{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T15:51:25Z","timestamp":1765554685231,"version":"3.48.0"},"reference-count":0,"publisher":"Walter de Gruyter GmbH","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>The objective of this research was to identify potential biological pathways associated with non-syndromic cleft lip with or without cleft palate (NSCL\/P), and to explore the potential biological mechanisms underlying these associated pathways on risk of NSCL\/P. This project was based on the dataset of a previously published genome-wide association (GWA) study on NSCL\/P (Beaty et al. 2010). Case-parent trios used here originated from an international consortium (The Gene, Environment Association Studies consortium, GENEVA) formed in 2007. A total of 5,742 individuals from 1,908 CL\/P case-parents trios (1,591 complete trios and 317 incomplete trios where one parent was missing) were collected and genotyped using the Illumina Human610-Quad array. Candidate pathways were selected using a list of 356 genes that may be related to oral clefts. In total, 42 candidate pathways, which included 1,564 genes and 40,208 SNPs were tested. Using a pathway-based analysis approach proposed by Wang et al (2007), we conducted a permutation-based test to assess the statistical significance of the nominal p-values of 42 candidate pathways. The analysis revealed several pathways yielding nominally significant p-values. However, controlling for the family wise error rate, none of these pathways could retain statistical significance. Nominal p-values of these pathways were concentrated at the lower tail of the distribution, with more than expected low p-values. A permutation based test for examining this type of distribution pattern yielded an overall p-value of 0.029. Thus, while this pathway-based analysis did not yield a clear significant result for any particular pathway, we conclude that one or more of the genes and pathways considered here likely do play a role in oral clefting.<\/jats:p>","DOI":"10.2202\/1544-6115.1717","type":"journal-article","created":{"date-parts":[[2014,8,11]],"date-time":"2014-08-11T09:49:03Z","timestamp":1407750543000},"source":"Crossref","is-referenced-by-count":8,"title":["Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate"],"prefix":"10.2202","volume":"11","author":[{"given":"Tian-Xiao","family":"Zhang","sequence":"first","affiliation":[{"name":"Johns Hopkins University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terri H.","family":"Beaty","sequence":"additional","affiliation":[{"name":"Johns Hopkins University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingo","family":"Ruczinski","sequence":"additional","affiliation":[{"name":"Johns Hopkins University"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"374","published-online":{"date-parts":[[2012,1,6]]},"container-title":["Statistical Applications in Genetics and Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.2202\/1544-6115.1717\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.2202\/1544-6115.1717\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T15:26:30Z","timestamp":1765553190000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.2202\/1544-6115.1717\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,6]]},"references-count":0,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2012,1,6]]}},"alternative-id":["10.2202\/1544-6115.1717"],"URL":"https:\/\/doi.org\/10.2202\/1544-6115.1717","relation":{},"ISSN":["1544-6115"],"issn-type":[{"type":"electronic","value":"1544-6115"}],"subject":[],"published":{"date-parts":[[2012,1,6]]}}}