Nathan Fortier’s webcast yesterday, CNV Analysis in VarSeq – A User’s Perspective, was an excellent demonstration of our CNV capabilites, so check it out if you missed it. There were a number of questions asked in the live event, so in today’s blog post I wanted to recap the Q&A session.

Question: Do the reference samples have to be from the same sequencing run as the samples that we need to call CNVs on?

Answer: No, they do not have to be from the same run. However, we do expect that they are from the same library preparation, so we expect they would be similar samples.

Question: What are you experiencing implementing this in high-throughput lab environments?

Answer: It really depends on what you mean by high-throughput. If we’re talking about running this sort of thing on gene panels, then it should be just fine running it on a standard desktop computer, and in fact, you should be able to get results within seconds. However, if you are running this algorithm in the context of exomes, there are increased computational requirements. We would probably recommend that you utilize our Varseq pipeline product and run your workflow on a server so that you can really utilize the multi core architecture of this algorithm. If you do this, it can take up to around 8 hours or so if you’re running it on 30-60 exomes.

Question: Can fusion events be detected?

Answer: No, currently this algorithm is not designed to detect fusion events.  The kinds of events this algorithm is designed to detect are heterozygous deletions, homozygous deletions and duplication events, although we have recently added the ability to detect LOH events as well.

Question: Did you perform experimental validations on the CNVs detected with Varseq?

Answer: Yes, we did and in fact we found that at the base pair level we obtained very high sensitivity and specificity. We’re talking over 98% sensitivity and over 99.9% specificity.

Question: When will the advanced karyotyper be available?

Answer: The advanced karyotyping functionality should be available at the next release which we estimate to occur around the middle to the end of May.

If you are interested in learning more or giving CNV analysis a try, please contact us at [email protected]!