Illumina Nextera for exome library prep versus sonicated approachs

[swNGS]

Hi

Does anyone have any experience comparing exome library prep coverage results using Illumina's Nextera library prep which relies on enzymatic 'tagmentation' (transposon-mediated addition of indexes and adapters and fragmentation) compared to alternate approaches that rely on sonication such as Agilent SureSelect or Illumina's TruSeq?

Thanks

[VanessaS]

I'm also curious about this. We are being strongly encouraged to use nextera over Truseq for exome sequencing and I'd like to get some feedback before we jump in. My understanding is that the lovely pricing we currently enjoy for the TruSeq Exome kits will be going away after the first of the year, but that the Nextera kits will remain affordable.

[ECO]

Moving to sample prep. Try to hit the right forum.

[dottomarco]

What is your esperience with the Nextera Exome kit so far?
Are you getting the same % of reads on targett? I am mostly interested about the coverage that I can get using these libraries compared to the TrueSeq exome enrichment libraries (62 Mb target) I have used so far.

If you have any suggestion when approaching Exome library prep with the Nextera' protocols, it will be much appreciated.

Marco

[james hadfield]

We've run 96 rapid-exomes but not done the direct comparison to TruSeq etal. The on-target rates were good, duplication rate was a bit higher than we'd previously seen and at some level I'd say the exome is not as "good". This is all relative though.

The biggest advantage from our perspective is the ability to perform exome analysis using 50ng of DNA routinely. Nextera also removes the need for any fragmentation or sonication making the lab work easier. I'd argue these workflow improvements need to be considered aginst other metrics.

You can only assesses the quality in light of your own very specific needs.

I'm sure comparisons will follow but they'll be out of date upon publication. I'd say just dive in a do an experiment, your almost certain to find something interesting!