Whole exome seuqencing capture sequence

Hi Everyone,

I am trying to solve a problem in my analysis and I want to make sure I understand the sequencing procedure that is happening for NGS.

Imagine we want to do a whole exome sequencing, the steps would be:

• Take the DNA
• Fragment the DNA
• Add the adapters to the end of fragments
• Use a cDNA based filter to only keep the coding region fragments
• Sequence …

So now here is my question, how do we know the cDNA sequence before the sequencing? Is it based on GRCh19/38?

For highly polymorphic regions, such as HLA or KIR regions, is the cDNA sequence based on reference genome? (and therefor it is possible some reads are not captured?)

Thanks,