How is it possible to differentiate CG or AT heterozygous in Illumina Infinium Genotype Microarrays?

Question

[igor.alcaras]

In illumina Infinium Genotype Microarrays Reference Guide, in the XSTain step, it is shown that biotin is associated with C and G, which will after have a green signal; and DNP with A and T, which will have a red signal.

But what if we have a CG heterozygous (like I do have in my data, a biallelic SNP C>G), how will the scan differentiate both green signals and not misinterpret it as being homozygous? (The same doubt about being AT heterozygous)

(Obs.: In my VCF files, this SNP does have homozygous, CC and GG, and heterozygous CG, and there were no problems in the sanning).

Answer 1

[LChart]

1: My impression always was that the biotin and DNP are used for two different alleles, and are not base specific.

2: I also thought that the probes are allele-specific, so rather than having a probe for upstream/downstream sequence and reading read/green intensity from the same "spot", I believe the major and minor alleles have separate spots on the array, so you you have separate intensities. This would mean that even if C/G always use green fluorescence, you still get separate major/minor intensities.