Formalin-Fixed, Paraffin-Embedded–Targeted Locus Capture

Journal of Molecular Diagnostics, vol. 25, pp. 758–770

Abstract

Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded-targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. We evaluated the utility of FFPE-TLC in bone and soft tissue tumor diagnostics. FFPE-TLC sequencing was successfully applied on noncalcified and decalcified FFPE samples (n = 44) and control samples (n = 19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples, and none was identified in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed due to either detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.

Authors 16

1. Ellen Stelloo

   Cergentis (Netherlands)

   Affiliation as printed

   Cergentis BV, Utrecht, the Netherlands

2. Ruud W. J. Meijers

   University Medical Center Utrecht

   Affiliation as printed

   Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands

   University Medical Center Utrecht, Department of Pathology, Utrecht, the Netherlands

3. Joost F. Swennenhuis

   Cergentis (Netherlands)

   Affiliation as printed

   Cergentis BV, Utrecht, the Netherlands

4. Amin Allahyar

   Royal Netherlands Academy of Arts and Sciences · University Medical Center Utrecht · Oncode Institute

   Affiliation as printed

   Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands

   Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands

5. Karima Hajo

   Cergentis (Netherlands)

   Affiliation as printed

   Cergentis BV, Utrecht, the Netherlands

6. Mario Cangiano

   Cergentis (Netherlands)

   Affiliation as printed

   Cergentis BV, Utrecht, the Netherlands

7. Wendy W.J. de Leng

   University Medical Center Utrecht

   Affiliation as printed

   Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands

   University Medical Center Utrecht, Department of Pathology, Utrecht, the Netherlands

8. Sjoerd van Helvert

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands

   Radboud University Medical Center, Department of Pathology, Nijmegen, the Netherlands

9. Joni Van der Meulen

   Ghent University Hospital

   Affiliation as printed

   Molecular Diagnostics, Ghent University Hospital, Ghent, Belgium

   Ghent University Hospital, Molecular Diagnostics, Ghent, Belgium

10. David Creytens

    Ghent University Hospital

    Affiliation as printed

    Department of Pathology, Ghent University Hospital, Ghent, Belgium

    Ghent University Hospital, Department of Pathology, Ghent, Belgium

11. Léon C.L.T. van Kempen

    University Medical Center Groningen · University of Antwerp · University of Groningen · Antwerp University Hospital

    Affiliation as printed

    Department of Pathology, University Hospital Antwerp, University of Antwerp, Antwerp, Belgium; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands

    University of Antwerp, University Hospital Antwerp, Department of Pathology, Antwerp, Belgium

    University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands

12. Anne‐Marie Cleton-Jansen Aachen Department of Pathology, Leiden University Medical Center Department of Pathology, Leiden

    Leiden University Medical Center

    Affiliation as printed

    Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands

    Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands

13. Judith V.M.G. Bovée Aachen Department of Pathology, Leiden University Medical Center Department of Pathology, Leiden

    Leiden University Medical Center

    Affiliation as printed

    Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands

    Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands

14. Wouter L. de Laat

    Royal Netherlands Academy of Arts and Sciences · University Medical Center Utrecht · Oncode Institute

    Affiliation as printed

    Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands

    Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands

15. Erik Splinter

    Cergentis (Netherlands)

    Affiliation as printed

    Cergentis BV, Utrecht, the Netherlands

16. Harma Feitsma corresponding

    Cergentis (Netherlands)

    Affiliation as printed

    Cergentis BV, Utrecht, the Netherlands. Electronic address: harma.feitsma@cergentis.com

    Cergentis BV, Utrecht, the Netherlands