Title :

Comparison of the ABC and ACMG systems for variant classification

Author(s) :

Houge, Gunnar [Auteur]
Haukeland University Hospital
Bratland, Eirik [Auteur]
Haukeland University Hospital
Aukrust, Ingvild [Auteur]
Haukeland University Hospital
Tveten, Kristian [Auteur]
Žukauskaitė, Gabrielė [Auteur]
Vilnius University [Vilnius]
Sansovic, Ivona [Auteur]
University of Zagreb
Brea-Fernández, Alejandro J. [Auteur]
CIBER de Enfermedades Raras (CIBERER)
Mayer, Karin [Auteur]
Paakkola, Teija [Auteur]
Mckenna, Caoimhe [Auteur]
Wright, William [Auteur]
Markovic, Milica Keckarevic [Auteur]
University of Belgrade [Belgrade]
Lildballe, Dorte L. [Auteur]
Aarhus University Hospital
Konecny, Michal [Auteur]
Trnava University
Smol, Thomas [Auteur]
Maladies Rares du Développement : Génétique, Régulation et Protéomique (RADEME) - ULR 7364
Institut de génétique médicale
Alhopuro, Pia [Auteur]
Helsinki University Hospital [Finland] [HUS]
Gouttenoire, Estelle Arnaud [Auteur]
Obeid, Katharina [Auteur]
Heidelberg University Hospital [Heidelberg]
Todorova, Albena [Auteur]
Jankovic, Milena [Auteur]
University of Belgrade [Belgrade]
Lubieniecka, Joanna M. [Auteur]
Ruhr University Bochum = Ruhr-Universität Bochum [RUB]
Stojiljkovic, Maja [Auteur]
University of Belgrade [Belgrade]
Buisine, Marie-Pierre [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Institut de Biochimie et Biologie Moléculaire [CHRU Lille]
Haukanes, Bjørn Ivar [Auteur]
Haukeland University Hospital
Lorans, Marie [Auteur]
Aarhus University Hospital
Roomere, Hanno [Auteur]
University of Tartu
Petit, François M. [Auteur]
Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] [UNICANCER/CAL]
Haanpää, Maria K. [Auteur]

Beneteau, Claire [Auteur]
Centre Hospitalier Universitaire de Bordeaux [CHU Bordeaux]
Pérez, Belén [Auteur]
Universidad Autónoma de Madrid [UAM]
Plaseska-Karanfilska, Dijana [Auteur]
Macedonian Academy of Sciences and Arts [Skopje, North Macedonia] [MASA]
Rath, Matthias [Auteur]
Medical School Hamburg
Universität Greifswald - University of Greifswald
Fuhrmann, Nico [Auteur]

Ferreira, Bibiana I. [Auteur]
University of Algarve [Portugal]
Stephanou, Coralea [Auteur]
Cyprus Institute of Neurology and Genetics
Sjursen, Wenche [Auteur]
St. Olavs Hospital HF [St. Olav's University Hospital]
Maver, Aleš [Auteur]
University Medical Centre Ljubljana [Ljubljana, Slovenia] [UMCL]
Rouzier, Cécile [Auteur]
Université Côte d'Azur [UniCA]
Centre Hospitalier Universitaire de Nice [CHU Nice]
Chirita-Emandi, Adela [Auteur]
Victor Babeş University of Medicine and Pharmacy [UMFT]
Gonçalves, João [Auteur]
Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] [INSA]
Kuek, Wei Cheng David [Auteur]
National University Hospital [Singapore] [NUH]
Broly, Martin [Auteur]

Haer-Wigman, Lonneke [Auteur]
Radboud University Medical Center [Nijmegen]
Thong, Meow-Keong [Auteur]
University of Malaya = Universiti Malaya [Kuala Lumpur, Malaisie] [UM]
Tae, Sok-Kun [Auteur]
Faculty of Medicine, University of Malaya [Kuala Lumpur, Malaisie]
Hyblova, Michaela [Auteur]
Slovak Medical University of Bratislava [SMU]
Den Dunnen, Johan T. [Auteur]
Leiden University Medical Center [LUMC]
Laner, Andreas [Auteur]

Journal title :

European Journal of Human Genetics

Abbreviated title :

Eur J Hum Genet

Volume number :

32

Pages :

858–863

Publisher :

Nature Publishing Group

Publication date :

2024-05-22

ISSN :

1018-4813

English keyword(s) :

Genetic predisposition to disease
Genetic testing

HAL domain(s) :

Sciences du Vivant [q-bio]

English abstract : [en]

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 ...
Show more >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.Show less >

Language :

Anglais

Audience :

Internationale

Popular science :

Non

Administrative institution(s) :

Université de Lille
CHU Lille

Collections :

• Cancer Heterogeneity, Plasticity and Resistance to Therapies (CANTHER) - UMR 9020 - UMR 1277
• Maladies Rares du Développement : Génétique, Régulation et Protéomique (RADEME) - ULR 7364

Submission date :

2024-06-26T21:08:52Z
2024-07-12T09:15:13Z