Why only heterogeneous SNVs for validation using genotyping arrays?

Question

I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called by the SNP array.

1) Performance comparison of whole-genome sequencing platforms

To further assess the accuracy of the variant calling, ... Of the 260,112 heterozygous calls detected with the Omni array, 99.5% were present in the entire SNV data set, 99.34% were concordant calls and only 0.16% were platform-specific SNVs. This demonstrates that both platforms are sensitive to known SNVs and that few known single-nucleotide polymorphisms (SNPs) are detected by only one platform.

2) Optimised filtering reduces the error rate in detecting genomic variants by short-read sequencing

To confirm that shared SNVs are indeed true variants, we used Illumina single-nucleotide polymorphism (SNP) arrays and selected all SNPs heterozygous on the SNP array.

My question is - why are only heterozygous SNPs chosen for validation when using Illumina Omni arrays?

Answer 1

The purpose of validating is to find genuine SNPs and not those caused by sequencing or amplification errors. It is extremely unlikely you will have a false homozygous SNP as a result of error. Just think about it. The same error, at the same base, occuring 80%+ of the time? Its not going to happen unless you have low coverage, and these SNPs should be thrown out anyway. You may have some cases where a genuine heterozygous SNP is called as a homozygous SNP. But that isnt much of a problem. It is still a genuine SNP. It would only be a problem if you were only interested in homozygous SNPs, in which case you will just need to validate everything biochemically, which you will need to do anyways.

Answer 2

i think the chance of a sequencing platform calling something A/A when the microarray calls it B/B is virtually nil. Just doesn't happen.