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two channel detection in SNP-chip

Hi - I have a clear understanding of the 2-channel detection technology when it has to identify one base (as in sequencing). I fail to fully get it in the SNPchip context. eg. if A and T are red (and C and G green), it is clear how I can identify AC, AG or TC and TG, but what if the genotype is AT or CG? What am I missing?

dna snpchip 2-channel
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updated by LChart LChart • written by Barma • Barma

1 answer

Two-channel detection helps to put more probes on a chip, but it doesn't really alter the mechanism of calling genotypes. The calling is still based on intensity just as in one-channel genotype chips. The probes themselves are allele-specific, so for an A/T SNP, the "AA" genotype has a high intensity for the ...NNNN A NNNN... probe, a "TT" genotype has a high intensity for the ...NNNN T NNNN.... probe, and an "AT" genotype has a moderate intensity for both. The variability of intensity with the number of alleles is significant enough to call copy number mutations, see https://mccarrolllab.org/wp-content/uploads/2015/02/Birdsuite.pdf

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written by LChart LChart

But, in the case of the Illumina Infinium II: the specificity is for the 50-mer preceding the position of interest, if annealing goes well there is the single-base extension and staining...so if A and G are stained with the same colour, I should not be able to distinguish any among AA AG GG (?)

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written by Barma • Barma

Again, there is an "A" probe separately from a "G" probe at different locations on the array, so you can use the intensity to distinguish.

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written by LChart LChart

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