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Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel

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Department of Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium
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Department of Clinical Biology, University Hospital Antwerp, 2650 Edegem, Belgium
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Center for Human Genetics, University Hospital Leuven, 3000 Leuven, Belgium
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Laboratory of Molecular Hematology, Ghent University Hospital, 9000 Ghent, Belgium
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AZ Sint-Jan Brugge-Oostende AV, Department of Laboratory Medicine, 8000 Brugge, Belgium
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Department of Laboratory Medicine, AZ Delta Hospital, 8800 Roeselare, Belgium
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Molecular Diagnostics, Ghent University Hospital, 9000 Ghent, Belgium
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Clinical Laboratory, AZ St-Lucas Hospital, 9000 Ghent, Belgium
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Department of Pathology, University Hospital Antwerp, 2650 Edegem, Belgium
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Laboratory of Pathology, University Hospital Leuven, 3000 Leuven, Belgium
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Cancer Centre, Sciensano, 1050 Brussels, Belgium
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Department of Quality Laboratories, Sciensano, 1050 Brussels, Belgium
*
Author to whom correspondence should be addressed.
Board member MolecularDiagnostics.be (https://moleculardiagnostics.be/).
Cancers 2019, 11(12), 2030; https://doi.org/10.3390/cancers11122030
Received: 13 November 2019 / Revised: 3 December 2019 / Accepted: 5 December 2019 / Published: 16 December 2019
(This article belongs to the Special Issue Targeting Solid Tumors)
In most diagnostic laboratories, targeted next-generation sequencing (NGS) is currently the default assay for the detection of somatic variants in solid as well as haematological tumours. Independent of the method, the final outcome is a list of variants that differ from the human genome reference sequence of which some may relate to the establishment of the tumour in the patient. A critical point towards a uniform patient management is the assignment of the biological contribution of each variant to the malignancy and its subsequent clinical impact in a specific malignancy. These so-called biological and clinical classifications of somatic variants are currently not standardized and are vastly dependent on the subjective analysis of each laboratory. This subjectivity can thus result in a different classification and subsequent clinical interpretation of the same variant. Therefore, the ComPerMed panel of Belgian experts in cancer diagnostics set up a working group with the goal to harmonize the biological classification and clinical interpretation of somatic variants detected by NGS. This effort resulted in the establishment of a uniform, two-level classification workflow system that should enable high consistency in diagnosis, prognosis, treatment and follow-up of cancer patients. Variants are first classified into a tumour-independent biological five class system and subsequently in a four tier ACMG clinical classification. Here, we describe the ComPerMed workflow in detail including examples for each step of the pipeline. Moreover, this workflow can be implemented in variant classification software tools enabling automatic reporting of NGS data, independent of panel, method or analysis software. View Full-Text
Keywords: cancer; classification; guideline; NGS; variant cancer; classification; guideline; NGS; variant
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Figure 1

MDPI and ACS Style

Froyen, G.; Le Mercier, M.; Lierman, E.; Vandepoele, K.; Nollet, F.; Boone, E.; Van der Meulen, J.; Jacobs, K.; Lambin, S.; Vander Borght, S.; Van Valckenborgh, E.; Antoniou, A.; Hébrant, A. Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel. Cancers 2019, 11, 2030. https://doi.org/10.3390/cancers11122030

AMA Style

Froyen G, Le Mercier M, Lierman E, Vandepoele K, Nollet F, Boone E, Van der Meulen J, Jacobs K, Lambin S, Vander Borght S, Van Valckenborgh E, Antoniou A, Hébrant A. Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel. Cancers. 2019; 11(12):2030. https://doi.org/10.3390/cancers11122030

Chicago/Turabian Style

Froyen, Guy; Le Mercier, Marie; Lierman, Els; Vandepoele, Karl; Nollet, Friedel; Boone, Elke; Van der Meulen, Joni; Jacobs, Koen; Lambin, Suzan; Vander Borght, Sara; Van Valckenborgh, Els; Antoniou, Aline; Hébrant, Aline. 2019. "Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel" Cancers 11, no. 12: 2030. https://doi.org/10.3390/cancers11122030

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