Detect exon deletion/duplication from NGS amplicon

Question

[sacha]

Hi,

I would like to detect exon duplication and deletion from NGS with panel amplicon strategy. For example, I have all exons of APC sequenced with an average depth > 100. ( exon 17 is covered by 34 amplicons ) How can I detect deletion of exon 3,4 or 5 ? is there any tool or method ?

My idea is:

• Split the exon region into bins ( or amplicon region )
• Count how many read fall into each bin
• Normalize bin count using %GC Lowess
• use normal sample data to create a model ( machin learning ... )
• Compare unknown sample to my model and check for a significant difference

Answer 1

[Eric T.]

The approach you described is similar to what CNVkit does -- see the bundled script cnv_ztest.py for single-exon testing.

There are other methods designed specifically for targeted amplicon sequencing that go beyond the above. For example, OncoCNV reportedly works well.