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Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites

Zhang, Peng, Chaldebas, Matthieu, Ogishi, Masato, Al Qureshah, Fahd, Ponsin, Khoren, Feng, Yi, Rinchai, Darawan, Milisavljevic, Baptiste, Han, Ji Eun, Moncada-Vélez, Marcela, Keles, Sevgi, Schröder, Bernd, Stenson, Peter D., Cooper, David N. ORCID:, Cobat, Aurélie, Boisson, Bertrand, Zhang, Qian, Boisson-Dupuis, Stéphanie, Abel, Laurent and Casanova, Jean-Laurent 2023. Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites. Proceedings of the National Academy of Sciences of the United States of America 120 (46) , e2314225120. 10.1073/pnas.2314225120

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Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Medicine
Publisher: National Academy of Sciences
ISSN: 0027-8424
Date of First Compliant Deposit: 13 March 2024
Date of Acceptance: 2 October 2023
Last Modified: 21 Mar 2024 15:35

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