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[…] Thirty-four SNPs in the ARNT2 gene were selected from 80704652 bp to 80889940 bp on chromosome 15 with a mean inter-SNP distance of 7 Kb (GRCH37.p10 Primary Assembly, National Center for Biotechnology Information [NCBI]). We did not have a specific hypothesis about any SNP in particular and tested multiple SNPs within the same gene to identify a possible association of the gene with a given phenotype []. All chosen SNPs had a minor allele frequency (MAF) > 0.05 in the HapMap CEU (Utah residents with northern and western European ancestry) population (HapMap genome browser, release 27) and were available in the TaqMan SNP Genotyping Assays (Applied Biosystems Inc., Foster City, CA, USA), that was used for genotyping in the current study. rs1446336, rs8034535 and rs7175825 are tag SNPs, as indicated by the HapMap genome browser (release 27). The most upstream SNP is rs1446336 (Chr 15: 80704652) and the most downstream is rs1139650 (Chr 15: 80889940) (see Table ). Buccal samples were collected by mail from the participants and DNA was extracted and anonymized []. SNP genotyping was performed following the protocol previously reported []. Hardy-Weinberg Equilibrium (HWE) was tested in controls using Plink v1.07 [] at α = 0.05, and all selected SNPs were in HWE. [...] The Chi-Square statistics was applied to test association between 34 SNPs in ARNT2 and AS, using Plink v1.07. We used Bonferroni correction to adjust P values at the α threshold of significance (α = 0.05). Since Bonferroni correction is conservative when the tests are not independent, we used the SNPSpD web interface [], to account for linkage disequilibrium (LD) patterns between all SNPs in the current sample. The effective number of independent loci was 21 and the subsequent threshold of significance after Bonferroni correction was α = 0.0024. We analysed LD blocks in our sample using Haploview [].Functional annotation of significant SNPs was conducted using the following softwares: HaploReg v2 [] allows analysis of non-coding genetic variants in terms of their effect on the organization of chromatin regions and regulatory motifs; F-SNP [] is a tool which combines multiple databases for providing the functional roles of genetic variants; the Genetic Association Database [] gives information about genetic studies which previously identified association between the SNPs we analysed and ASC; SNPnexus [] is an online database which was used to define regulatory elements and conserved regions; the University of California Santa Cruz (UCSC) genome browser [] permits to validate functions of the SNPs analysed. […]

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