I have some problems with the understanding of the part of exome sequencing where the targets (exons) are captured. And how the SNPs (or SNVs) can be detected.
Firstly, the genomic DNA is shared, so we have exomes, introns there and intergeneric regions there. The primers are attached and then the hybridization takes place which helps to get rid of non-exome sequences. It means that we need to know the sequences of exons in forehand. So, I need to design exon sequences that already include all possible SNPs and due to those sequences I can capture my patient's exons with SNPs, that I know in forehand. If some sequence do not hybridize, it means there is no SNP which is associated with this sequence in my patient. How can I detect then the novel SNPs or SNVs in exome sequencing if for capturing the targets I had to know the corresponding SNPs and SNVs?
Thank you in advance.