{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T22:42:46Z","timestamp":1789512166044,"version":"build-2803163510"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:00:00Z","timestamp":1767830400000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DP2AG072437"],"award-info":[{"award-number":["DP2AG072437"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AG070921"],"award-info":[{"award-number":["R01AG070921"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R56AG079857"],"award-info":[{"award-number":["R56AG079857"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AG088082"],"award-info":[{"award-number":["R01AG088082"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AG070921"],"award-info":[{"award-number":["R01AG070921"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Somatic variants are increasingly recognized as contributors to diverse non-cancer, developmental, and aging-related disorders. However, most tools for detecting somatic single-nucleotide variants (sSNVs) were designed for DNA sequencing and primarily tailored to cancer datasets, leaving a critical gap in harnessing the rich potential of RNA-seq for sSNV identification, particularly in non-cancer tissues with low mutation rates. Here, we introduce RNA-MosaicHunter, a novel bioinformatic tool for accurate sSNV detection from bulk RNA-seq. In two benchmarking datasets, it demonstrated high precision (94.7% in TCGA and 99.3% in a cell-line mixture) with sensitivities of 53.4% and 38.9%, respectively, in the default mode that maximizes precision. We then applied RNA-MosaicHunter to profile 827 RNA-seq samples in three tissue types from the Genotype Tissue Expression project (GTEx), where it outperformed previous methods in capturing mutational characteristics associated with normal aging. We further utilized RNA-MosaicHunter to analyze RNA-seq data from 382 Alzheimer\u2019s disease (AD) brain samples and 480 age-matched controls and revealed a significantly higher burden of sSNVs in AD cerebral cortex, suggesting the potential contribution of sSNVs to AD pathogenesis. RNA-MosaicHunter enables accurate profiling and characterization of sSNVs from RNA-seq data, advancing the understanding of the role of somatic variants across diverse tissues and diseases.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1450","type":"journal-article","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T12:34:48Z","timestamp":1765197288000},"source":"Crossref","is-referenced-by-count":5,"title":["Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter"],"prefix":"10.1093","volume":"54","author":[{"given":"August Yue","family":"Huang","sequence":"first","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5903-9773","authenticated-orcid":false,"given":"Yuchen","family":"Cheng","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayoung","family":"Ku","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boxun","family":"Zhao","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junseok","family":"Park","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dachan","family":"Kim","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Otorhinolaryngology, Severance Hospital, Yonsei University Health System, Yonsei University College of Medicine , Seoul 03722 ,","place":["South Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaejoon","family":"Choi","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunjung Alice","family":"Lee","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics and Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital , Boston, MA 02115 ,","place":["United States"]},{"name":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115 ,","place":["United States"]},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,1,8]]},"reference":[{"key":"2026010810165919900_B1","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/S1383-5742(00)00015-6","article-title":"Molecular epidemiology and carcinogenesis: endogenous and exogenous carcinogens","volume":"462","author":"Hussain","year":"2000","journal-title":"Mutat Res"},{"key":"2026010810165919900_B2","doi-asserted-by":"publisher","first-page":"16895","DOI":"10.1074\/jbc.R400006200","article-title":"DNA replication fidelity","volume":"279","author":"Kunkel","year":"2004","journal-title":"J Biol Chem"},{"key":"2026010810165919900_B3","doi-asserted-by":"publisher","first-page":"e1007395","DOI":"10.1371\/journal.pgen.1007395","article-title":"Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs","volume":"14","author":"Huang","year":"2018","journal-title":"PLoS Genet"},{"key":"2026010810165919900_B4","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/nature05610","article-title":"Patterns of somatic mutation in human cancer genomes","volume":"446","author":"Greenman","year":"2007","journal-title":"Nature"},{"key":"2026010810165919900_B5","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1038\/nrg3539","article-title":"Emerging patterns of somatic mutations in cancer","volume":"14","author":"Watson","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2026010810165919900_B6","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1056\/NEJMoa1104017","article-title":"A mosaic activating mutation in AKT1 associated with the Proteus syndrome","volume":"365","author":"Lindhurst","year":"2011","journal-title":"N Engl J Med"},{"key":"2026010810165919900_B7","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1056\/NEJMoa1314432","article-title":"Somatic mutations in cerebral cortical malformations","volume":"371","author":"Jamuar","year":"2014","journal-title":"N Engl J Med"},{"key":"2026010810165919900_B8","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1016\/j.ajhg.2017.01.018","article-title":"Somatic MAP2K1 mutations are associated with extracranial arteriovenous malformation","volume":"100","author":"Couto","year":"2017","journal-title":"Am J Hum Genet"},{"key":"2026010810165919900_B9","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/s13073-020-00738-1","article-title":"EM-mosaic detects mosaic point mutations that contribute to congenital heart disease","volume":"12","author":"Hsieh","year":"2020","journal-title":"Genome Med"},{"key":"2026010810165919900_B10","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/s41593-020-00765-6","article-title":"The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing","volume":"24","author":"Rodin","year":"2021","journal-title":"Nat Neurosci"},{"key":"2026010810165919900_B11","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1038\/nature23672","article-title":"A somatic mutation in erythro-myeloid progenitors causes neurodegenerative disease","volume":"549","author":"Mass","year":"2017","journal-title":"Nature"},{"key":"2026010810165919900_B12","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1126\/science.abe1544","article-title":"Landmarks of human embryonic development inscribed in somatic mutations","volume":"371","author":"Bizzotto","year":"2021","journal-title":"Science"},{"key":"2026010810165919900_B13","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/s41586-022-05448-9","article-title":"Common and rare variant associations with clonal haematopoiesis phenotypes","volume":"612","author":"Kessler","year":"2022","journal-title":"Nature"},{"key":"2026010810165919900_B14","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1038\/s41586-019-1670-9","article-title":"Somatic mutations and clonal dynamics in healthy and cirrhotic human liver","volume":"574","author":"Brunner","year":"2019","journal-title":"Nature"},{"key":"2026010810165919900_B15","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/s43587-022-00261-5","article-title":"Somatic mutations in single human cardiomyocytes reveal age-associated DNA damage and widespread oxidative genotoxicity","volume":"2","author":"Choudhury","year":"2022","journal-title":"Nat Aging"},{"key":"2026010810165919900_B16","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1126\/science.aao4426","article-title":"Aging and neurodegeneration are associated with increased mutations in single human neurons","volume":"359","author":"Lodato","year":"2018","journal-title":"Science"},{"key":"2026010810165919900_B17","doi-asserted-by":"publisher","first-page":"1921","DOI":"10.1038\/s41591-021-01521-4","article-title":"Distinction of lymphoid and myeloid clonal hematopoiesis","volume":"27","author":"Niroula","year":"2021","journal-title":"Nat Med"},{"key":"2026010810165919900_B18","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1056\/NEJMoa1701719","article-title":"Clonal hematopoiesis and risk of atherosclerotic cardiovascular disease","volume":"377","author":"Jaiswal","year":"2017","journal-title":"N Engl J Med"},{"key":"2026010810165919900_B19","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/s13059-019-1659-6","article-title":"Analysis of error profiles in deep next-generation sequencing data","volume":"20","author":"Ma","year":"2019","journal-title":"Genome Biol"},{"key":"2026010810165919900_B20","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"Koboldt","year":"2012","journal-title":"Genome Res"},{"key":"2026010810165919900_B21","doi-asserted-by":"publisher","first-page":"1811","DOI":"10.1093\/bioinformatics\/bts271","article-title":"Strelka: accurate somatic small-variant calling from sequenced tumor\u2013normal sample pairs","volume":"28","author":"Saunders","year":"2012","journal-title":"Bioinformatics"},{"key":"2026010810165919900_B22","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1038\/cr.2014.131","article-title":"Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals","volume":"24","author":"Huang","year":"2014","journal-title":"Cell Res"},{"key":"2026010810165919900_B23","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2026010810165919900_B24","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1038\/s41587-019-0368-8","article-title":"Accurate detection of mosaic variants in sequencing data without matched controls","volume":"38","author":"Dou","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026010810165919900_B25","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1038\/nmeth.2722","article-title":"Systematic evaluation of spliced alignment programs for RNA-seq data","volume":"10","author":"Engstr\u00f6m","year":"2013","journal-title":"Nat Methods"},{"key":"2026010810165919900_B26","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/s41576-018-0006-1","article-title":"A-to-I RNA editing\u2014immune protector and transcriptome diversifier","volume":"19","author":"Eisenberg","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2026010810165919900_B27","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.gde.2020.10.007","article-title":"Allele-specific expression: applications in cancer and technical considerations","volume":"66","author":"Robles-Espinoza","year":"2021","journal-title":"Curr Opin Genet Dev"},{"key":"2026010810165919900_B28","doi-asserted-by":"publisher","first-page":"865313","DOI":"10.3389\/fgene.2022.865313","article-title":"RNA-SSNV: a reliable somatic single nucleotide variant identification framework for bulk RNA-seq data","volume":"13","author":"Long","year":"2022","journal-title":"Front Genet"},{"key":"2026010810165919900_B29","doi-asserted-by":"publisher","first-page":"e161","DOI":"10.1093\/nar\/gkw757","article-title":"RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data","volume":"44","author":"Movassagh","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B30","doi-asserted-by":"publisher","first-page":"e5362","DOI":"10.7717\/peerj.5362","article-title":"Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data","volume":"6","author":"Coudray","year":"2018","journal-title":"PeerJ"},{"key":"2026010810165919900_B31","doi-asserted-by":"publisher","first-page":"2256","DOI":"10.1038\/srep02256","article-title":"Novel insights into breast cancer genetic variance through RNA sequencing","volume":"3","author":"Horvath","year":"2013","journal-title":"Sci Rep"},{"key":"2026010810165919900_B32","doi-asserted-by":"publisher","first-page":"eaaw0726","DOI":"10.1126\/science.aaw0726","article-title":"RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues","volume":"364","author":"Yizhak","year":"2019","journal-title":"Science"},{"key":"2026010810165919900_B33","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/s13073-020-00746-1","article-title":"The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues","volume":"12","author":"Muyas","year":"2020","journal-title":"Genome Med"},{"key":"2026010810165919900_B34","doi-asserted-by":"publisher","first-page":"e76","DOI":"10.1093\/nar\/gkx024","article-title":"MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples","volume":"45","author":"Huang","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B35","doi-asserted-by":"publisher","first-page":"D925","DOI":"10.1093\/nar\/gkae977","article-title":"The evolution of dbSNP: 25 years of impact in genomic research","volume":"53","author":"Phan","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B36","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B37","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/s41586-023-06045-0","article-title":"A genomic mutational constraint map using variation in 76,156 human genomes","volume":"625","author":"Chen","year":"2024","journal-title":"Nature"},{"key":"2026010810165919900_B38","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202","article-title":"BLAT\u2014The BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2026010810165919900_B39","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1093\/bioinformatics\/btq285","article-title":"DARNED: a DAtabase of RNa EDiting in humans","volume":"26","author":"Kiran","year":"2010","journal-title":"Bioinformatics"},{"key":"2026010810165919900_B40","doi-asserted-by":"publisher","first-page":"D750","DOI":"10.1093\/nar\/gkw767","article-title":"REDIportal: a comprehensive database of A-to-I RNA editing events in humans","volume":"45","author":"Picardi","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B41","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2026010810165919900_B42","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat Genet"},{"key":"2026010810165919900_B43","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"The 1000 Genomes Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2026010810165919900_B44","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1126\/science.1219240","article-title":"Evolution and functional impact of rare coding variation from deep sequencing of human exomes","volume":"337","author":"Tennessen","year":"2012","journal-title":"Science"},{"key":"2026010810165919900_B45","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Consortium","year":"2016","journal-title":"Nature"},{"key":"2026010810165919900_B46","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/nature20805","article-title":"Integrated genomic characterization of oesophageal carcinoma","volume":"541","author":"The Cancer Genome Atlas Research Network","year":"2017","journal-title":"Nature"},{"key":"2026010810165919900_B47","doi-asserted-by":"publisher","first-page":"3426","DOI":"10.1016\/j.cell.2022.08.004","article-title":"High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios","volume":"185","author":"Byrska-Bishop","year":"2022","journal-title":"Cell"},{"key":"2026010810165919900_B48","doi-asserted-by":"publisher","DOI":"10.1101\/201178","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","volume-title":"bioRxiv","author":"Poplin"},{"key":"2026010810165919900_B49","doi-asserted-by":"crossref","unstructured":"Danecek P, Bonfield JK, Liddle J \u00a0et al. \u00a0Twelve years of SAMtools and BCFtools. GigaScience. 2021;10:giab008. 10.1093\/gigascience\/giab008.","DOI":"10.1093\/gigascience\/giab008"},{"key":"2026010810165919900_B50","doi-asserted-by":"publisher","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B51","doi-asserted-by":"publisher","first-page":"D243","DOI":"10.1093\/nar\/gkae1038","article-title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","volume":"53","author":"Goldfarb","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B52","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1126\/science.aai8690","article-title":"DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification","volume":"355","author":"Chen","year":"2017","journal-title":"Science"},{"key":"2026010810165919900_B53","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1093\/dnares\/dsw038","article-title":"Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications","volume":"23","author":"Arbeithuber","year":"2016","journal-title":"DNA Res"},{"key":"2026010810165919900_B54","doi-asserted-by":"publisher","first-page":"e67","DOI":"10.1093\/nar\/gks1443","article-title":"Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation","volume":"41","author":"Costello","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B55","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/s41593-020-00765-6","article-title":"The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing","volume":"24","author":"Rodin","year":"2021","journal-title":"Nat Neurosci"},{"key":"2026010810165919900_B56","doi-asserted-by":"publisher","first-page":"1747","DOI":"10.1101\/gr.239244.118","article-title":"Maftools: efficient and comprehensive analysis of somatic variants in cancer","volume":"28","author":"Mayakonda","year":"2018","journal-title":"Genome Res"},{"key":"2026010810165919900_B57","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1038\/s41586-020-2819-2","article-title":"Inherited causes of clonal haematopoiesis in 97,691 whole genomes","volume":"586","author":"Bick","year":"2020","journal-title":"Nature"},{"key":"2026010810165919900_B58","doi-asserted-by":"publisher","first-page":"1662","DOI":"10.1038\/s41591-023-02397-2","article-title":"Clonal hematopoiesis is associated with protection from Alzheimer\u2019s disease","volume":"29","author":"Bouzid","year":"2023","journal-title":"Nat Med"},{"key":"2026010810165919900_B59","doi-asserted-by":"publisher","first-page":"S161","DOI":"10.3233\/JAD-179939","article-title":"Religious orders study and rush memory and Aging Project","volume":"64","author":"Bennett","year":"2018","journal-title":"J Alzheimers Dis"},{"key":"2026010810165919900_B60","doi-asserted-by":"publisher","first-page":"160089","DOI":"10.1038\/sdata.2016.89","article-title":"Human whole genome genotype and transcriptome data for Alzheimer\u2019s and other neurodegenerative diseases","volume":"3","author":"Allen","year":"2016","journal-title":"Sci Data"},{"key":"2026010810165919900_B61","doi-asserted-by":"publisher","first-page":"Unit7.20","DOI":"10.1002\/0471142905.hg0720s76","article-title":"Predicting functional effect of human missense mutations using PolyPhen-2","volume":"Chapter 7","author":"Adzhubei","year":"2013","journal-title":"Curr Protoc Hum Genet"},{"key":"2026010810165919900_B62","doi-asserted-by":"publisher","first-page":"3812","DOI":"10.1093\/nar\/gkg509","article-title":"SIFT: predicting amino acid changes that affect protein function","volume":"31","author":"Ng","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B63","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","author":"Newman","year":"2015","journal-title":"Nat Methods"},{"key":"2026010810165919900_B64","doi-asserted-by":"publisher","first-page":"eaat8464","DOI":"10.1126\/science.aat8464","article-title":"Comprehensive functional genomic resource and integrative model for the human brain","volume":"362","author":"Wang","year":"2018","journal-title":"Science"},{"key":"2026010810165919900_B65","doi-asserted-by":"publisher","first-page":"R14","DOI":"10.1186\/gb-2010-11-2-r14","article-title":"Gene ontology analysis for RNA-seq: accounting for selection bias","volume":"11","author":"Young","year":"2010","journal-title":"Genome Biol"},{"key":"2026010810165919900_B66","doi-asserted-by":"publisher","first-page":"eaax2659","DOI":"10.1126\/sciadv.aax2659","article-title":"Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver","volume":"6","author":"Brazhnik","year":"2020","journal-title":"Sci Adv"},{"key":"2026010810165919900_B67","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/s41586-022-04640-1","article-title":"Somatic genomic changes in single Alzheimer\u2019s disease neurons","volume":"604","author":"Miller","year":"2022","journal-title":"Nature"},{"key":"2026010810165919900_B68","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"key":"2026010810165919900_B69","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1016\/j.cell.2012.04.024","article-title":"Mutational processes molding the genomes of 21 breast cancers","volume":"149","author":"Nik-Zainal","year":"2012","journal-title":"Cell"},{"key":"2026010810165919900_B70","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1038\/s41588-024-01755-1","article-title":"Analysis of somatic mutations in whole blood from 200,618 individuals identifies pervasive positive selection and novel drivers of clonal hematopoiesis","volume":"56","author":"Bernstein","year":"2024","journal-title":"Nat Genet"},{"key":"2026010810165919900_B71","doi-asserted-by":"publisher","first-page":"8866","DOI":"10.1038\/ncomms9866","article-title":"Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution","volume":"6","author":"Kasar","year":"2015","journal-title":"Nat Commun"},{"key":"2026010810165919900_B72","doi-asserted-by":"publisher","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the catalogue of somatic mutations in cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026010810165919900_B73","doi-asserted-by":"publisher","first-page":"3090","DOI":"10.1038\/s41467-019-11000-7","article-title":"Brain somatic mutations observed in Alzheimer\u2019s disease associated with aging and dysregulation of tau phosphorylation","volume":"10","author":"Park","year":"2019","journal-title":"Nat Commun"},{"key":"2026010810165919900_B74","doi-asserted-by":"publisher","first-page":"105021","DOI":"10.1016\/j.nbd.2020.105021","article-title":"Somatic mutations in neurodegeneration: an update","volume":"144","author":"Proukakis","year":"2020","journal-title":"Neurobiol Dis"},{"key":"2026010810165919900_B75","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1007\/BF00308809","article-title":"Neuropathological stageing of Alzheimer-related changes","volume":"82","author":"Braak","year":"1991","journal-title":"Acta Neuropathol"},{"key":"2026010810165919900_B76","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s42003-018-0254-9","article-title":"Regional protein expression in human Alzheimer\u2019s brain correlates with disease severity","volume":"2","author":"Xu","year":"2019","journal-title":"Commun Biol"},{"key":"2026010810165919900_B77","doi-asserted-by":"publisher","first-page":"4257","DOI":"10.1038\/s41467-018-06331-w","article-title":"High prevalence of focal and multi-focal somatic genetic variants in the human brain","volume":"9","author":"Keogh","year":"2018","journal-title":"Nat Commun"},{"key":"2026010810165919900_B78","doi-asserted-by":"publisher","DOI":"10.1101\/2024.01.03.574078","article-title":"Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer\u2019s disease microglia","volume-title":"bioRxiv","author":"Huang"},{"key":"2026010810165919900_B79","doi-asserted-by":"publisher","first-page":"RP96519","DOI":"10.7554\/eLife.96519.1","article-title":"A microglia clonal inflammatory disorder in Alzheimer\u2019s Disease","author":"Vicario","year":"2024","journal-title":"eLife"},{"key":"2026010810165919900_B80","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1016\/j.cels.2022.05.001","article-title":"Diploid hepatocytes drive physiological liver renewal in adult humans","volume":"13","author":"Heinke","year":"2022","journal-title":"Cell Syst"},{"key":"2026010810165919900_B81","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1111\/acel.12311","article-title":"Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover","volume":"14","author":"Westera","year":"2015","journal-title":"Aging Cell"},{"key":"2026010810165919900_B82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.aanat.2015.09.002","article-title":"The association between total leukocyte count and longevity: evidence from longitudinal and cross-sectional data","volume":"204","author":"Chmielewski","year":"2016","journal-title":"Ann Anat"},{"key":"2026010810165919900_B83","doi-asserted-by":"publisher","first-page":"9014","DOI":"10.1073\/pnas.1902510116","article-title":"Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan","volume":"116","author":"Zhang","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026010810165919900_B84","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/s41586-022-04786-y","article-title":"Clonal dynamics of haematopoiesis across the human lifespan","volume":"606","author":"Mitchell","year":"2022","journal-title":"Nature"},{"key":"2026010810165919900_B85","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/s41586-021-03974-6","article-title":"Convergent somatic mutations in metabolism genes in chronic liver disease","volume":"598","author":"Ng","year":"2021","journal-title":"Nature"},{"key":"2026010810165919900_B86","doi-asserted-by":"publisher","first-page":"1791","DOI":"10.1212\/WNL.58.12.1791","article-title":"Phases of a\u03b2-deposition in the human brain and its relevance for the development of AD","volume":"58","author":"Thal","year":"2002","journal-title":"Neurology"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/1\/gkaf1450\/66308118\/gkaf1450.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/1\/gkaf1450\/66308118\/gkaf1450.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T15:17:03Z","timestamp":1767885423000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf1450\/8417347"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":86,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf1450","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1,13]]},"published":{"date-parts":[[2026,1,5]]},"article-number":"gkaf1450"}}