Rapid exome

[james hadfield]

has anyone used the newest rapid exome capture kits from Ilumina. Our first run generated huge amounts of library pre-caprute and again in teh final PCR. I'm worried about over-amplifying and adding in too many PCR artefacts.

The QC run has just gone on MiSeq but if anyone has experience I'd be interested in comparing notes?

[ymc]

Nope. I think its coverage is still not as good as Nimblegen v3. For me, if Nimblegen v4 also has miRNA genes, it will be perfect

[buckybadger]

Hi ymc,

I believe the Nimblegen v3 does contain miRNA. At least, the annotation on their web site (http://www.nimblegen.com/products/se.../v3/index.html) includes the following among the v3 targets:
- miRNAs from miRBase (version 16)
- miRNAs from snoRNABase (version 3)

Cheers,

--BB

[ymc]

Hi ymc,

I believe the Nimblegen v3 does contain miRNA. At least, the annotation on their web site (http://www.nimblegen.com/products/se.../v3/index.html) includes the following among the v3 targets:
- miRNAs from miRBase (version 16)
- miRNAs from snoRNABase (version 3)

Cheers,

--BB

It might contain miRNA but the two I am interested in (RMRP, KCNQ1OT1) are not there.

[buckybadger]

Nimblegen has something called "exome plus" where they add custom probes to their exome probes, for just that situation. Another option (probably lower cost) is to get biotinylated probes for just those two miRNA from IDT, and spike them into the exome probes yourself. It works, and I believe IDT does the probe design and can provide guidance on the amounts to mix in.
- BB