc:PMC5442522},
      doi          = {10.1128/JCM.01463-16},
      url          = {https://inrepo02.dkfz.de/record/125288},
}