Halo Genomics Selector Technology

[BTS]

I'm wondering if anyone has experience with Halo Genomics' Selector Technology (formerly O-link Genomics)? We are considering this technology for targeted resequencing of a panel of about 500-600 genes. Could this step negate the need to use custom designed probes for hybridization and capture via Agilent or Nimblegen?

I'm envisioning that this could be done before fragmentation and post fragmentation steps would only include ligation of adaptors but I'm not positive...

Thanks in advance

[james hadfield]

Yes you would not need t do any Agilent or Nimblegen caputre, they are a competitor although not for whole exomes. The HaloGenomics technology could possibly be made to work as a no-PCR protocol but it neds some tweaking. Looks good thouigh, I meant to follow up after AGBT. Must get that email sent!

[krobison]

Well, you wouldn't need custom Agilent or Nimblegen probes -- but would need custom Halo Selector probes. No fragmentation though (they use restriction enzyme digestion).

Have you gotten pricing? When I talked to them a year plus ago, it seemed they were pricing for large projects (many samples) -- which perhaps yours is. In general, anything requiring custom oligos that aren't made on microarrays is going to have economics skewed towards large projects.

[BTS]

We are going to be sequencing on a GAIIx with 2x75 bp reads. Wouldn't we still have to fragment to remove bias towards the ends of the fragments?

I don't have the exact pricing but from what I understand it is comparable to Nimblegen or Agilent custom captures.

[krobison]

You are correct -- my mistake. The difference vs. the Agilent & Nimblegen schemes is the fragmentation & library construction is after selection, not before.

This NAR paper seems to have a good M&M section explaining all of it.

[Seqasaurus]

Uppsala Genome Centre plans to start sometime in the autumn

[epistatic]

I have made 30 libraries with the Halo Genomics selector probes. The process was very straightforward and I am waiting to hear back from the analysis how specific the capture was.

The capture was backwards from our exome work, it occurs prior to library construction. The end product is high molecular weight genomic DNA produced from circle dependent amplification with phi29, so I did have to shear all of the captured samples with the Covaris before going into standard library construction.

I have not yet tried their PCR version that should bypass the library construction. We find their process fits well in the space between PCR enrichment and Agilent/Nimblegen/Illumina biotinylated bait capture.

[TonyBrooks]

We are seriously considering it as an alternative to Agilent capture for a few projects. Price-wise, it's very competitive to Agilent if you are running a high enough sample number. When you add in the time saving, apparently 50 preps can be done in a day, then it looks good. We also only have access to a S2 Covaris, so just shearing our samples for Agilent capture would probably take two days.
Sequencing needs to be 100bp paired end and they support up to 96 indexes (soon to be up to 384, I think).
We've found it looks to be particularly helpful for repetitive areas of the genome. We could design to 95.2% of our region of interest using Halo. By contrast we designed baits to 63% using SureSelect, and (when discounting the small gaps that would still be sequenced), we estimated we'd still miss around 15-20% as some of those gaps are large (>1kb).
They also expect <95% of reads to hit target, so all quoted specs look good.
Now we have to make a decision on which technology to go for.

[genomehacker]

Agilent acquires Halo!

http://www.genomeweb.com/sequencing/agilent-acquires-halo-genomics-complement-sureselect-small-captures