{"doi":"10.1093/jamia/ocad205","title":"Systematic replication of smoking disease associations using survey responses and EHR data in the <i>All of Us</i> Research Program","abstract":"OBJECTIVE: The All of Us Research Program (All of Us) aims to recruit over a million participants to further precision medicine. Essential to the verification of biobanks is a replication of known associations to establish validity. Here, we evaluated how well All of Us data replicated known cigarette smoking associations. MATERIALS AND METHODS: We defined smoking exposure as follows: (1) an EHR Smoking exposure that used International Classification of Disease codes; (2) participant provided information (PPI) Ever Smoking; and, (3) PPI Current Smoking, both from the lifestyle survey. We performed a phenome-wide association study (PheWAS) for each smoking exposure measurement type. For each, we compared the effect sizes derived from the PheWAS to published meta-analyses that studied cigarette smoking from PubMed. We defined two levels of replication of meta-analyses: (1) nominally replicated: which required agreement of direction of effect size, and (2) fully replicated: which required overlap of confidence intervals. RESULTS: PheWASes with EHR Smoking, PPI Ever Smoking, and PPI Current Smoking revealed 736, 492, and 639 phenome-wide significant associations, respectively. We identified 165 meta-analyses representing 99 distinct phenotypes that could be matched to EHR phenotypes. At P < .05, 74 were nominally replicated and 55 were fully replicated. At P < 2.68 × 10-5 (Bonferroni threshold), 58 were nominally replicated and 40 were fully replicated. DISCUSSION: Most phenotypes found in published meta-analyses associated with smoking were nominally replicated in All of Us. Both survey and EHR definitions for smoking produced similar results. CONCLUSION: This study demonstrated the feasibility of studying common exposures using All of Us data.","journal":"Journal of the American Medical Informatics Association","year":2023,"id":364748,"datarank":0.42306017191783696,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.11114394066586154,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.11114394066586154,"corpus_percentile":56.115107913669064,"corpus_rank":5674,"citation_count":7,"citer_count":4,"citers_with_citation_signal":4,"citers_with_endowment":4,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7567,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":555874,"name":"Lina Sulieman","orcid":"0000-0002-2680-8230","position":1,"is_corresponding":false},{"id":756161,"name":"Huan Mo","orcid":"0000-0001-6029-458X","position":2,"is_corresponding":false},{"id":279178,"name":"Jacob M. Keaton","orcid":"0000-0002-6371-7530","position":3,"is_corresponding":false},{"id":278321,"name":"Tracey M. Ferrara","orcid":"0000-0001-9599-413X","position":4,"is_corresponding":false},{"id":361229,"name":"Ariel Williams","orcid":"0000-0001-5343-8274","position":5,"is_corresponding":false},{"id":1119845,"name":"Jun Qian","orcid":"0000-0002-8105-1306","position":6,"is_corresponding":false},{"id":1120318,"name":"Onajia Stubblefield","orcid":null,"position":7,"is_corresponding":false},{"id":510075,"name":"Chenjie Zeng","orcid":"0000-0002-0149-5661","position":8,"is_corresponding":false},{"id":1048329,"name":"Tam C. Tran","orcid":"0009-0007-5343-8822","position":9,"is_corresponding":false},{"id":31022,"name":"Lisa Bastarache","orcid":null,"position":10,"is_corresponding":false},{"id":449652,"name":"Jian Dai","orcid":"0000-0002-8784-7487","position":11,"is_corresponding":false},{"id":1120319,"name":"Anav Babbar","orcid":null,"position":12,"is_corresponding":false},{"id":279182,"name":"Andrea H. Ramirez","orcid":"0000-0002-6460-0182","position":13,"is_corresponding":false},{"id":477291,"name":"Slavina B. Goleva","orcid":"0000-0001-5177-9286","position":14,"is_corresponding":false},{"id":22022,"name":"Joshua C. Denny","orcid":"0000-0002-3049-7332","position":15,"is_corresponding":false},{"id":556653,"name":"David J. Schlueter","orcid":null,"position":0,"is_corresponding":true}],"reference_count":191,"raw_metadata":null,"created_at":"2026-07-19T01:14:41.218128Z","pmid":"37885303","pmcid":"PMC10746325","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":[]}