{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T16:20:28Z","timestamp":1768926028749,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,12,12]],"date-time":"2018-12-12T00:00:00Z","timestamp":1544572800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"SNSF Starting"},{"name":"Significant Pattern Mining"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Combinatorial association mapping aims to assess the statistical association of higher-order interactions of genetic markers with a phenotype of interest. This article presents combinatorial association mapping (CASMAP), a software package that leverages recent advances in significant pattern mining to overcome the statistical and computational challenges that have hindered combinatorial association mapping. CASMAP can be used to perform region-based association studies and to detect higher-order epistatic interactions of genetic variants. Most importantly, unlike other existing significant pattern mining-based tools, CASMAP allows for the correction of categorical covariates such as age or gender, making it suitable for genome-wide association studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The R and Python packages can be downloaded from our GitHub repository http:\/\/github.com\/BorgwardtLab\/CASMAP. The R package is also available on CRAN.<\/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\/bty1020","type":"journal-article","created":{"date-parts":[[2018,12,10]],"date-time":"2018-12-10T20:16:21Z","timestamp":1544472981000},"page":"2680-2682","source":"Crossref","is-referenced-by-count":9,"title":["CASMAP: detection of statistically significant combinations of SNPs in association mapping"],"prefix":"10.1093","volume":"35","author":[{"given":"Felipe","family":"Llinares-L\u00f3pez","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laetitia","family":"Papaxanthos","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damian","family":"Roqueiro","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dean","family":"Bodenham","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karsten","family":"Borgwardt","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,12,12]]},"reference":[{"key":"2023062713263670800_bty1020-B1","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nature12625","article-title":"The causes and consequences of genetic heterogeneity in cancer evolution","volume":"501","author":"Burrell","year":"2013","journal-title":"Nature"},{"key":"2023062713263670800_bty1020-B2","doi-asserted-by":"crossref","first-page":"2463.","DOI":"10.1093\/hmg\/11.20.2463","article-title":"Epistasis: what it means, what it doesn\u2019t mean, and statistical methods to detect it in humans","volume":"11","author":"Cordell","year":"2002","journal-title":"Hum. Mol. Genet"},{"key":"2023062713263670800_bty1020-B3","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.ajhg.2014.06.009","article-title":"Rare-variant association analysis: study designs and statistical tests","volume":"95","author":"Lee","year":"2014","journal-title":"Am. J. Hum. Genet"},{"key":"2023062713263670800_bty1020-B4","doi-asserted-by":"crossref","first-page":"i240.","DOI":"10.1093\/bioinformatics\/btv263","article-title":"Genome-wide detection of intervals of genetic heterogeneity associated with complex traits","volume":"31","author":"Llinares-L\u00f3pez","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062713263670800_bty1020-B5","doi-asserted-by":"crossref","first-page":"1820","DOI":"10.1093\/bioinformatics\/btx071","article-title":"Genome-wide genetic heterogeneity discovery with categorical covariates","volume":"33","author":"Llinares-L\u00f3pez","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062713263670800_bty1020-B6","first-page":"2271","article-title":"Finding significant combinations of features in the presence of categorical covariates","volume-title":"Advances in Neural Information Processing Systems","author":"Papaxanthos","year":"2016"},{"key":"2023062713263670800_bty1020-B7","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet"},{"key":"2023062713263670800_bty1020-B8","doi-asserted-by":"crossref","first-page":"32","DOI":"10.3109\/15412550903499522","article-title":"Genetic epidemiology of COPD (COPDGene) study design","volume":"7","author":"Regan","year":"2011","journal-title":"COPD"},{"key":"2023062713263670800_bty1020-B9","doi-asserted-by":"crossref","first-page":"515","DOI":"10.2307\/2531456","article-title":"A modified Bonferroni method for discrete data","volume":"46","author":"Tarone","year":"1990","journal-title":"Biometrics"},{"key":"2023062713263670800_bty1020-B10","doi-asserted-by":"crossref","first-page":"12996","DOI":"10.1073\/pnas.1302233110","article-title":"Statistical significance of combinatorial regulations","volume":"110","author":"Terada","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062713263670800_bty1020-B11","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/bty219","article-title":"MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms","volume":"34","author":"Yoshizoe","year":"2018","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/15\/2680\/50722499\/bioinformatics_35_15_2680.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/15\/2680\/50722499\/bioinformatics_35_15_2680.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T13:26:56Z","timestamp":1687872416000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/15\/2680\/5239654"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,12,12]]},"references-count":11,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2019,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty1020","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,8,1]]},"published":{"date-parts":[[2018,12,12]]}}}