Samples were hybridised to the Illumina HumanCoreExome-12 Beadchip according to the manufacturer's guidelines. Four microlitres (200 ng) of DNA is required for the pre-amplification reaction using a Tecan Freedom Evo. The process is automated except for manual agitation/centrifugation step midway through and at the end of the process. Post-amplification processes (fragmentation, precipitation, resuspension, hybridization to beadchip and xStaining) were completed over three days as per Illumina protocol. Following the staining process, beadchips were coated for protection and dried completely under vacuum before scanning on the Illumina iScan paired with Illumina Autoloader 2.x. Prior to downstream analysis, all samples were subjected to initial quality control to establish that the assay was successful. Sample call-rates below 92.5% were flagged before loading samples into Illumina’s GenomeStudio software. Using Illumina’s QC dashboard, sample performance was assessed by measuring dependant and non-dependent controls that are manufactured onto each beadchip during production.
