{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Chen X"],"funding":["NICHD NIH HHS","NHGRI NIH HHS","Wellcome Trust"],"pagination":["2340"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11890787"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["16(1)"],"pubmed_abstract":["Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions. We identified 23 paralog groups with exceptionally low within-group diversity, where extensive gene conversion and unequal crossing over contribute to highly similar gene copies. Furthermore, our analysis of 36 trios identified 7 de novo SNVs and 4 de novo gene conversion events, 2 of which are non-allelic. Finally, we sum"],"journal":["Nature communications"],"pubmed_title":["Genome-wide profiling of highly similar paralogous genes using HiFi sequencing."],"pmcid":["PMC11890787"],"funding_grant_id":["U01 HG011745","R01 HD093450"],"pubmed_authors":["Belhadj S","Ko A","Pitsava G","Kasperaviciute D","Baker D","Devaney JM","Kruszka P","Almalvez M","Delaney M","Bluske K","Delot E","Eberle MA","Harting J","Berlyoung AS","Fraser J","Lochovsky L","Chen X","Newman S","Fusaro V","Losic B","Dolzhenko E","Hruska KS","Brandon R","LoTempio J","UCI Genomics Research to Elucidate the Genetics of Rare diseases (UCI GREGoR) Consortium","de Dios I","Li W","Pastinen T","Cohen A","King CH","Hoischen A","Auriga L","Thiffault I","Gilissen C","Vilain E","Cui Y","Karam R","Vissers L","Boukas L","Farrow E","Noya J","Xiao C","Berger S","Hsiao EY"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide profiling of highly similar paralogous genes using HiFi sequencing.","description":"Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions. We identified 23 paralog groups with exceptionally low within-group diversity, where extensive gene conversion and unequal crossing over contribute to highly similar gene copies. Furthermore, our analysis of 36 trios identified 7 de novo SNVs and 4 de novo gene conversion events, 2 of which are non-allelic. Finally, we sum","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Mar","modification":"2026-06-01T20:13:50.107Z","creation":"2025-04-04T08:22:44.085Z"},"accession":"S-EPMC11890787","cross_references":{"pubmed":["40057485"],"doi":["10.1038/s41467-025-57505-2"]}}