{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T20:01:55Z","timestamp":1776456115653,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009487","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,5,2]],"date-time":"2022-05-02T00:00:00Z","timestamp":1651449600000}}],"reference-count":17,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T00:00:00Z","timestamp":1650412800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["R01MH100914"],"award-info":[{"award-number":["R01MH100914"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["U01MH106876"],"award-info":[{"award-number":["U01MH106876"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011541","name":"Division of Cancer Epidemiology and Genetics, National Cancer Institute","doi-asserted-by":"publisher","award":["U24CA220242"],"award-info":[{"award-number":["U24CA220242"]}],"id":[{"id":"10.13039\/100011541","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["399558"],"award-info":[{"award-number":["399558"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["399558"],"award-info":[{"award-number":["399558"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Accurate discovery of somatic mutations in a cell is a challenge that partially lays in immaturity of dedicated analytical approaches. Approaches comparing a cell\u2019s genome to a control bulk sample miss common mutations, while approaches to find such mutations from bulk suffer from low sensitivity. We developed a tool, All\n                    <jats:sup>2<\/jats:sup>\n                    , which enables accurate filtering of mutations in a cell without the need for data from bulk(s). It is based on pair-wise comparisons of all cells to each other where every call for base pair substitution and indel is classified as either a germline variant, mosaic mutation, or false positive. As All\n                    <jats:sup>2<\/jats:sup>\n                    allows for considering dropped-out regions, it is applicable to whole genome and exome analysis of cloned and amplified cells. By applying the approach to a variety of available data, we showed that its application reduces false positives, enables sensitive discovery of high frequency mutations, and is indispensable for conducting high resolution cell lineage tracing.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009487","type":"journal-article","created":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T13:36:54Z","timestamp":1650461814000},"page":"e1009487","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3070-8582","authenticated-orcid":true,"given":"Vivekananda","family":"Sarangi","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7816-3278","authenticated-orcid":true,"given":"Yeongjun","family":"Jang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5839-9611","authenticated-orcid":true,"given":"Milovan","family":"Suvakov","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4626-3725","authenticated-orcid":true,"given":"Taejeong","family":"Bae","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6840-658X","authenticated-orcid":true,"given":"Liana","family":"Fasching","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8273-9022","authenticated-orcid":true,"given":"Shobana","family":"Sekar","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7144-6964","authenticated-orcid":true,"given":"Livia","family":"Tomasini","sequence":"additional","affiliation":[]},{"given":"Jessica","family":"Mariani","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2167-981X","authenticated-orcid":true,"given":"Flora M.","family":"Vaccarino","sequence":"additional","affiliation":[]},{"given":"Alexej","family":"Abyzov","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,4,20]]},"reference":[{"issue":"6417","key":"pcbi.1009487.ref001","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1126\/science.aau3879","article-title":"Somatic mutant clones colonize the human esophagus with age","volume":"362","author":"I Martincorena","year":"2018","journal-title":"Science"},{"issue":"7739","key":"pcbi.1009487.ref002","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/s41586-018-0811-x","article-title":"Age-related remodelling of oesophageal epithelia by mutated cancer drivers","volume":"565","author":"A Yokoyama","year":"2019","journal-title":"Nature"},{"issue":"7724","key":"pcbi.1009487.ref003","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/s41586-018-0497-0","article-title":"Population dynamics of normal human blood inferred from somatic mutations","volume":"561","author":"H Lee-Six","year":"2018","journal-title":"Nature"},{"issue":"18","key":"pcbi.1009487.ref004","doi-asserted-by":"crossref","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":"L Zhang","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6375","key":"pcbi.1009487.ref005","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1126\/science.aan8690","article-title":"Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis","volume":"359","author":"T Bae","year":"2018","journal-title":"Science"},{"issue":"6535","key":"pcbi.1009487.ref006","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1126\/science.abe0981","article-title":"Early developmental asymmetries in cell lineage trees in living individuals","volume":"371","author":"L Fasching","year":"2021","journal-title":"Science"},{"issue":"8","key":"pcbi.1009487.ref007","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"X Chen","year":"2016","journal-title":"Bioinformatics"},{"issue":"12","key":"pcbi.1009487.ref008","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1101\/gr.262667.120","article-title":"Complex mosaic structural variations in human fetal brains","volume":"30","author":"S Sekar","year":"2020","journal-title":"Genome Res"},{"issue":"1","key":"pcbi.1009487.ref009","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1186\/s12859-020-03858-y","article-title":"SCELLECTOR: ranking amplification bias in single cells using shallow sequencing","volume":"21","author":"V Sarangi","year":"2020","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"pcbi.1009487.ref010","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1101\/gr.215517.116","article-title":"One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin","volume":"27","author":"A Abyzov","year":"2017","journal-title":"Genome Res"},{"key":"pcbi.1009487.ref011","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.compbiolchem.2019.03.013","article-title":"SCOUT: A new algorithm for the inference of pseudo-time trajectory using single-cell data","volume":"80","author":"J Wei","year":"2019","journal-title":"Comput Biol Chem"},{"issue":"3","key":"pcbi.1009487.ref012","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/j.cell.2012.09.035","article-title":"Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain","volume":"151","author":"GD Evrony","year":"2012","journal-title":"Cell"},{"issue":"14","key":"pcbi.1009487.ref013","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pcbi.1009487.ref014","first-page":"201178","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","author":"R Poplin","year":"2018","journal-title":"bioRxiv"},{"issue":"3","key":"pcbi.1009487.ref015","doi-asserted-by":"crossref","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":"K Cibulskis","year":"2013","journal-title":"Nat Biotechnol"},{"issue":"14","key":"pcbi.1009487.ref016","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1093\/bioinformatics\/bts271","article-title":"Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs","volume":"28","author":"CT Saunders","year":"2012","journal-title":"Bioinformatics"},{"key":"pcbi.1009487.ref017","article-title":"CNVpytor: a tool for CNV\/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing","author":"M Suvakov","year":"2021","journal-title":"bioRxiv"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1009487","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,5,2]],"date-time":"2022-05-02T00:00:00Z","timestamp":1651449600000}},{"DOI":"10.1371\/journal.pcbi.1010703","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2022,11,15]],"date-time":"2022-11-15T00:00:00Z","timestamp":1668470400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1009487","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,2]],"date-time":"2022-05-02T13:39:45Z","timestamp":1651498785000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1009487"}},"subtitle":[],"editor":[{"given":"Anna R.","family":"Panchenko","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,4,20]]},"references-count":17,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2022,4,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1009487","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.09.29.462281","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,20]]}}}