{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:39Z","timestamp":1772138079981,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM59507"],"award-info":[{"award-number":["R01 GM59507"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01 HG005718"],"award-info":[{"award-number":["U01 HG005718"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks. Under such circumstances, a computational approach that may increase signal replication rate and identify potential functional sites among correlated markers is urgently needed.<\/jats:p>\n                  <jats:p>Results: We describe GenoWAP, a GWAS signal prioritization method that integrates genomic functional annotation and GWAS test statistics. The effectiveness of GenoWAP is demonstrated through its applications to Crohn\u2019s disease and schizophrenia using the largest studies available, where highly ranked loci show substantially stronger signals in the whole dataset after prioritization based on a subset of samples. At the single nucleotide polymorphism (SNP) level, top ranked SNPs after prioritization have both higher replication rates and consistently stronger enrichment of eQTLs. Within each risk locus, GenoWAP may be able to distinguish functional sites from groups of correlated SNPs.<\/jats:p>\n                  <jats:p>Availability and implementation: GenoWAP is freely available on the web at http:\/\/genocanyon.med.yale.edu\/GenoWAP<\/jats:p>\n                  <jats:p>Contact: \u00a0hongyu.zhao@yale.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv610","type":"journal-article","created":{"date-parts":[[2015,10,26]],"date-time":"2015-10-26T20:20:03Z","timestamp":1445890803000},"page":"542-548","source":"Crossref","is-referenced-by-count":45,"title":["GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation"],"prefix":"10.1093","volume":"32","author":[{"given":"Qiongshi","family":"Lu","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA,"}]},{"given":"Xinwei","family":"Yao","sequence":"additional","affiliation":[{"name":"2 Yale College, New Haven, CT, USA,"}]},{"given":"Yiming","family":"Hu","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA,"}]},{"given":"Hongyu","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA,"},{"name":"3 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA and"},{"name":"4 VA Cooperative Studies Program Coordinating Center, West Haven, CT, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,10,25]]},"reference":[{"key":"2023020110321816100_btv610-B1","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Ardlie","year":"2015","journal-title":"Science"},{"key":"2023020110321816100_btv610-B2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Bernstein","year":"2012","journal-title":"Nature"},{"key":"2023020110321816100_btv610-B3","doi-asserted-by":"crossref","first-page":"e1004787","DOI":"10.1371\/journal.pgen.1004787","article-title":"GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation","volume":"10","author":"Chung","year":"2014","journal-title":"PLoS Genet."},{"key":"2023020110321816100_btv610-B6","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1038\/nrg3046","article-title":"Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data","volume":"12","author":"Cooper","year":"2011","journal-title":"Nat. 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