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Exome sequencing identified FGF12 as a novel candidate gene for Kashin-Beck disease.
Funct Integr Genomics. 2016 Jan; 16(1):13-7.FI

Abstract

The objective of this study was to identify novel causal genes involved in the pathogenesis of Kashin-Beck disease (KBD). A representative grade III KBD sib pair with serious skeletal growth and development failure was subjected to exome sequencing using the Illumina Hiseq2000 platform. The detected gene mutations were then filtered against the data of 1000 Genome Project, dbSNP database, and BGI inhouse database, and replicated by a genome-wide association study (GWAS) of KBD. Ninety grade II or III KBD patients with extreme KBD phenotypes and 1627 healthy controls were enrolled in the GWAS. Affymetrix Genome-Wide Human SNP Array 6.0 was applied for genotyping. PLINK software was used for association analysis. We identified a novel 106T>C at the 3'UTR of the FGF12 gene, which has not been reported by now. Sequence alignment observed high conversation at the mutated 3'UTR+106T>C locus across various vertebrates. In the GWAS of KBD, we detected nine SNPs of the FGF12 gene showing association evidence (P value < 0.05) with KBD. The most significant association signal was observed at rs1847340 (P value = 1.90 × 10(-5)). This study suggests that FGF12 was a susceptibility gene of KBD. Our results provide novel clues for revealing the pathogenesis of KBD and the biological function of FGF12.

Authors+Show Affiliations

Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.BGI-Shenzhen, Shenzhen, 518083, China.Department of Nephrology and Traditional Chinese Medicine, The People's Liberating Army 451 Hospital, Xi'an, People's Republic of China.Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.BGI-Shenzhen, Shenzhen, 518083, China.BGI-Shenzhen, Shenzhen, 518083, China.Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China.Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China.Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA. Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China.Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China.Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA. Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA. Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.BGI-Shenzhen, Shenzhen, 518083, China. xuxun@genomics.org.cn.Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China. guox@mail.xjtu.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26290467

Citation

Zhang, Feng, et al. "Exome Sequencing Identified FGF12 as a Novel Candidate Gene for Kashin-Beck Disease." Functional & Integrative Genomics, vol. 16, no. 1, 2016, pp. 13-7.
Zhang F, Dai L, Lin W, et al. Exome sequencing identified FGF12 as a novel candidate gene for Kashin-Beck disease. Funct Integr Genomics. 2016;16(1):13-7.
Zhang, F., Dai, L., Lin, W., Wang, W., Liu, X., Zhang, J., Yang, T., Liu, X., Shen, H., Chen, X., Tan, L., Tian, Q., Deng, H. W., Xu, X., & Guo, X. (2016). Exome sequencing identified FGF12 as a novel candidate gene for Kashin-Beck disease. Functional & Integrative Genomics, 16(1), 13-7. https://doi.org/10.1007/s10142-015-0462-z
Zhang F, et al. Exome Sequencing Identified FGF12 as a Novel Candidate Gene for Kashin-Beck Disease. Funct Integr Genomics. 2016;16(1):13-7. PubMed PMID: 26290467.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Exome sequencing identified FGF12 as a novel candidate gene for Kashin-Beck disease. AU - Zhang,Feng, AU - Dai,Lanlan, AU - Lin,Weimin, AU - Wang,Wenyu, AU - Liu,Xuanzhu, AU - Zhang,Jianguo, AU - Yang,Tielin, AU - Liu,Xiaogang, AU - Shen,Hui, AU - Chen,Xiangding, AU - Tan,Lijun, AU - Tian,Qing, AU - Deng,Hong-Wen, AU - Xu,Xun, AU - Guo,Xiong, Y1 - 2015/08/20/ PY - 2015/05/04/received PY - 2015/08/02/accepted PY - 2015/07/30/revised PY - 2015/8/21/entrez PY - 2015/8/21/pubmed PY - 2016/10/26/medline KW - Exome sequencing KW - Fibroblast growth factor KW - Genome-wide association study KW - Kashin-Beck disease SP - 13 EP - 7 JF - Functional & integrative genomics JO - Funct. Integr. Genomics VL - 16 IS - 1 N2 - The objective of this study was to identify novel causal genes involved in the pathogenesis of Kashin-Beck disease (KBD). A representative grade III KBD sib pair with serious skeletal growth and development failure was subjected to exome sequencing using the Illumina Hiseq2000 platform. The detected gene mutations were then filtered against the data of 1000 Genome Project, dbSNP database, and BGI inhouse database, and replicated by a genome-wide association study (GWAS) of KBD. Ninety grade II or III KBD patients with extreme KBD phenotypes and 1627 healthy controls were enrolled in the GWAS. Affymetrix Genome-Wide Human SNP Array 6.0 was applied for genotyping. PLINK software was used for association analysis. We identified a novel 106T>C at the 3'UTR of the FGF12 gene, which has not been reported by now. Sequence alignment observed high conversation at the mutated 3'UTR+106T>C locus across various vertebrates. In the GWAS of KBD, we detected nine SNPs of the FGF12 gene showing association evidence (P value < 0.05) with KBD. The most significant association signal was observed at rs1847340 (P value = 1.90 × 10(-5)). This study suggests that FGF12 was a susceptibility gene of KBD. Our results provide novel clues for revealing the pathogenesis of KBD and the biological function of FGF12. SN - 1438-7948 UR - https://www.unboundmedicine.com/medline/citation/26290467/Exome_sequencing_identified_FGF12_as_a_novel_candidate_gene_for_Kashin_Beck_disease_ L2 - https://dx.doi.org/10.1007/s10142-015-0462-z DB - PRIME DP - Unbound Medicine ER -