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Shallow whole-genome sequencing: a useful, easy to apply molecular technique for CNA detection on FFPE tumor tissue—a glioma-driven study

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Abstract

Copy number alterations (CNAs) have increasingly become part of the diagnostic algorithm of glial tumors. Alterations such as homozygous deletion of CDKN2A/B, 7 +/ 10 - chromosome copy number changes or EGFR amplification are predictive of a poor prognosis. The codeletion of chromosome arms 1p and 19q, typically associated with oligodendroglioma, implies a more favorable prognosis. Detection of this codeletion by the current diagnostic standard, being fluorescence in situ hybridization (FISH), is sometimes however subject to technical and interpretation problems. In this study, we evaluated CNA detection by shallow whole-genome sequencing (sWGS) as an inexpensive, complementary molecular technique. A cohort of 36 glioma tissue samples, enriched with “difficult” and “ambiguous” cases, was analyzed by sWGS. sWGS results were compared with FISH assays of chromosomes 1p and 19q. In addition, CNAs relevant to glioblastoma diagnosis were explored. In 4/36 samples, EGFR (7p11.2) amplifications and homozygous loss of CDKN2A/B were identified by sWGS. Six out of 8 IDH–wild-type glioblastomas demonstrated a prognostic chromosome 7/chromosome 10 signature. In 11/36 samples, local interstitial and terminal 1p/19q alterations were detected by sWGS, implying that FISH’s targeted nature might promote false arm–level extrapolations. In this cohort, differences in overall survival between patients with and without codeletion were better pronounced by the sequencing-based distinction (likelihood ratio of 7.48) in comparison to FISH groupings (likelihood ratio of 0.97 at diagnosis and 1.79 ± 0.62 at reobservation), suggesting sWGS is more accurate than FISH. We recognized adverse effects of tissue block age on FISH signals. In addition, we show how sWGS reveals relevant aberrations beyond the 1p/19q state, such as EGFR amplification, combined gain of chromosome 7 and loss of chromosome 10, and homozygous loss of CDKN2A/B. The findings presented by this study might stimulate implementation of sWGS as a complementary, easy to apply technique for copy number detection.

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Data supporting this study are available within the published article or supplementary information or are available from the corresponding author on reasonable request.

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Acknowledgements

We thank Bart Matthys and Lynn Supply for their critical advice and excellent technical assistance with FISH analysis.

Funding

This work was supported by Bijzonder Onderzoeksfonds (BE), Ghent University, in the form of a doctoral research grant (BOF.STA.2017.0002.01 to LR).

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Author notes

  1. Kim Van der Eecken, Malaïka Van der Linden and Lennart Raman contributed equally to this work.

Authors and Affiliations

  1. Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium

    Kim Van der Eecken, Malaïka Van der Linden, Lennart Raman, David Creytens, Liesbeth Ferdinande, Isabelle Rottiers, Bram Van Gaever, Koen Van de Vijver, Sofie Verbeke & Jo Van Dorpe

  2. Cancer Research Institute (CRIG), Ghent, Belgium

    Kim Van der Eecken, Malaïka Van der Linden, David Creytens, Liesbeth Ferdinande, Björn Menten, Isabelle Rottiers, Koen Van de Vijver, Nadine Van Roy, Sofie Verbeke & Jo Van Dorpe

  3. Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent, Belgium

    Malaïka Van der Linden, Lennart Raman, Björn Menten & Nadine Van Roy

  4. Department of Pathology, AZ Delta, Roeselare, Belgium

    Franceska Dedeurwaerdere

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

    Koen De Winne & Martin Lammens

  6. Department of Pathology, AZ Sint-Lucas, Ghent, Belgium

    Caroline Van den Broecke

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  1. Kim Van der Eecken
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Contributions

JVD had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. JVD performed study concept and design; FD, CVdB, DC, KDW, ML, NR, BM, LF, IR, KVdV, SV, JVD, MVdL, and KVdE performed data acquisition; LR and BVG carried out bioinformatic and statistical analysis; KVdE, LR, and MVdL provided interpretation of data and writing of the paper; all the authors read and approved the final paper.

Corresponding author

Correspondence to Jo Van Dorpe.

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This study was approved by the institutional ethics committee at Ghent University Hospital (BC-07259) and executed conforming with the principles of good clinical practice (ICH/GCP) and the Helsinki Declaration. The need for consent to participate was waived by the ethics committee.

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This work has not been published before, and it is not under consideration for publication anywhere else. Its publication has been approved by all authors.

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The authors declare no competing interests.

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Van der Eecken, K., Van der Linden, M., Raman, L. et al. Shallow whole-genome sequencing: a useful, easy to apply molecular technique for CNA detection on FFPE tumor tissue—a glioma-driven study. Virchows Arch 480, 677–686 (2022). https://doi.org/10.1007/s00428-022-03268-w

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