{"doi":"10.1101/2025.11.25.690514","title":"SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction","abstract":"Sum of Single Effects regression (SuSiE) has become widely adopted for genetic fine-mapping, yet its original implementation faces architectural limitations that hinder extensibility and performance. We present SuSiE 2.0, featuring a modular redesign for extensibility, up to 5x speed improvements for summary statistics applications, and several useful extensions including SuSiE-ash, a new method that improves calibration when strong signals coexist with moderate effects. Simulations and real data benchmarks demonstrate performance across diverse genetic architectures, highlighting improved calibration of SuSiE-ash for fine-mapping under complex polygenic backgrounds with 1.5-3x FDR reduction while maintaining power, and revealing SuSiE-based methods as effective yet underappreciated tools for TWAS prediction.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":555302,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9436,"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":1453608,"name":"Yanghyeon Cho","orcid":"0000-0002-3641-0162","position":1,"is_corresponding":false},{"id":888436,"name":"Ruixi Li","orcid":"0000-0003-4763-5436","position":2,"is_corresponding":false},{"id":29407,"name":"Daniel Nachun","orcid":"0000-0002-0271-1135","position":3,"is_corresponding":false},{"id":1453609,"name":"Hao Gan","orcid":"0000-0003-3926-6239","position":4,"is_corresponding":false},{"id":106843,"name":"Peter Carbonetto","orcid":"0000-0003-1144-6780","position":5,"is_corresponding":false},{"id":5157,"name":"Matthew Stephens","orcid":"0000-0001-5397-9257","position":6,"is_corresponding":false},{"id":660310,"name":"William R. P. Denault","orcid":"0000-0002-9690-3890","position":7,"is_corresponding":false},{"id":29324,"name":"Gao Wang","orcid":"0000-0001-9336-402X","position":8,"is_corresponding":false},{"id":1454120,"name":"Alexander McCreight","orcid":null,"position":0,"is_corresponding":true}],"reference_count":21,"raw_metadata":null,"created_at":"2026-07-19T02:54:59.329539Z","pmid":"41394690","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":[]}