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Reporting of somatic variants in clinical cancer care: recommendations of the Swiss Society of Molecular Pathology

Authors: Christinat, Yann; Hamelin, Baptiste; Alborelli, Ilaria; Angelino, Paolo; Barbié, Valérie; Bisig, Bettina; Dawson, Heather; +13 Authors

Reporting of somatic variants in clinical cancer care: recommendations of the Swiss Society of Molecular Pathology

Abstract

AbstractSomatic variant testing through next-generation sequencing (NGS) is well integrated into Swiss molecular pathology laboratories and has become a standard diagnostic method for numerous indications in cancer patient care. Currently, there is a wide variation in reporting practices within our country, and as patients move between different hospitals, it is increasingly necessary to standardize NGS reports to ease their reinterpretation. Additionally, as many different stakeholders—oncologists, hematologists, geneticists, pathologists, and patients—have access to the NGS report, it needs to contain comprehensive and detailed information in order to answer the questions of experts and avoid misinterpretation by non-experts. In 2017, the Swiss Institute of Bioinformatics conducted a survey to assess the differences in NGS reporting practices across ten pathology institutes in Switzerland. The survey examined 68 reporting items and identified 48 discrepancies. Based on these findings, the Swiss Society of Molecular Pathology initiated a Delphi method to reach a consensus on a set of recommendations for NGS reporting. Reports should include clinical information about the patient and the diagnosis, technical details about the sample and the test performed, and a list of all clinically relevant variants and variants of uncertain significance. In the absence of a consensus on an actionability scheme, the five-class pathogenicity scheme proposed by the ACMG/AMP guideline must be included in the reports. The Swiss Society of Molecular Pathology recognizes the importance of including clinical actionability in the report and calls on the European community of molecular pathologists and oncologists to reach a consensus on this issue.

Keywords

Consensus, Genetic Variation, High-Throughput Nucleotide Sequencing, 610 Medicine & health, Swiss Society of Molecular Pathology, 616.07, Guidelines, NGS reporting, 2734 Pathology and Forensic Medicine, 1307 Cell Biology, 10049 Institute of Pathology and Molecular Pathology, Neoplasms, 1312 Molecular Biology, Humans, Original Article, Genetic Testing, Pathology, Molecular, Humans; Consensus; Genetic Testing/methods; Genetic Variation/genetics; High-Throughput Nucleotide Sequencing; Neoplasms/genetics; Neoplasms/pathology; Neoplasms/diagnosis; Pathology, Molecular/standards; Societies, Medical/standards; Switzerland; Cancer; Guidelines; NGS reporting; Swiss Society of Molecular Pathology, Societies, Medical, Switzerland, Cancer

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
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Average
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Cancer Research