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

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Protocol publication

[…] The detailed description of these procedures has been reported previously [, ]. Briefly, DNA samples were genotyped with the Affymetrix GeneChip Mapping 100K kit, at a commercial laboratory (National Engineering Center for Biochip at Shanghai, China). Genotype data of all the subjects were generated using a GeneChip DNA analysis Software (GDAS, Affymetrix). The pedigree information, allele frequencies, and map position of the SNPs were combined with the genotype data. To determine the LD SNPs from this KDS family, we performed a simulation study using Agilent Varia software [, ]. The following steps were automatically executed in the computer workstation of the laboratory. (a) likelihoods, L (θ), are calculated for each possible θ value ranging from 0 to 0.5, in increments of 0.02, that is, 0, 0.02, 0.04,…, 0.46, 0.48, 0.5. (b) Choose θ which maximizes the likelihood ratio, L(θ)/L(1/2), of the occurrence of linkage to no linkage. (c) Calculate the lod adds (LOD) score for this θ. Genes located within 100 bp of the flanks of LD SNPs were mined via an authoritative web tool, GeneView ( Their biological functions were then annotated by employing FatiGO (http://fatigo.bioinfo.ochoa.fib/es). [...] All of the 29 exons of DCDC5 were covered by 29 pairs of PCR primers (). These primers were designed based on the DCDC5 version issued on 26 June, 2007 (NM_198462.2). A website primer design platform, Primer3 (, was employed under the default primer selection conditions. All samples, including twelve KDS patients and three spouses from the KDS pedigree were resequenced and compared for variation discovery in DCDC5. A detailed laboratory protocol can be found on the SeattleSNPs website ( PCR products were sequenced using each pair of above PCR primers and BigDye Terminator Cycle Sequencing v2.0 kit (Applied Biosystems, Applera, USA). Sequencing reactions were electrophoresed on an ABI 377 automated sequencers. Finally, the substitution effect was evaluated by a free software, PolyPhen ( […]

Pipeline specifications

Software tools Primer3, PolyPhen
Application qPCR
Diseases Kidney Diseases