Figure 1

Examples of SNP Chart Application. Examples of SNP Charts for the SNP rs1106577 to illustrate the data structure (e.g., Table 1). Template DNA from three Coriell samples with three possible genotypes (CC, CT and TT) and one negative control (NN) are shown in four different charts. Each chart shows four-channel fluorescent intensity data (A, C, G, and T) on the vertical axes, from 12 rs1106577-specific array spots (duplicate spots for six different probes). On the horizontal axes, 12 probe-names corresponding to 12 spots are given sequentially. 1st and 2nd spots from the left ("LEFT C/T") refer to the left-hand APEX probe that will give either a single C (green) signal (for homozygous CC genotypes) or a T (blue) signal (for homozygous TT genotypes) or a mixture of C and T (heterozygous CT). 3rd and 4th spots from the left ("RIGHT G/A") refer to the right-hand APEX probe that interrogates the DNA strand nucleotide complementary to that of the left-hand APEX probe, thus giving a single G (red) signal (for CC), a single A (yellow) signal (for TT), or a mixed G and A signal (for CT). From left, spots 5 to 12, inclusive, represent allele-specific APEX probes in which a base-specific fluorescence signifies the presence of the allele. Among them, spots 5 to 8 refer to the "_1" probes corresponding to the first allele (C in the case of rs1106577) and spots 9 to 12 refer to the "_2" probes corresponding to the second allele (T). The redundancy and consistency of the data across different probes give high confidence in the assigned genotypes.