A likelihood ratio approach for utilizing case-control data in the clinical classification of rare sequence variants: application to
ACMG/AMP
BRCA
PS4
VUS
case-control
likelihood ratio
variant classification
Journal
Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429
Informations de publication
Date de publication:
2023
2023
Historique:
medline:
1
1
2023
pubmed:
1
1
2023
entrez:
10
5
2024
Statut:
ppublish
Résumé
A large number of variants identified through clinical genetic testing in disease susceptibility genes, are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion), can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analyses of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of
Identifiants
pubmed: 38725546
doi: 10.1155/2023/9961341
pmc: PMC11080979
pii:
doi:
Substances chimiques
BRCA2 Protein
0
BRCA1 Protein
0
BRCA1 protein, human
0
BRCA2 protein, human
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM