Genotyping forward and reverse polymerase chain reaction (PCR) primers and a extension primer were designed using the Sequenom MassARRAY Assay Design (version 3.0) software (Sequenom Inc., San Diego, CA) and purchased from Bioneer Corporation (Daejeon, Korea). Genotyping was carried out in standard 384-well plates with 12.5 ng genomic DNA used per sample. We used a modified Sequenom protocol where half reaction volumes were used in each of the PCR, SAP and iPLEX stages giving a total reaction volume of 5.5 μL. The iPLEX reaction products were desalted by diluting samples with 18 μL of water and 3 μL SpectroCLEAN resin (Sequenom) and then were spotted on a SpectroChip (Sequenom), processed and analyzed on a Compact MALDI-TOF Mass Spectrometer by MassARRAY Workstation software (version 3.3) (Sequenom). Allele calls for each 384-well plate were reviewed using the cluster tool in the SpectroTyper software (Sequenom) to evaluate assay quality. Genotype error checking, sample identity and zygosity assessment and Hardy-Weinberg equilibrium analyses were completed in PEDSTATS (Wigginton and Abecasis, 2005).
