Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

6 Issues per year


IMPACT FACTOR 2016: 0.646
5-year IMPACT FACTOR: 1.191

CiteScore 2016: 0.94

SCImago Journal Rank (SJR) 2016: 0.625
Source Normalized Impact per Paper (SNIP) 2016: 0.596

Mathematical Citation Quotient (MCQ) 2016: 0.06

Online
ISSN
1544-6115
See all formats and pricing
More options …
Volume 11, Issue 2 (Jan 2012)

Issues

Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate

Tian-Xiao Zhang / Terri H. Beaty / Ingo Ruczinski
Published Online: 2012-01-06 | DOI: https://doi.org/10.2202/1544-6115.1717

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.

Keywords: case-parent trios; oral clefts; single nucleotide polymorphisms; genes; pathways

About the article

Published Online: 2012-01-06


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1717.

Export Citation

©2012 Walter de Gruyter GmbH & Co. KG, Berlin/Boston. Copyright Clearance Center

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Dong Shang, Li Dong, Lingfang Zeng, Rui Yang, Jing Xu, Yue Wu, Ran Xu, Hong Tao, and Nan Zhang
Scientific Reports, 2016, Volume 5, Number 1
[2]
Qianqian Chen, Hong Wang, Holger Schwender, Tianxiao Zhang, Jacqueline B. Hetmanski, Yah-Huei Wu Chou, Xiaoqian Ye, Vincent Yeow, Samuel S. Chong, Bo Zhang, Ethylin Wang Jabs, Margaret M. Parker, Alan F. Scott, Terri H. Beaty, and Maranke I. Koster
PLoS ONE, 2014, Volume 9, Number 10, Page e109038

Comments (0)

Please log in or register to comment.
Log in