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Splicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants.

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cam.depositDate2022-01-06
cam.issuedOnline2021-12-28
dc.contributor.authorValenzuela-Palomo, Alberto
dc.contributor.authorBueno-Martínez, Elena
dc.contributor.authorSanoguera-Miralles, Lara
dc.contributor.authorLorca, Víctor
dc.contributor.authorFraile-Bethencourt, Eugenia
dc.contributor.authorEsteban-Sánchez, Ada
dc.contributor.authorGómez-Barrero, Susana
dc.contributor.authorCarvalho, Sara
dc.contributor.authorAllen, Jamie
dc.contributor.authorGarcía-Álvarez, Alicia
dc.contributor.authorPérez-Segura, Pedro
dc.contributor.authorDorling, Leila
dc.contributor.authorEaston, Douglas
dc.contributor.authorDevilee, Peter
dc.contributor.authorVreeswijk, Maaike Pg
dc.contributor.authorde la Hoya, Miguel
dc.contributor.authorVelasco, Eladio A
dc.contributor.orcidEaston, Douglas [0000-0003-2444-3247]
dc.contributor.orcidde la Hoya, Miguel [0000-0002-8113-1410]
dc.contributor.orcidVelasco, Eladio A [0000-0002-9682-5589]
dc.date.accessioned2022-01-07T00:32:05Z
dc.date.available2022-01-07T00:32:05Z
dc.date.issued2021-11-30
dc.date.updated2022-01-06T15:07:19Z
dc.description.abstractPALB2 loss-of-function variants confer high risk of developing breast cancer. Here we present a systematic functional analysis of PALB2 splice-site variants detected in approximately 113,000 women in the large-scale sequencing project Breast Cancer After Diagnostic Gene Sequencing (BRIDGES; https://bridges-research.eu/). Eighty-two PALB2 variants at the intron-exon boundaries were analyzed with MaxEntScan. Forty-two variants were selected for the subsequent splicing functional assays. For this purpose, three splicing reporter minigenes comprising exons 1-12 were constructed. The 42 potential spliceogenic variants were introduced into the minigenes by site-directed mutagenesis and assayed in MCF-7/MDA-MB-231 cells. Splicing anomalies were observed in 35 variants, 23 of which showed no traces or minimal amounts of the expected full-length transcripts of each minigene. More than 30 different variant-induced transcripts were characterized, 23 of which were predicted to truncate the PALB2 protein. The pathogenicity of all variants was interpreted according to an in-house adaptation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) variant classification scheme. Up to 23 variants were classified as pathogenic/likely pathogenic. Remarkably, three ±1,2 variants (c.49-2A>T, c.108+2T>C, and c.211+1G>A) were classified as variants of unknown significance, as they produced significant amounts of either in-frame transcripts of unknown impact on the PALB2 protein function or the minigene full-length transcripts. In conclusion, we have significantly contributed to the ongoing effort of identifying spliceogenic variants in the clinically relevant PALB2 cancer susceptibility gene. Moreover, we suggest some approaches to classify the findings in accordance with the ACMG-AMP rationale. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
dc.format.mediumPrint-Electronic
dc.identifier.doi10.17863/CAM.79711
dc.identifier.eissn1096-9896
dc.identifier.issn0022-3417
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/332266
dc.language.isoeng
dc.publisherWiley
dc.publisher.departmentDepartment of Public Health And Primary Care, Cancer Genetic Epidemiology
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectPALB2
dc.subjectVUS
dc.subjectaberrant splicing
dc.subjectbreast cancer
dc.subjectclinical interpretation
dc.subjectfunctional assay
dc.subjectminigene
dc.subjectsplicing
dc.subjectsusceptibility genes
dc.titleSplicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants.
dc.typeArticle
dcterms.dateAccepted2021-11-26
prism.publicationDate2021
prism.publicationNameJ Pathol
pubs.funder-project-idEuropean Commission Horizon 2020 (H2020) Societal Challenges (634935)
pubs.licence-display-nameApollo Repository Deposit Licence Agreement
pubs.licence-identifierapollo-deposit-licence-2-1
rioxxterms.typeJournal Article/Review
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1002/path.5839

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