Genotyping of ADAR1 SNPs from Genomic DNA

Genomic DNA was extracted from anus or cervical samples^{38 (link)} using the QuickExtract™ DNA Extraction Solution 1.0 (QE09050, Epicentre Biotechnologies). Extracted DNA was used for each genotyping. Six ADAR1 SNPs (rs6699729, rs3766927, rs3766925, rs3766924, rs9616 and rs9427097) were selected based on linkage disequilibrium testing and cover all described variation in ADAR1 gene^{23 (link),42 (link)}. The variants were typed using TaqMan SNP genotyping assay (Assay num: C__30114879_10, C__11259682_10, C___222942_10, C__25800598_10, C___8724401_10 and C__303121822_10, respectively, Applied Biosystems) following manufacturer’s protocol. Reactions were analyzed on an ABI PRISM 7500 (Applied Biosystems) and allele calling was performed by AutoCaller Software v 1.1 (Applied Biosystems).
Genotyping data, minor allele frequency and Hardy-Weinberg equilibrium of selected SNPs are found in Supplementary Table 1.

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Pujantell M., Badia R., Galván-Femenía I., Garcia-Vidal E., de Cid R., Alcalde C., Tarrats A., Piñol M., Garcia F., Chamorro A.M., Revollo B., Videla S., Parés D., Corral J., Tural C., Sirera G., Esté J.A., Ballana E, & Riveira-Muñoz E. (2019). ADAR1 function affects HPV replication and is associated to recurrent human papillomavirus-induced dysplasia in HIV coinfected individuals. Scientific Reports, 9, 19848.

Publication 2019

QuickExtract™ DNA Extraction Solution 1.0 TaqMan SNP genotyping assay ABI PRISM 7500

Allele Anus Assay Cervical Genomic Prism Snps

Corresponding Organization :

Other organizations : IrsiCaixa, Institute of Predictive and Personalized Medicine of Cancer, Red de Investigación en Sida, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol

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Variable analysis

independent variables

ADAR1 SNPs (rs6699729, rs3766927, rs3766925, rs3766924, rs9616 and rs9427097)

dependent variables

Genotyping data

control variables

Genomic DNA extracted from anus or cervical samples
QuickExtract™ DNA Extraction Solution 1.0 used for DNA extraction
TaqMan SNP genotyping assay used for variant typing
Reactions analyzed on an ABI PRISM 7500
Allele calling performed by AutoCaller Software v 1.1

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