{"doi":"10.1016/j.xgen.2025.100769","title":"Secure and federated quantitative trait loci mapping with privateQTL","abstract":"Understanding the relationship between genotypes and phenotypes is crucial for advancing personalized medicine. Expression quantitative trait loci (eQTL) mapping plays a significant role by correlating genetic variants to gene expression levels. Despite the progress made by large-scale projects, eQTL mapping still faces challenges in statistical power and privacy concerns. Multi-site studies can increase sample sizes but are hindered by privacy issues. We present privateQTL, a novel framework leveraging secure multi-party computation for secure and federated eQTL mapping. When tested in a real-world scenario with data from different studies, privateQTL outperformed meta-analysis by accurately correcting for covariates and batch effect and retaining higher accuracy and precision for both eGene-eVariant mapping and effect size estimation. In addition, privateQTL is modular and scalable, making it adaptable for other molecular phenotypes and large-scale studies. Our results indicate that privateQTL is a practical solution for privacy-preserving collaborative eQTL mapping.","journal":"Cell Genomics","year":2025,"id":550161,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9511,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1445831,"name":"Yebin Kim","orcid":null,"position":1,"is_corresponding":false},{"id":1445832,"name":"Peihan Miao","orcid":null,"position":2,"is_corresponding":false},{"id":14836,"name":"Tuuli Lappalainen","orcid":"0000-0002-7746-8109","position":3,"is_corresponding":false},{"id":6259,"name":"Gamze Gürsoy","orcid":"0000-0002-1352-8686","position":4,"is_corresponding":false},{"id":856934,"name":"Yoolim A. Choi","orcid":null,"position":0,"is_corresponding":true}],"reference_count":58,"raw_metadata":null,"created_at":"2026-07-19T02:54:16.596730Z","pmid":"39947138","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":[]}