Whole-exome sequencing for the identification of susceptibility genes of Kashin-Beck disease

Yang, Zhenxing, Xu, Yu, Luo, Hongrong, Ma, Xiaohong, Wang, Qiang, Wang, Yingcheng, Deng, Wei, Jiang, Tao, Sun, Guangqing, He, Tingting, Hu, Jingchu, Li, Yingrui, Wang, Jun, Li, Tao and Hu, Xun (2014) Whole-exome sequencing for the identification of susceptibility genes of Kashin-Beck disease. PLoS ONE, 9 4: . doi:10.1371/journal.pone.0092298


Author Yang, Zhenxing
Xu, Yu
Luo, Hongrong
Ma, Xiaohong
Wang, Qiang
Wang, Yingcheng
Deng, Wei
Jiang, Tao
Sun, Guangqing
He, Tingting
Hu, Jingchu
Li, Yingrui
Wang, Jun
Li, Tao
Hu, Xun
Title Whole-exome sequencing for the identification of susceptibility genes of Kashin-Beck disease
Journal name PLoS ONE   Check publisher's open access policy
ISSN 1932-6203
Publication date 2014-04
Year available 2014
Sub-type Article (original research)
DOI 10.1371/journal.pone.0092298
Open Access Status DOI
Volume 9
Issue 4
Total pages 6
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
Formatted abstract
Objective

To identify and investigate the susceptibility genes of Kashin–Beck disease (KBD) in Chinese population.

Methods


Whole-exome capturing and sequencing technology was used for the detection of genetic variations in 19 individuals from six families with high incidence of KBD. A total of 44 polymorphisms from 41 genes were genotyped from a total of 144 cases and 144 controls by using MassARRAY under the standard protocol from Sequenom. Association was applied on the data by using PLINK1.07.

Results

In the sequencing stage, each sample showed approximately 70-fold coverage, thus covering more than 99% of the target regions. Among the single nucleotide polymorphisms (SNPs) used in the transmission disequilibrium test, 108 had a p-value of <0.01, whereas 1056 had a p-value of <0.05. Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis indicates that these SNPs focus on three major pathways: regulation of actin cytoskeleton, focal adhesion, and metabolic pathways. In the validation stage, single locus effects revealed that two of these polymorphisms (rs7745040 and rs9275295) in the human leukocyte antigen (HLA)-DRB1 gene and one polymorphism (rs9473132) in CD2-associated protein (CD2AP) gene have a significant statistical association with KBD.

Conclusions

HLA-DRB1 and CD2AP gene were identified to be among the susceptibility genes of KBD, thus supporting the role of the autoimmune response in KBD and the possibility of shared etiology between osteoarthritis, rheumatoid arthritis, and KBD.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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