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Article: Identification of linkage disequilibrium SNPs from a Kidney-yang deficiency syndrome pedigree

TitleIdentification of linkage disequilibrium SNPs from a Kidney-yang deficiency syndrome pedigree
Authors
Issue Date2009
PublisherWorld Scientific Publishing Co Pte Ltd. The Journal's web site is located at http://www.worldscinet.com/ajcm/ajcm.shtml
Citation
American Journal Of Chinese Medicine, 2009, v. 37 n. 3, p. 427-438 How to Cite?
AbstractIn order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required. © 2009 World Scientific Publishing Company.
Persistent Identifierhttp://hdl.handle.net/10722/179149
ISSN
2015 Impact Factor: 2.959
2015 SCImago Journal Rankings: 0.797
References

 

DC FieldValueLanguage
dc.contributor.authorDing, WJen_US
dc.contributor.authorZeng, YZen_US
dc.contributor.authorLi, WHen_US
dc.contributor.authorZhang, TEen_US
dc.contributor.authorLiu, WWen_US
dc.contributor.authorTeng, XKen_US
dc.contributor.authorMa, YXen_US
dc.contributor.authorYan, SLen_US
dc.contributor.authorWan, JMFen_US
dc.contributor.authorWang, MQen_US
dc.date.accessioned2012-12-19T09:52:23Z-
dc.date.available2012-12-19T09:52:23Z-
dc.date.issued2009en_US
dc.identifier.citationAmerican Journal Of Chinese Medicine, 2009, v. 37 n. 3, p. 427-438en_US
dc.identifier.issn0192-415Xen_US
dc.identifier.urihttp://hdl.handle.net/10722/179149-
dc.description.abstractIn order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required. © 2009 World Scientific Publishing Company.en_US
dc.languageengen_US
dc.publisherWorld Scientific Publishing Co Pte Ltd. The Journal's web site is located at http://www.worldscinet.com/ajcm/ajcm.shtmlen_US
dc.relation.ispartofAmerican Journal of Chinese Medicineen_US
dc.subject.meshFamily Healthen_US
dc.subject.meshFemaleen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHumansen_US
dc.subject.meshKidney Diseases - Geneticsen_US
dc.subject.meshLinkage Disequilibriumen_US
dc.subject.meshMaleen_US
dc.subject.meshMedicine, Chinese Traditionalen_US
dc.subject.meshPedigreeen_US
dc.subject.meshPolymorphism, Single Nucleotideen_US
dc.subject.meshYang Deficiency - Geneticsen_US
dc.titleIdentification of linkage disequilibrium SNPs from a Kidney-yang deficiency syndrome pedigreeen_US
dc.typeArticleen_US
dc.identifier.emailWan, JMF: jmfwan@hku.hken_US
dc.identifier.authorityWan, JMF=rp00798en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1142/S0192415X09006953en_US
dc.identifier.pmid19606505-
dc.identifier.scopuseid_2-s2.0-68149171589en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-68149171589&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume37en_US
dc.identifier.issue3en_US
dc.identifier.spage427en_US
dc.identifier.epage438en_US
dc.publisher.placeSingaporeen_US
dc.identifier.scopusauthoridDing, WJ=26639234000en_US
dc.identifier.scopusauthoridZeng, YZ=35217125600en_US
dc.identifier.scopusauthoridLi, WH=24348010700en_US
dc.identifier.scopusauthoridZhang, TE=35207537500en_US
dc.identifier.scopusauthoridLiu, WW=26643405200en_US
dc.identifier.scopusauthoridTeng, XK=24081680800en_US
dc.identifier.scopusauthoridMa, YX=7404700917en_US
dc.identifier.scopusauthoridYan, SL=33167837600en_US
dc.identifier.scopusauthoridWan, JMF=8930305000en_US
dc.identifier.scopusauthoridWang, MQ=13605467900en_US

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