{"doi":"10.1101/2020.07.23.206391","title":"A novel haplotype-based eQTL approach identifies genetic associations not detected through conventional SNP-based methods","abstract":"Abstract Motivation The high accuracy of current haplotype phasing tools has enabled the interrogation of haplotype (or phase) information more widely in genetic investigations. Including such information in eQTL analysis complements SNP-based approaches as it has the potential to detect associations that may otherwise be missed. Results We have developed a haplotype-based eQTL approach called eQTLHap to investigate associations between gene expression and haplotype blocks. Using simulations, we demonstrate that eQTLHap significantly outperforms typical SNP-based eQTL methods when the causal genetic architecture involves multiple SNPs. We show that phasing errors slightly impact the sensitivity of the proposed method (< 4%). Finally, the application of eQTLHap to real GEUVADIS and GTEx datasets finds 22 associations that replicated in larger studies or other tissues and could not be detected using a single-SNP approach. Availability https://github.com/ziadbkh/eQTLHap .","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":130505,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9543,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":583195,"name":"Gursharan Chana","orcid":"0000-0002-1096-1986","position":1,"is_corresponding":false},{"id":583196,"name":"Cheng Soon Ong","orcid":"0000-0002-2302-9733","position":2,"is_corresponding":false},{"id":583197,"name":"Benjamin Goudey","orcid":"0000-0002-2318-985X","position":3,"is_corresponding":false},{"id":258989,"name":"Kotagiri Ramamohanarao","orcid":"0000-0003-3304-9268","position":4,"is_corresponding":false},{"id":583194,"name":"Ziad Al Bkhetan","orcid":"0000-0002-4032-5331","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":null,"created_at":"2026-07-18T23:15:56.698770Z","pmid":null,"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":[]}