Computational protocol: Associations between RET tagSNPs and their haplotypes and susceptibility, clinical severity, and thyroid function in patients with differentiated thyroid cancer

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Protocol publication

[…] HapMap genotype data of the Chinese Han Beijing (CHB) population (Release 27, Phase I +II +III, http://www.HapMap.org) were extracted within extended gene regions of RET in 2016, which encompassed 2 kb of upstream and downstream flanking sequence. The CHB RET gene has 33 common SNPs. As described in our previous studies, tagSNPs were selected by using the Haploview software[, ]. Briefly, tagSNPs were chosen initially based on pairwise linkage disequilibrium information to maximally represent (r2 > 0.8) common SNPs (minor allele frequency (MAF) > 0.05) by Haploview 4.2. We then used bioinformatics search to prioritize the tagSNPs for genotyping, based on their predicted functional effects (http://snpinfo.niehs.nih.gov/). For example, rs1799939 was predicted to be located at a splicing site, suggesting a potential effect on this gene's splicing regulation. […]

Pipeline specifications

Software tools Haploview, SNPinfo
Application GWAS
Organisms Homo sapiens