I have three independent GWAS studies and they were genotyped using Illumina's HumanHap300, HumanHap550v3.0 and Illumina HumanOmni1 Quad. However for our disocveries we found consistency between the two HumanHap data but not the HumanOmni1 Quad.
May I make a conclusion that the false replication on the third data is due to the platform difference?
Thanks in advance for your inputs!
chances are higher you have a sample mixup somewhere, better check that.
you definately don't expect genotyping differences between different platforms. So all SNP's which are on all platforms should be called exactly the same.
(ps. since they are all illumina platforms, they'l most likely have the exact same probe sequences for 99,9% of the SNP's)
I assume you refer to the list of SNPs in each platform. The list of SNPs are specific to a particular platform. The same platform with a higher version may have few thousands additional SNPs in it.
Hi,
I wouldn't rule out the possibility of chip effects as colleagues of mine have observed a clustering difference when genotyping the same set of samples on the Illumina omni2.5M quad and the 2.5M octo array, despite Illumina guaranteeing 99% identity of the bead pools. This clustering difference was caused by a few thousand SNPs so a small fraction of SNPs on the array. However, there could be several more plausible reasons that your SNP didn't replicate and checking the signal intensity plot, allele frequencies etc is a good place to start.
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