Figure 3.

Cluster analyses of candidate EST–SNP sites of GBA genotype data from two contigs. The contig number and library source (3′ or 5′) are given. Each GBA experiment assayed 18 genomic DNA samples from three ethnic groups: eight Caucasian DNA samples (+), five African American DNA samples (o), and five Hispanic DNA samples (x), as well as two positive (/) and two negative controls (\ , −). Raw optical density values from the two-color ELISA system were plotted on an xy scatterplot. Allele 1 data (fluorescein–PNPP reactions) were captured by a standard plate reader at 405 nm and were plotted on the x-axis. Allele 2 readings (biotin–TMB reactions, 620 nm) were plotted on the y-axis. Thus, the axes represent the base analog extension signals determined by primer extension. Homozygotes for allele 1 lie on the x-axis, homozygotes for allele 2 lie on the y-axis, and heterozygotes lie on the diagonal. Negative PCR controls (\, reactions controlling for cross-hybridization of the PCR primer and capture–extension primer) and negative GBA controls (−, reactions controlling for self-extension of the capture–extension primer) lie near the plot origins. Synthetic templates (/) were also included as positive controls to monitor hybridization and extension efficiency. Cluster analyses for genotype determination were done automatically by an in-house software program.