Exome enrichment, How does Nextera Exome Enrichment compares to TrueseqNimbleAgilent?

[dottomarco]

I have been trying all the different exome enrichment kits available during the last years.
I am now wondering what the real performance of the new Nextera Rapid Exome enrichment kit (37 or 62 Mb target) is compared to the competitors.

I used a lot of the TrueSeq exome enrichment which was a good deal considering quality and costs compared to Nimblegen and Agilent.

Now that the TrueSeq libraries are only available until the end of 2013 and the TrueSeq exome enrichment have been eliminated, the only choice is between Agilent or Nextera.
Nimblegen does not have an optimized protocol for the enrichment of Nextera libraries so when the TrueSeq library prep kit will be over, there will be nothing to enrich with the Nimblegen kits.
Agilent is not my favourite for many reasons (high quantity requested in input or high # of PCR Cycles requested, high costs, low % of reads on target when a few samples are pooled prior to enrichment etc.).

Can someone tell me what's the % of reads on target with the Nextera libraries and exome enrichment? Did you compare it to previous exomes using other kits?
With the other kits I could expect 65-80% of reads on target depending on the condition and kit used.

What real coverage do you get on avarage pooling n ( ... you name it) Nextera samples per lane?
With Illumina TrueSeq libraries and Enrichment I used to get a 35-45X coverage from a pool of 6 samples per lane (2x100bp) (62 Mb target).

Thank you in advance for sharing your experience.

[daantje]

Hi,

No reactions... I would also be interested in this question!

Anybody tested this?

[buckybadger]

I don't have an answer to the Nextera question, but perhaps the anticipated demise of the TruSeq library prep kits shouldn't concern you too much if you prefer to stay with the standard approach and avoid Nextera. Library preps and oligos aren't too complicated (genome centers and larger lab often develop their own homebrew kits) and there are a number of Illumina-compatible library prep options on the market that have been demonstrated to work well with the same applications. For example, Kapa Biosciences and Bioo both make kits that work well in targeted enrichment with Nimblegen probes:

(1) http://www.kapabiosystems.com/public...eNimbleGen.pdf
(2) http://www.biooscientific.com/Detail...ext-Generation Sequencing&SubName=Illumina-Compatible&Name=DNA Sequencing

I hope these examples will be helpful to you,

Cheers,

--BB

[hide23]

I've heard that Nimblegen is coming out with their own library kit soon.

[SeqHealth]

NimbleGen will offer all reagents from library prep through sequencing. From what I've heard these kits will come out in mid-December.

Best
SH

[buckybadger]

Kapa Biosystems-Roche Nimblegen Partnership

http://www.nimblegen.com/news/press_rel/news_2013_12_18.html

Roche NimbleGen and Kapa Biosystems Team Up to Provide Optimized Next-Generation Sequencing (NGS) Target Enrichment Workflow Solution
Madison, WI, USA, December 18, 2013

Roche (SIX: RO, ROG; OTCQX: RHHBY) and Kapa Biosystems announced today a partnership to provide an optimized NGS target enrichment workflow solution. Kapa Biosystems will custom manufacture NGS library preparation products for Roche NimbleGen to distribute to its customers.

Roche NimbleGen's new offering combines KAPA Library Preparation Kits with Roche NimbleGen sequence capture products for complete workflow coverage, prior to sequencing. This validated protocol provides customers with the ability to work with low DNA quantity or quality, including FFPE DNA for whole exome or targeted sequencing. Compared to other workflows, this offering significantly reduces GC bias and obtains better molecular complexity, resulting in further improved enrichment performance.

[etc.]