Repository logo
 

Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants.

Simple item page
cam.depositDate2022-06-30
cam.issuedOnline2022-06-18
cam.orpheus.success2022-07-04 - Embargo set during processing via Fast-track
dc.contributor.authorBueno-Martínez, Elena
dc.contributor.authorSanoguera-Miralles, Lara
dc.contributor.authorValenzuela-Palomo, Alberto
dc.contributor.authorEsteban-Sánchez, Ada
dc.contributor.authorLorca, Víctor
dc.contributor.authorLlinares-Burguet, Inés
dc.contributor.authorAllen, Jamie
dc.contributor.authorGarcía-Álvarez, Alicia
dc.contributor.authorPérez-Segura, Pedro
dc.contributor.authorDurán, Mercedes
dc.contributor.authorEaston, Douglas
dc.contributor.authorDevilee, Peter
dc.contributor.authorVreeswijk, Maaike PG
dc.contributor.authorde la Hoya, Miguel
dc.contributor.authorVelasco-Sampedro, Eladio A
dc.contributor.orcidEaston, Douglas [0000-0003-2444-3247]
dc.contributor.orcidVelasco-Sampedro, Eladio A [0000-0002-9682-5589]
dc.date.accessioned2022-07-04T23:30:06Z
dc.date.available2022-07-04T23:30:06Z
dc.date.issued2022-06-18
dc.date.updated2022-06-30T13:51:05Z
dc.description.abstractThe ataxia telangiectasia-mutated (ATM) protein is a major coordinator of the DNA damage response pathway. ATM loss-of-function variants are associated with two-fold increased breast cancer risk. We aimed at identifying and classifying spliceogenic ATM variants detected in subjects of the large-scale sequencing project BRIDGES. A total of 381 variants at the intron-exon boundaries were identified, 128 of which were predicted to be spliceogenic. After further filtering, we ended up selecting 56 variants for splicing analysis. Four functional minigenes (mgATM) spanning exons 4-9, 11-17, 25-29 and 49-52 were constructed in the splicing plasmid pSAD. Selected variants were genetically engineered into the four constructs and assayed in MCF-7/HeLa cells. Forty-eight variants (85.7%) impaired splicing, 32 of which did not show any trace of the full-length (FL)-transcript. A total of 43 transcripts were identified where the most prevalent event was exon/multi-exon skipping. Twenty-seven transcripts were predicted to truncate the ATM protein. A tentative ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme that integrates mgATM data allowed us to classify 29 ATM variants as pathogenic/likely pathogenic and 7 variants as likely benign. Interestingly, the likely pathogenic variant c.1898+2T>G generated 13% of the minigene FL-transcript due to the use of a non-canonical GG-5'-splice-site (0.014% of human donor sites). Circumstantial evidence in three ATM variants (leakiness uncovered by our mgATM analysis together with clinical data) provides some support for a dosage-sensitive expression model in which variants producing ≥30% of FL-transcripts would be predicted benign, while variants producing ≤13% of FL-transcripts might be pathogenic. This article is protected by copyright. All rights reserved.
dc.identifier.doi10.17863/CAM.86153
dc.identifier.eissn1096-9896
dc.identifier.issn0022-3417
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/338743
dc.language.isoeng
dc.publisherWiley
dc.publisher.departmentDepartment of Public Health And Primary Care, Cancer Genetic Epidemiology
dc.rightsAll Rights Reserved
dc.rights.urihttp://www.rioxx.net/licenses/all-rights-reserved
dc.titleMinigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants.
dc.typeArticle
dcterms.dateAccepted2022-06-08
prism.publicationNameJ Pathol
pubs.licence-display-nameApollo Repository Deposit Licence Agreement
pubs.licence-identifierapollo-deposit-licence-2-1
rioxxterms.typeJournal Article/Review
rioxxterms.versionAM
rioxxterms.versionofrecord10.1002/path.5979

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
JPath 2022 Bueno-Martinez et al.pdf
Size:
6.81 MB
Format:
Adobe Portable Document Format
Description:
Accepted version
Licence
http://www.rioxx.net/licenses/all-rights-reserved
Download

Collections

Cambridge University Research Outputs