{"doi":"10.1371/journal.pcbi.1009487","title":"All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons","abstract":"Accurate discovery of somatic mutations in a cell is a challenge that partially lays in immaturity of dedicated analytical approaches. Approaches comparing a cell's 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, All2, 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 All2 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.","journal":"PLoS Computational Biology","year":2022,"id":283403,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9532,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":552241,"name":"Yeongjun Jang","orcid":"0000-0002-7816-3278","position":1,"is_corresponding":false},{"id":830335,"name":"Milovan Šuvakov","orcid":"0000-0002-5839-9611","position":2,"is_corresponding":false},{"id":27807,"name":"Taejeong Bae","orcid":"0000-0002-4626-3725","position":3,"is_corresponding":false},{"id":480990,"name":"Liana Fasching","orcid":"0000-0002-6840-658X","position":4,"is_corresponding":false},{"id":533716,"name":"Shobana Sekar","orcid":"0000-0002-8273-9022","position":5,"is_corresponding":false},{"id":552240,"name":"Livia Tomasini","orcid":"0000-0001-7144-6964","position":6,"is_corresponding":false},{"id":21440,"name":"Jessica Mariani","orcid":"0000-0003-3657-1748","position":7,"is_corresponding":false},{"id":21357,"name":"Flora M. Vaccarino","orcid":"0000-0003-2167-981X","position":8,"is_corresponding":false},{"id":21363,"name":"Alexej Abyzov","orcid":"0000-0001-5405-6729","position":9,"is_corresponding":false},{"id":336442,"name":"Vivekananda Sarangi","orcid":"0000-0002-3070-8582","position":0,"is_corresponding":true}],"reference_count":18,"raw_metadata":null,"created_at":"2026-07-19T00:29:28.452697Z","pmid":"35442945","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}