{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kadam A"],"funding":["Ernest and Bonnie Beutler Research Program","ISF-IPMP-Israel Precision Medicine Program","Rising Tide Foundation","Steven B. Rubenstein research fund","Barry and Eleanore Reznik Family Cancer Research fund","Sagol Institute for Longevity Research","Applebaum Foundation"],"pagination":["e106"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11662932"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["52(22)"],"pubmed_abstract":["We developed Del-read, an algorithm targeting medium-sized deletions (6-100 bp) in short-reads, which are challenging for current variant callers relying on alignment. Our focus was on Micro-Homolog mediated End Joining deletions (MMEJ-dels), prevalent in myeloid malignancies. MMEJ-dels follow a distinct pattern, occurring between two homologies, allowing us to generate a comprehensive list of MMEJ-dels in the exome. Using Del-read, we identified numerous novel germline and somatic MMEJ-dels in BEAT-AML and TCGA-breast datasets. Validation in 672 healthy individuals confirmed their presence. These novel MMEJ-dels were linked to genomic features associated with replication stress, like G-quadruplexes and minisatellite. Additionally, we observed a new category of MMEJ-dels with an imperfect-"],"journal":["Nucleic acids research"],"pubmed_title":["Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms."],"pmcid":["PMC11662932"],"funding_grant_id":["rtf6005-19","3165/19","isf-nsfc 2427/18","1123/21"],"pubmed_authors":["Chapal-Ilani N","Kadam A","Shlush L","Wainstein A","Minden M","Feldman T","Kaushansky N","Naor H","Shilo S","Brilon Y"],"additional_accession":[]},"is_claimable":false,"name":"Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms.","description":"We developed Del-read, an algorithm targeting medium-sized deletions (6-100 bp) in short-reads, which are challenging for current variant callers relying on alignment. Our focus was on Micro-Homolog mediated End Joining deletions (MMEJ-dels), prevalent in myeloid malignancies. MMEJ-dels follow a distinct pattern, occurring between two homologies, allowing us to generate a comprehensive list of MMEJ-dels in the exome. Using Del-read, we identified numerous novel germline and somatic MMEJ-dels in BEAT-AML and TCGA-breast datasets. Validation in 672 healthy individuals confirmed their presence. These novel MMEJ-dels were linked to genomic features associated with replication stress, like G-quadruplexes and minisatellite. Additionally, we observed a new category of MMEJ-dels with an imperfect-","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Dec","modification":"2025-04-18T12:52:29.041Z","creation":"2025-04-06T22:14:19.768Z"},"accession":"S-EPMC11662932","cross_references":{"pubmed":["39607705"],"doi":["10.1093/nar/gkae1132"]}}