Protocol detail

Genotyping and Annotation of SLC30A8 Variants

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Study participants were previously genotyped for approximately 995,321 SNP markers using several Illumina genotyping arrays, including the HumanHap550v3, HumanExon510Sv1, Human1Mv1, and Human1M-Duov3. Details of the data cleaning and imputing steps for the genotypic data have been detailed elsewhere [24 (link)]. We used all the SNPs within the SLC30A8 gene as well those within 50 kb upstream and downstream of this gene. A total of 118 SNPs were found in this region. Detailed characteristics along with genomic locations of these 118 SNPs are provided in Supplementary Table 1 in Supplementary Material available online at http://dx.doi.org/10.1155/2016/6463214. The variants were annotated using ANNOVAR [25 (link)] that used human genome Build 19 and SNP version 138 databases for annotation.

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Kulkarni H., Mamtani M., Peralta J.M., Diego V., Dyer T.D., Goring H., Almasy L., Mahaney M.C., Williams-Blangero S., Duggirala R., Curran J.E, & Blangero J. (2016). Lack of Association between SLC30A8 Variants and Type 2 Diabetes in Mexican American Families. Journal of Diabetes Research, 2016, 6463214.

Publication 2016

genotyping arrays

Gene Genomic Genotypic Human genome Slc30a8

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Variable analysis

independent variables

Genotyping of approximately 995,321 SNP markers using several Illumina genotyping arrays, including the HumanHap550v3, HumanExon510Sv1, Human1Mv1, and Human1M-Duov3

dependent variables

Not explicitly mentioned

control variables

Details of the data cleaning and imputing steps for the genotypic data have been detailed elsewhere [24 (link)]
All the SNPs within the SLC30A8 gene as well those within 50 kb upstream and downstream of this gene
A total of 118 SNPs were found in this region
The variants were annotated using ANNOVAR [25 (link)] that used human genome Build 19 and SNP version 138 databases for annotation

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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