{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:52:00Z","timestamp":1776214320456,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T00:00:00Z","timestamp":1614124800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases P30 Center for the Advancement of Precision Medicine in Rheumatology","award":["P30AR070155"],"award-info":[{"award-number":["P30AR070155"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01HG008140"],"award-info":[{"award-number":["R01HG008140"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sandler Asthma Basic Research Center"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21AI1280471"],"award-info":[{"award-number":["R21AI1280471"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000884","name":"Cancer Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014220","name":"Innovative Genomics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014220","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014547","name":"Parker Institute for Cancer Immunotherapy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014547","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The Probabilistic Identification of Causal SNPs (PICS) algorithm and web application was developed as a fine-mapping tool to determine the likelihood that each single nucleotide polymorphism (SNP) in LD with a reported index SNP is a true causal polymorphism. PICS is notable for its ability to identify candidate causal SNPs within a locus using only the index SNP, which are widely available from published GWAS, whereas other methods require full summary statistics or full genotype data. However, the original PICS web application operates on a single SNP at a time, with slow performance, severely limiting its usability. We have developed a next-generation PICS tool, PICS2, which enables performance of PICS analyses of large batches of index SNPs with much faster performance. Additional updates and extensions include use of LD reference data generated from 1000 Genomes phase 3; annotation of variant consequences; annotation of GTEx eQTL genes and downloadable PICS SNPs from GTEx eQTLs; the option of generating PICS probabilities from experimental summary statistics; and generation of PICS SNPs from all SNPs of the GWAS catalog, automatically updated weekly. These free and easy-to-use resources will enable efficient determination of candidate loci for biological studies to investigate the true causal variants underlying disease processes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PICS2 is available at https:\/\/pics2.ucsf.edu.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab122","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T15:42:10Z","timestamp":1614094930000},"page":"3004-3007","source":"Crossref","is-referenced-by-count":35,"title":["PICS2: next-generation fine mapping via probabilistic identification of causal SNPs"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6848-9074","authenticated-orcid":false,"given":"Kimberly E","family":"Taylor","sequence":"first","affiliation":[{"name":"Russell\/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco , CA,","place":["USA"]}]},{"given":"K Mark","family":"Ansel","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of California , San Francisco, CA,","place":["USA"]},{"name":"Sandler Asthma Basic Research Center, University of California , San Francisco, CA,","place":["USA"]}]},{"given":"Alexander","family":"Marson","sequence":"additional","affiliation":[{"name":"Russell\/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco , CA,","place":["USA"]},{"name":"Department of Microbiology and Immunology, University of California , San Francisco, CA,","place":["USA"]},{"name":"Gladstone Institutes, University of California , San Francisco, CA,","place":["USA"]}]},{"given":"Lindsey A","family":"Criswell","sequence":"additional","affiliation":[{"name":"Russell\/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco , CA,","place":["USA"]}]},{"given":"Kyle Kai-How","family":"Farh","sequence":"additional","affiliation":[{"name":"Illumina, Inc , San Diego, CA 92122","place":["USA"]}]}],"member":"286","published-online":{"date-parts":[[2021,2,24]]},"reference":[{"key":"2026041420022504000_btab122-B1","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026041420022504000_btab122-B2","doi-asserted-by":"crossref","first-page":"D745","DOI":"10.1093\/nar\/gky1113","article-title":"Ensembl 2019","volume":"47","author":"Cunningham","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026041420022504000_btab122-B3","doi-asserted-by":"crossref","first-page":"e60646","DOI":"10.1371\/journal.pone.0060646","article-title":"Evidence of new risk genetic factor to systemic lupus erythematosus: the UBASH3A gene","volume":"8","author":"Diaz-Gallo","year":"2013","journal-title":"PLoS One"},{"key":"2026041420022504000_btab122-B4","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature13835","article-title":"Genetic and epigenetic fine mapping of causal autoimmune disease variants","volume":"518","author":"Farh","year":"2015","journal-title":"Nature"},{"key":"2026041420022504000_btab122-B5","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/s41431-018-0123-5","article-title":"Molecular-genetic characterization of common, noncoding UBASH3A variants associated with type 1 diabetes","volume":"26","author":"Ge","year":"2018","journal-title":"Eur. 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