Question: Detect exon deletion/duplication from NGS amplicon
gravatar for sacha
23 months ago by
sacha1.9k wrote:


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
cnv ngs amplicon • 776 views
ADD COMMENTlink modified 23 months ago by Eric T.2.6k • written 23 months ago by sacha1.9k
gravatar for Eric T.
23 months ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

The approach you described is similar to what CNVkit does -- see the bundled script 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.

ADD COMMENTlink written 23 months ago by Eric T.2.6k
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