Forum:Is WGS reliable for larges indels and duplication?
0
0
Entering edit mode
14 days ago
vpsev3 • 0

I came across this site https://www.centogene.com/diagnostics/whole-genome-sequencing-with-centogenome.html

enter image description here

Are these low sensitivity rates related to an alignment problem?

I was wondering if, for example, PE150bp shotgun sequencing with 30X depth could detect these variants (like a 22q11.3 microduplication) with higher confidence.

sequencing • 173 views
ADD COMMENT
0
Entering edit mode

I think you need to create one post "what can you detect with PE150bp shotgun sequencing with 30X depth " and not discussing each variant in a separate topics =)

I don't really understand what is large indel - 50 bp? Usually these ones are fine.

I don't see why they call some deletions as "copy-number deletions".

If you want to get good SV calling accuracy, check the long read alternatives to short-read WGS.

ADD REPLY
0
Entering edit mode

In our experience, with WGS you can get better sensitivity than this with large deletions at least, but it really depends on the analysis. @German.M.Demidov, maybe the distinction between deletions (for <10kb) and copy-number deletion (>10kb) is related to the software they use to identify them.

In any case, I think this low sensitivity might be due to the specificity guarantee (>99.9%), which will force them to be very stringent and only report very clear variants. There's always a tension between specificity and sensitivity and it seems they have decided to g all-in on specificity.

ADD REPLY
0
Entering edit mode

ah I see, thanks, however any deletion is a copy-number change of this particular piece - first time I see anyone using this terminology...Yeap, I assume that >10kb they detected with read depths and <10kb with paired-ends - maybe it was easier for them to call them differently...

ADD REPLY
1
Entering edit mode

Completely agree that any deletion is a copy-number change and that it does not make sense to call it otherwise.

ADD REPLY

Login before adding your answer.

Traffic: 2519 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6