{"doi":"10.1016/j.stem.2022.01.011","title":"Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation","abstract":"Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.","journal":"Cell stem cell","year":2022,"id":237328,"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":61,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8569,"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":479357,"name":"Sulagna Ghosh","orcid":"0000-0003-1833-7296","position":1,"is_corresponding":false},{"id":3813,"name":"Giulio Genovese","orcid":"0000-0003-3066-5575","position":2,"is_corresponding":false},{"id":16701,"name":"Robert E. Handsaker","orcid":"0000-0002-3128-3547","position":3,"is_corresponding":false},{"id":29310,"name":"Seva Kashin","orcid":"0009-0008-1432-8249","position":4,"is_corresponding":false},{"id":815149,"name":"Daniel Meyer","orcid":"0000-0003-4720-9891","position":5,"is_corresponding":false},{"id":47,"name":"Konrad J. Karczewski","orcid":"0000-0003-2878-4671","position":6,"is_corresponding":false},{"id":552190,"name":"Colm O’Dushlaine","orcid":"0000-0003-2858-3642","position":7,"is_corresponding":false},{"id":1161,"name":"Carlos N. Pato","orcid":"0000-0002-5858-266X","position":8,"is_corresponding":false},{"id":5042,"name":"Michele T. Pato","orcid":"0000-0002-4589-7398","position":9,"is_corresponding":false},{"id":1085,"name":"Daniel G. MacArthur","orcid":"0000-0002-5771-2290","position":10,"is_corresponding":false},{"id":1158,"name":"Steven A. McCarroll","orcid":"0000-0002-6954-8184","position":11,"is_corresponding":false},{"id":33055,"name":"Kevin Eggan","orcid":"0000-0003-4436-8467","position":12,"is_corresponding":false},{"id":310510,"name":"Florian T. Merkle","orcid":"0000-0002-8513-2998","position":0,"is_corresponding":true}],"reference_count":91,"raw_metadata":null,"created_at":"2026-07-19T00:22:08.925400Z","pmid":"35176222","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":[]}