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Article: Identification of genes for bone mineral density variation by computational disease gene identification strategy

TitleIdentification of genes for bone mineral density variation by computational disease gene identification strategy
Authors
KeywordsAssociation
Bone mineral density
Genetics
MATN3
Osteoporosis
Issue Date2011
PublisherSpringer Japan. The Journal's web site is located at http://link.springer.de/link/service/journals/00774/index.htm
Citation
Journal Of Bone And Mineral Metabolism, 2011, v. 29 n. 6, p. 709-716 How to Cite?
AbstractWe previously used five freely available bioinformatics tools (Prioritizer, Geneseeker, PROSPECTR and SUSPECTS, Disease Gene Prediction, and Endeavour) to analyze the thirteen well-replicated osteoporosis susceptibility loci and identify a subset of most likely candidate osteoporosis susceptibility genes (Huang et al. in J Hum Genet 53:644-655, 2008). In the current study, we experimentally tested the association between bone mineral density (BMD) and the 9 most likely candidate genes [LAMC2(1q25-q31), MATN3(2p24-p23), ITGAV(2q31-q32), ACVR1(2q23-q24), TDGF1(3p21.31), EGF(4q25), IGF1(12q22-q23), ZIC2(13q32), BMP2(20p12)] which were pinpointed by 4 or more bioinformatics tools. Forty tag SNPs in nine candidate genes were genotyped in a southern Chinese female case-control cohort consisting of 1643 subjects. Single- and multi-marker association analyses were performed using logistic regression analysis implemented by PLINK. Potential transcription factor binding sites were predicted by MatInspector. The strongest association was observed between rs10178256 (MATN3) and trochanter (P < 0.001) and total hip BMD (P = 0.002). The SNP rs6214 (IGF1) showed consistent association with BMD at all the four measured skeletal sites (P = 0.005-0.044). Prediction of transcription factor binding suggested that the minor allele G of rs10178256 might abolish the binding of MESP1 and MESP2 which play vital roles in bone homeostasis, whereas the minor allele G of rs6214 might create an additional binding site for XBP1, a constitutive regulator of endoplasmic reticulum stress response. Our data suggested that variants in MATN3 and IGF1 were involved in BMD regulation in southern Chinese women. © 2011 The Japanese Society for Bone and Mineral Research and Springer.
Persistent Identifierhttp://hdl.handle.net/10722/163430
ISSN
2015 Impact Factor: 2.312
2015 SCImago Journal Rankings: 0.775
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLi, GHYen_HK
dc.contributor.authorDeng, HWen_HK
dc.contributor.authorKung, AWCen_HK
dc.contributor.authorHuang, QYen_HK
dc.date.accessioned2012-09-05T05:31:16Z-
dc.date.available2012-09-05T05:31:16Z-
dc.date.issued2011en_HK
dc.identifier.citationJournal Of Bone And Mineral Metabolism, 2011, v. 29 n. 6, p. 709-716en_HK
dc.identifier.issn0914-8779en_HK
dc.identifier.urihttp://hdl.handle.net/10722/163430-
dc.description.abstractWe previously used five freely available bioinformatics tools (Prioritizer, Geneseeker, PROSPECTR and SUSPECTS, Disease Gene Prediction, and Endeavour) to analyze the thirteen well-replicated osteoporosis susceptibility loci and identify a subset of most likely candidate osteoporosis susceptibility genes (Huang et al. in J Hum Genet 53:644-655, 2008). In the current study, we experimentally tested the association between bone mineral density (BMD) and the 9 most likely candidate genes [LAMC2(1q25-q31), MATN3(2p24-p23), ITGAV(2q31-q32), ACVR1(2q23-q24), TDGF1(3p21.31), EGF(4q25), IGF1(12q22-q23), ZIC2(13q32), BMP2(20p12)] which were pinpointed by 4 or more bioinformatics tools. Forty tag SNPs in nine candidate genes were genotyped in a southern Chinese female case-control cohort consisting of 1643 subjects. Single- and multi-marker association analyses were performed using logistic regression analysis implemented by PLINK. Potential transcription factor binding sites were predicted by MatInspector. The strongest association was observed between rs10178256 (MATN3) and trochanter (P < 0.001) and total hip BMD (P = 0.002). The SNP rs6214 (IGF1) showed consistent association with BMD at all the four measured skeletal sites (P = 0.005-0.044). Prediction of transcription factor binding suggested that the minor allele G of rs10178256 might abolish the binding of MESP1 and MESP2 which play vital roles in bone homeostasis, whereas the minor allele G of rs6214 might create an additional binding site for XBP1, a constitutive regulator of endoplasmic reticulum stress response. Our data suggested that variants in MATN3 and IGF1 were involved in BMD regulation in southern Chinese women. © 2011 The Japanese Society for Bone and Mineral Research and Springer.en_HK
dc.languageengen_US
dc.publisherSpringer Japan. The Journal's web site is located at http://link.springer.de/link/service/journals/00774/index.htmen_HK
dc.relation.ispartofJournal of Bone and Mineral Metabolismen_HK
dc.subjectAssociationen_HK
dc.subjectBone mineral densityen_HK
dc.subjectGeneticsen_HK
dc.subjectMATN3en_HK
dc.subjectOsteoporosisen_HK
dc.subject.meshAdulten_US
dc.subject.meshAgeden_US
dc.subject.meshBone Density - Geneticsen_US
dc.subject.meshComputational Biology - Methodsen_US
dc.subject.meshFemaleen_US
dc.subject.meshGenetic Predisposition To Disease - Geneticsen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHumansen_US
dc.subject.meshMiddle Ageden_US
dc.subject.meshPolymorphism, Single Nucleotide - Geneticsen_US
dc.titleIdentification of genes for bone mineral density variation by computational disease gene identification strategyen_HK
dc.typeArticleen_HK
dc.identifier.emailKung, AWC: awckung@hku.hken_HK
dc.identifier.emailHuang, QY: qyhuang@hotmail.comen_HK
dc.identifier.authorityKung, AWC=rp00368en_HK
dc.identifier.authorityHuang, QY=rp00521en_HK
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1007/s00774-011-0271-yen_HK
dc.identifier.pmid21638018-
dc.identifier.scopuseid_2-s2.0-83055181535en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-83055181535&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume29en_HK
dc.identifier.issue6en_HK
dc.identifier.spage709en_HK
dc.identifier.epage716en_HK
dc.identifier.isiWOS:000297199100009-
dc.publisher.placeJapanen_HK
dc.identifier.scopusauthoridLi, GHY=35080710200en_HK
dc.identifier.scopusauthoridDeng, HW=7401775190en_HK
dc.identifier.scopusauthoridKung, AWC=7102322339en_HK
dc.identifier.scopusauthoridHuang, QY=7403630787en_HK
dc.identifier.citeulike9412458-

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