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Roberto Pappesch

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    Lunch & Poster Display session (ID 58)

    • Event: ELCC 2019
    • Type: Poster Display session
    • Track:
    • Presentations: 1
    • Moderators:
    • Coordinates: 4/11/2019, 12:30 - 13:00, Hall 1
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      27P - Comparison of three different gene panels for determination of tumor mutational burden by next generation sequencing (ID 371)

      12:30 - 13:00  |  Presenting Author(s): Roberto Pappesch

      • Abstract


      The introduction of cancer immunotherapies has improved survival rates of certain groups of patients. According to first studies, that used whole exome sequencing, the accumulation of tumor neoantigens and therefore tumor mutational burden (TMB) could be used as molecular marker for prediction. In this study, large gene panel assays of different suppliers were tested on 28 DNA samples derived from formalin fixed, paraffin-embedded (FFPE) tumor tissue with regard to implementation in routine diagnostics.

      a9ded1e5ce5d75814730bb4caaf49419 Methods

      After DNA isolation the following kits of three different suppliers have been used for library preparation: A custom SureSelectXTHS Target Assay (Agilent Technologies, Santa Clara, CA, USA), the NEOplus v2 RUO assay (New Oncology, Cologne, Germany) and the TruSight Oncology 500 kit (Ilumina, San Diego, CA, USA, TSO500) following manufacturers’ protocol. All assays were sequenced on the NextSeq 500 system (Illumina). For quality control the TapeStation 4200 System (Agilent Technologies) was used.

      20c51b5f4e9aeb5334c90ff072e6f928 Results

      All kits tested showed different final concentration after library preparation. Fragment sizes were as expected and libraries were suitable for sequencing. In terms of time needed for library preparation the NEOplus v2 RUO assay was the most laborious kit. The resulting TMB-scores showed similar picture for all kits and samples tested. For all panels access to the results of the sequenced genes and detected variants is possible. Data access differs between the developers in terms of availability and manageability. Since not all kits use unique molecular identifiers (UMI) the filtering capabilities are different.

      fd69c5cf902969e6fb71d043085ddee6 Conclusions

      In this study, three different gene panel assays for TMB-determination were tested. All panels provided a similar TMB-score for the analysed samples. In terms of usage and in respect of implementation in routine diagnostics, time and efficiency are the most important parameters. Here, the TSO500 kit and the SureSelectXTHS Target Assay showed the best potential for the use in routine diagnostics.

      b651e8a99c4375feb982b7c2cad376e9 Legal entity responsible for the study

      The authors.

      213f68309caaa4ccc14d5f99789640ad Funding

      Has not received any funding.

      682889d0a1d3b50267a69346a750433d Disclosure

      C. Heydt: Honoraria: AstraZeneca, BMS, Illumina. S. Merkelbach-Bruse: Honoraria: AstraZeneca; Advisory role: AstraZeneca, Roche. All other authors have declared no conflicts of interest.