Genotyping Common Variants in CELSR Genes

The Agena (http://agenabio.com/, San Diego, US, previously Sequenom) MassARRAY^® System, combined with iPLEX^® chemistry, was used to genotype a set of common variants in CELSR1, 2 and 3. The variants were chosen using the LD TAG SNP Selection tool at https://snpinfo.niehs.nih.gov/snpinfo/snptag.php, [32 (link)]) to tag each gene with an LD threshold of r² = 0.8. For practical reasons, only the variants fitting into two iPLEX pools were selected. The 20 common variants in CELSR1-3 were genotyped in the same cohort of Swedish-Danish cases and controls as used previously [15 (link)]. The HWE of each marker in controls was assessed, and any sample with <80% call-rate was removed.