Pros and Cons of DNA Mass Spectrometry versus WES/WGS?

Question

[Pratik]

Hey Biostars Community,

What are some pros and cons of DNA Mass Spec versus Whole Genome/Exome Sequencing?

The very obvious con is that DNA Mass Spec will only detect the mutations that have been selected to be profiled. Whereas for WGS/WES will be able to profile the whole genome/exome for any mutations including the ones that DNA Mass Spec will be looking at.

Is DNA Mass Spec... I guess... more specific and sensitive (than WES/WGS) for detecting the mutations that it does profile? Thereby giving more confidence in the results from it?

Is there sometimes uncertainty/less confidence with your results from WGS/WES?

I guess an experiment could be done with WGS/WES and then maybe verified by some type of Sanger Sequencing? Thoughts?

Thank you in advance! Pratik

Answer 1

[Prash]

Dear Pratik

We did use Sequenom/KASPAr based technologies and we found them invariably sensitive than the Sanger which is the usual best. The bona fidelity of calling a variant for validation is higher in these approaches than the Sanger where we could see blobs. The turn around time is higher too with amplification of flank sequences in the latter.

The less confident SNPs could then be used fo rmutational spectrum assay or again used for Sanger.

Regards Prash

[Pratik]

Thank you Prash : )