title: Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants.
abstract: Assessing the impact of variants of unknown significance (VUS) on splicing is a key issue in molecular diagnosis. This impact can be predicted by in silico tools, but proper evaluation and user guidelines are lacking. To fill this gap, we embarked upon the largest BRCA1 and BRCA2 splice study to date by testing 272 VUSs (327 analyses) within the BRCA splice network of Unicancer. All these VUSs were analyzed by using six tools (splice site prediction by neural network, splice site finder (SSF), MaxEntScan (MES), ESE finder, relative enhancer and silencer classification by unanimous enrichment, and human splicing finder) and the predictions obtained were compared with transcript analysis results. Combining MES and SSF gave 96% sensitivity and 83% specificity for VUSs occurring in the vicinity of consensus splice sites, that is, the surrounding 11 and 14 bases for the 5' and 3' sites, respectively. This study was also an opportunity to define guidelines for transcript analysis along with a tentative classification of splice variants. The guidelines drawn from this large series should be useful for the whole community, particularly in the context of growing sequencing capacities that require robust pipelines for variant interpretation.
authors.affiliation: Service de Génétique, Institut Curie et Université Paris Descartes, Sorbonne Paris Cité, Paris, France. claude.houdayer@curie.net
authors.forename: Claude
authors.initials: C
authors.lastname: Houdayer
authors.forename: Virginie
authors.initials: V
authors.lastname: Caux-Moncoutier
authors.forename: Sophie
authors.initials: S
authors.lastname: Krieger
authors.forename: Michel
authors.initials: M
authors.lastname: Barrois
authors.forename: Françoise
authors.initials: F
authors.lastname: Bonnet
authors.forename: Violaine
authors.initials: V
authors.lastname: Bourdon
authors.forename: Myriam
authors.initials: M
authors.lastname: Bronner
authors.forename: Monique
authors.initials: M
authors.lastname: Buisson
authors.forename: Florence
authors.initials: F
authors.lastname: Coulet
authors.forename: Pascaline
authors.initials: P
authors.lastname: Gaildrat
authors.forename: Cédrick
authors.initials: C
authors.lastname: Lefol
authors.forename: Mélanie
authors.initials: M
authors.lastname: Léone
authors.forename: Sylvie
authors.initials: S
authors.lastname: Mazoyer
authors.forename: Danielle
authors.initials: D
authors.lastname: Muller
authors.forename: Audrey
authors.initials: A
authors.lastname: Remenieras
authors.forename: Françoise
authors.initials: F
authors.lastname: Révillion
authors.forename: Etienne
authors.initials: E
authors.lastname: Rouleau
authors.forename: Joanna
authors.initials: J
authors.lastname: Sokolowska
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Vert
authors.forename: Rosette
authors.initials: R
authors.lastname: Lidereau
authors.forename: Florent
authors.initials: F
authors.lastname: Soubrier
authors.forename: Hagay
authors.initials: H
authors.lastname: Sobol
authors.forename: Nicolas
authors.initials: N
authors.lastname: Sevenet
authors.forename: Brigitte
authors.initials: B
authors.lastname: Bressac-de Paillerets
authors.forename: Agnès
authors.initials: A
authors.lastname: Hardouin
authors.forename: Mario
authors.initials: M
authors.lastname: Tosi
authors.forename: Olga M
authors.initials: OM
authors.lastname: Sinilnikova
authors.forename: Dominique
authors.initials: D
authors.lastname: Stoppa-Lyonnet
mesh_terms: D019313:BRCA1 Protein / Q000235:genetics*; D024682:BRCA2 Protein / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005260:Female; D006801:Humans; D057089:Pathology, Molecular / Q000379:methods* / Q000592:standards*; D012326:RNA Splicing / Q000235:genetics*
chemical_list: D019313:BRCA1 Protein; D024682:BRCA2 Protein