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Pipeline publication

[…] 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 (http://www.ncbi.nlm.nih.gov/SNP/). 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 (http://www.genome.wi.mit.edu/cgi-bin/primer/primer3.cgi), 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 (http://pga.gs.washington.edu/). 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 (http://genetics.bwh.harvard.edu/pph/)., 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 []. Twelve available KDS subjects () 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., Five SNPs obtained from the KDS family were identified as LD SNPs. The sequences of alleles of LD SNPs identified from the KDS family were displa […]

Pipeline specifications

Software tools Primer Premier, Primer3, PolyPhen