{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:46Z","timestamp":1753875886247,"version":"3.41.2"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12325110","12288201"],"award-info":[{"award-number":["12325110","12288201"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The Sequence Kernel Association Test (SKAT) and its extensions are the most popular methods for studying the association between phenotypes and a set of single nucleotide polymorphisms. Their practical application is very wide, but most of these methods are designed for continuous and binary phenotypes. Ordered categorical phenotypes are also very common in practice, so there is an urgent need to develop SKAT-type tests for proportional odds model.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To accommodate ordered categorical phenotypes, we propose a test named the Sequence Kernel Association Test for the Proportional Odds Model (POM-SKAT). It constructs a score test for the variance of the coefficients of interest using a quasi-likelihood and the P-value is evaluated by approximating the asymptotic distribution of the test statistic with the Pearson Type III distribution. Simulation studies demonstrate that our method performs well and achieves high power in detecting gene-phenotype associations. We apply POM-SKAT to rheumatoid arthritis data provided by Genetic Analysis Workshop 16, identifying multiple relevant gene variants.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code is available at GitHub (https:\/\/github.com\/amss-stat\/POM-SKAT).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf304","type":"journal-article","created":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T05:36:02Z","timestamp":1751002562000},"source":"Crossref","is-referenced-by-count":0,"title":["The sequence kernel association test for the proportional odds model"],"prefix":"10.1093","volume":"41","author":[{"given":"Jingxin","family":"Yan","sequence":"first","affiliation":[{"name":"State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","place":["China"]},{"name":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049,","place":["China"]}]},{"given":"Xiaoyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","place":["China"]}]},{"given":"Shuying","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Changchun University of Technology , Changchun 130012,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4320-8528","authenticated-orcid":false,"given":"Jinjuan","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Beijing Institute of Technology , Beijing 100081,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3325-8265","authenticated-orcid":false,"given":"Qizhai","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","place":["China"]},{"name":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,6,23]]},"reference":[{"key":"2025070408270840800_btaf304-B1","doi-asserted-by":"crossref","DOI":"10.1002\/9780470594001","volume-title":"Analysis of Ordinal Categorical Data","author":"Agresti","year":"2010"},{"key":"2025070408270840800_btaf304-B2","doi-asserted-by":"crossref","first-page":"2739","DOI":"10.1093\/hmg\/ddq155","article-title":"Genome-wide association study of circulating vitamin D levels","volume":"19","author":"Ahn","year":"2010","journal-title":"Hum Mol 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