Forum:What can you detect with PE150bp shotgun sequencing with 100X depth

Question

[vpsev3]

Hello,

I wonder if it is possible to detect large deletions or duplications with the NGS and with an acceptable sensitivity rate, such as 22q11.3 microduplication

Because I read that it could be complicated with this technique, like here https://www.longdom.org/open-access/structural-variation-detection-from-next-generation-sequencing-2469-9853-S1-007.pdf

[German.M.Demidov]

yes, it is possible. use read-depth callers - they are way superior to paired-end methods for large CNVs with breakpoints in "low mappability" regions. I'd say the sensitivity of 22q11.3 should be 100% after we exclude ~3% of QC failed samples (depending on the initial DNA quality more than on sequencing)