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Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family.

Zhou LP, Liu WW, Zhang TE, Li WH, Tan LL, Li WZ, Qin YH, Yang HY, Duan A, Wang MQ, Ding WJ - Evid Based Complement Alternat Med (2011)

Bottom Line: The S1172P substitution effect was evaluated as "possibly damaging" by PolyPhen.Conclusion.DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.

View Article: PubMed Central - PubMed

Affiliation: Department of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.

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 Ser(1172) was substituted by Pro(1172). 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.

No MeSH data available.


Pedigree tree of the collected KDS family. This family comprise four generations and 35 members that display an autosomal dominant model of inheritance. The KDS subjects were evaluated by a 40-item scoring table based on TCM criteria system of KDS promulgated by the Health Department of China (GB/T15657-1995). Dark color indicates KDS. The mark “?” indicates those were not evaluated due to death, nonaccessibility, or babies who were too young to be easily checked. The mark “∗” indicates those genome SNP were checked by SNP chip.  KDS: kidney-yang deficiency syndrome. TCM: traditional chinese medicine. SNP: single nucleotide polymorphism.
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Related In: Results  -  Collection


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fig1: Pedigree tree of the collected KDS family. This family comprise four generations and 35 members that display an autosomal dominant model of inheritance. The KDS subjects were evaluated by a 40-item scoring table based on TCM criteria system of KDS promulgated by the Health Department of China (GB/T15657-1995). Dark color indicates KDS. The mark “?” indicates those were not evaluated due to death, nonaccessibility, or babies who were too young to be easily checked. The mark “∗” indicates those genome SNP were checked by SNP chip. KDS: kidney-yang deficiency syndrome. TCM: traditional chinese medicine. SNP: single nucleotide polymorphism.

Mentions: A typical KDS pedigree, including 17 KDS patients distributed in four generations who live in the area surrounding Chengdu, China, was selected as the subject for the present study. Their KDS symptoms were confirmed by repeated TCM diagnosis and clinic biochemistry assays [8]. Twelve available KDS subjects (Figure 1) were collected for genetic analysis. Simultaneously, three healthy spouses, whose life environment and ages were best matched with those of the KDS subjects, were recruited as non-KDS controls.


Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family.

Zhou LP, Liu WW, Zhang TE, Li WH, Tan LL, Li WZ, Qin YH, Yang HY, Duan A, Wang MQ, Ding WJ - Evid Based Complement Alternat Med (2011)

Pedigree tree of the collected KDS family. This family comprise four generations and 35 members that display an autosomal dominant model of inheritance. The KDS subjects were evaluated by a 40-item scoring table based on TCM criteria system of KDS promulgated by the Health Department of China (GB/T15657-1995). Dark color indicates KDS. The mark “?” indicates those were not evaluated due to death, nonaccessibility, or babies who were too young to be easily checked. The mark “∗” indicates those genome SNP were checked by SNP chip.  KDS: kidney-yang deficiency syndrome. TCM: traditional chinese medicine. SNP: single nucleotide polymorphism.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3106376&req=5

fig1: Pedigree tree of the collected KDS family. This family comprise four generations and 35 members that display an autosomal dominant model of inheritance. The KDS subjects were evaluated by a 40-item scoring table based on TCM criteria system of KDS promulgated by the Health Department of China (GB/T15657-1995). Dark color indicates KDS. The mark “?” indicates those were not evaluated due to death, nonaccessibility, or babies who were too young to be easily checked. The mark “∗” indicates those genome SNP were checked by SNP chip. KDS: kidney-yang deficiency syndrome. TCM: traditional chinese medicine. SNP: single nucleotide polymorphism.
Mentions: A typical KDS pedigree, including 17 KDS patients distributed in four generations who live in the area surrounding Chengdu, China, was selected as the subject for the present study. Their KDS symptoms were confirmed by repeated TCM diagnosis and clinic biochemistry assays [8]. Twelve available KDS subjects (Figure 1) were collected for genetic analysis. Simultaneously, three healthy spouses, whose life environment and ages were best matched with those of the KDS subjects, were recruited as non-KDS controls.

Bottom Line: The S1172P substitution effect was evaluated as "possibly damaging" by PolyPhen.Conclusion.DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.

View Article: PubMed Central - PubMed

Affiliation: Department of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.

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 Ser(1172) was substituted by Pro(1172). 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.

No MeSH data available.