TruseqDNA and Nimblegen capture

[chiaraf]

Dear community,
I ask your help to understand if someone can give me an idea of what's the best thing to do.
In the next months I need to do some custom exome capture with nimblegene kit.
Before the nimblegene capture the nimblegen protocol told me to make a library with truseqDNA kit.
I know that the truseqDNA will be not available the next year...can someone suggest me another kit than can work efficiently ?
For me the new illumina kits TRuseqPCR free and the Truseq nano are not suitable for that purpose.
Many thanks,
Chiara

[buckybadger]

Hi Chiara,
The KAPA Library Preparation Kits/Illumina series (Kapa Biosystems) work very well as a TruSeq substitute, and the KAPA HiFi HotStart ReadyMix polymerase has one of the best performances I've seen in this application compared to other polymerases, showing less bias against high- and low-(G+C) content and little inhibition by SA-beads when you amplify captured products directly from SA-beads. Kapa does not provide the Illumina-compatible Y-adapters, but these are easy to obtain from commercial oligo vendors, pre-annealed and with the sample indexes you want. BioO, also provides library-prep kits and adapter kits.
-- BB

[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.]

[chiaraf]

Many thanks for your help!!!!
Ciao
Chiara

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.]

[Bioo Scientific]

The NEXTflex™ Pre-Capture Combo Kit is available with 96 barcodes for multiplexing both upstream and downstream of SeqCap target capture. Here is a whitepaper written in conjunction with Roche that illustrates how the NEXTflex Pre-Capture Combo Kit works with their Nimblegen SeqCap EZ Library capture systems for targeted exome sequencing.

[ECO]

I don't think Kapa (or Nimblegen) offers adapters. Bioo or homebrew are the only way to go for adapters. You can buy blockers from Roche, Bioo, or IDT.

[buckybadger]

Nimblegen did launch a couple of adapter kits to accompany the Kapa library prep kit. Here's a link to descriptions on their web site:

http://www.nimblegen.com/products/kits/seqcap/index.html

-- BB