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

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).

heterozygous genotype microarray infinium illumina
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updated by LChart LChart • written by igor.alcaras • igor.alcaras

1 answer

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.

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written by LChart LChart

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