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Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA repor

AuthorsLopez Periolo, Irene; Leman, Raphaël; Behar, Raquel; Lattimore, Vanessa; Pearson, John F.; Castéra, Laurent; Martins, Alexandra; Vaur, Dominique; Goardon, Nicolas; Davy, Grégoire; Garre, Pilar; García-Barberán, Vanesa; Llovet, Patricia; Pérez-Segura, Pedro; Díaz Rubio, Eduardo; Caldés, Trinidad; Hruska, Kathleen S.; Hsuan, Vickie; Wu, Sitao; Pesaran, Tina; Karam, Rachid; Vallon-Christersson, Johan; Borg, Ake; KConFab Investigators; Valenzuela-Palomo, Alberto; Velasco, Eladio ; Southey, Melissa; Vreeswijk, Maaike P. G.; Devilee, Peter; Kvist, Anders; Spurdle, Amanda B.; Walker, Logan C.; Krieger, Sophie; Hoya, Miguel de la
Issue Date2019
PublisherBMJ Publishing Group
CitationJournal of Medical Genetics 56(7): 453-460 (2019)
Abstract[Background] PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2—without incurring overprediction—is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines.
[Methods] Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212–1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant.
[Results] We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies.
[Conclusions] PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.
DescriptionCancer genetics: Original article.
Publisher version (URL)http://dx.doi.org/10.1136/jmedgenet-2018-105834
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