SNP rs4236 Expression Analysis

We chose to analyse MGP transcript SNP rs4236 (T > C, OA risk allele = C, minor allele frequency = 0.37) as the difference in expression between its risk and non-risk alleles was the largest of those SNPs investigated in the original study [8 (link)]. The SNP was genotyped by pyrosequencing using the primers listed in Additional file 2: Table S2. The assay was designed using PyroMark assay design 2.0 (Qiagen), and the sequencing was performed using the PyroMark Q24 Advanced platform (Qiagen).

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Shepherd C., Reese A.E., Reynard L.N, & Loughlin J. (2019). Expression analysis of the osteoarthritis genetic susceptibility mapping to the matrix Gla protein gene MGP. Arthritis Research & Therapy, 21, 149.

Publication 2019

PyroMark assay design 2.0 PyroMark Q24 Advanced platform

Alleles Assay Primers

Corresponding Organization : Newcastle University

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Variable analysis

independent variables

Genotype of SNP rs4236 (T > C, OA risk allele = C, minor allele frequency = 0.37)

dependent variables

Difference in expression between risk and non-risk alleles of SNP rs4236

control variables

Primers used for pyrosequencing (listed in Additional file 2: Table S2)
PyroMark assay design 2.0 (Qiagen) for assay design
PyroMark Q24 Advanced platform (Qiagen) for sequencing

controls

No positive or negative controls were explicitly mentioned in the provided information.

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