Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family
Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibri...
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| creator | Yang, Hong Ya Duan, Azure Wang, Mi Qu Ding, Wei Jun Zhou, Li Ping Qin, Yu Hua Li, Wan Zhen Tan, Ling Ling Liu, Wei Wei Zhang, Tian E. Li, Wei Hong |
| description | Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced. Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172 was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen. Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS. |
| doi_str_mv | 10.1155/2011/215653 |
| format | Article |
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To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced. Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172 was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen. Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.</description><identifier>ISSN: 1741-427X</identifier><identifier>EISSN: 1741-4288</identifier><identifier>DOI: 10.1155/2011/215653</identifier><identifier>PMID: 21647313</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Puplishing Corporation</publisher><subject>Alternative medicine ; Deoxyribonucleic acid ; Diabetes ; Disease ; DNA ; Doublecortin protein ; Exons ; Flanks ; Gene polymorphism ; Genes ; Genetic testing ; Genetics ; Genomes ; Genomics ; Kidneys ; Laboratories ; Leucine-tRNA ligase ; Linkage disequilibrium ; Mutation ; Single-nucleotide polymorphism ; Software ; tRNA</subject><ispartof>Evidence-based complementary and alternative medicine, 2011, Vol.2011 (2011), p.1-7</ispartof><rights>Copyright © 2011 Li Ping Zhou et al.</rights><rights>Copyright © 2011 Li Ping Zhou et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. https://creativecommons.org/licenses/by/4.0</rights><rights>Copyright © 2011 Li Ping Zhou et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3803-f49919c433eaa4451fa6b9803ffa33e51864b68c712e5d3c34d42d9a27fa6bc03</citedby><cites>FETCH-LOGICAL-c3803-f49919c433eaa4451fa6b9803ffa33e51864b68c712e5d3c34d42d9a27fa6bc03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106376/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106376/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,887,4026,27930,27931,27932,53798,53800</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21647313$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Hong Ya</creatorcontrib><creatorcontrib>Duan, Azure</creatorcontrib><creatorcontrib>Wang, Mi Qu</creatorcontrib><creatorcontrib>Ding, Wei Jun</creatorcontrib><creatorcontrib>Zhou, Li Ping</creatorcontrib><creatorcontrib>Qin, Yu Hua</creatorcontrib><creatorcontrib>Li, Wan Zhen</creatorcontrib><creatorcontrib>Tan, Ling Ling</creatorcontrib><creatorcontrib>Liu, Wei Wei</creatorcontrib><creatorcontrib>Zhang, Tian E.</creatorcontrib><creatorcontrib>Li, Wei Hong</creatorcontrib><title>Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family</title><title>Evidence-based complementary and alternative medicine</title><addtitle>Evid Based Complement Alternat Med</addtitle><description>Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced. Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172 was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen. Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.</description><subject>Alternative medicine</subject><subject>Deoxyribonucleic acid</subject><subject>Diabetes</subject><subject>Disease</subject><subject>DNA</subject><subject>Doublecortin protein</subject><subject>Exons</subject><subject>Flanks</subject><subject>Gene polymorphism</subject><subject>Genes</subject><subject>Genetic testing</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Kidneys</subject><subject>Laboratories</subject><subject>Leucine-tRNA ligase</subject><subject>Linkage disequilibrium</subject><subject>Mutation</subject><subject>Single-nucleotide 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Hong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family</atitle><jtitle>Evidence-based complementary and alternative medicine</jtitle><addtitle>Evid Based Complement Alternat Med</addtitle><date>2011</date><risdate>2011</risdate><volume>2011</volume><issue>2011</issue><spage>1</spage><epage>7</epage><pages>1-7</pages><issn>1741-427X</issn><eissn>1741-4288</eissn><abstract>Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced. Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172 was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen. Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.</abstract><cop>Cairo, Egypt</cop><pub>Hindawi Puplishing Corporation</pub><pmid>21647313</pmid><doi>10.1155/2011/215653</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Alternative medicine Deoxyribonucleic acid Diabetes Disease DNA Doublecortin protein Exons Flanks Gene polymorphism Genes Genetic testing Genetics Genomes Genomics Kidneys Laboratories Leucine-tRNA ligase Linkage disequilibrium Mutation Single-nucleotide polymorphism Software tRNA |
| title | Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family |
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