Based on results from the MH test (5th column on Table 8 ), 19 out of the top 30 SNP markers were genotyped for 1,586 individuals from 220 Wave I & II families. We used the Sequenom MassArray technology for SNP genotyping [81]. PCR primers, extension primers, and multiplexing capabilities were determined with Sequenom MassARRAY Assay Designer software v3.1.2.2. Standard procedures were used to amplify PCR products; unincorporated nucleotides were deactivated with shrimp alkaline phosphatase. A single base pair extension step was completed with the mass extension primer and the terminator (iPLEX). The primer extension products were cleaned with resin and spotted onto a silicon SpectroChip. The chip was scanned with a mass spectrometry workstation (Bruker). The resulting genotype spectra were analyzed with Sequenom SpectroTYPER software v3.4.
