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Title: | Comparison of the ABC and ACMG systems for variant classification | Authors: | Houge, Gunnar Bratland, Eirik Aukrust, Ingvild Tveten, Kristian Žukauskaitė, Gabrielė Sansovic, Ivona Brea-Fernández, Alejandro J Mayer, Karin Paakkola, Teija McKenna, Caoimhe Wright, William Keckarević-Marković, Milica Lildballe, Dorte L Konecny, Michal Smol, Thomas Alhopuro, Pia Gouttenoire, Estelle Arnaud Obeid, Katharina Todorova, Albena Jankovic, Milena Lubieniecka, Joanna M Stojiljkovic, Maja Buisine, Marie-Pierre Haukanes, Bjørn Ivar Lorans, Marie Roomere, Hanno Petit, François M Haanpää, Maria K Beneteau, Claire Pérez, Belén Plaseska-Karanfilska, Dijana Rath, Matthias Fuhrmann, Nico Ferreira, Bibiana I Stephanou, Coralea Sjursen, Wenche Maver, Aleš Rouzier, Cécile Chirita-Emandi, Adela Gonçalves, João Kuek, Wei Cheng David Broly, Martin Haer-Wigman, Lonneke Thong, Meow-Keong Tae, Sok-Kun Hyblova, Michaela den Dunnen, Johan T Laner, Andreas |
Issue Date: | 22-May-2024 | Rank: | M21 | Publisher: | Nature Publishing Group | Journal: | European journal of human genetics : EJHG | Abstract: | The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known. |
URI: | https://biore.bio.bg.ac.rs/handle/123456789/7205 | ISSN: | 10184813 | DOI: | 10.1038/s41431-024-01617-8 |
Appears in Collections: | Journal Article |
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