Efficient targeted resequencing of human germline and cancer genomes by oligonucleoti

[JBuenrostro]

Hi everyone, check out our new sequence capture method, recently published in NBT. We are calling the method oligonucleotide-selective sequencing (OS-Seq). The major innovation involves integrating the capture reaction directly on the Illumina flow cell. This eliminates user error (all capture manipulations are done automatically by the sequencer), high cost and laborious sample preparation steps associated with commercial technologies. Let me know what you guys think/ if you have any questions!


Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing

With the cost of DNA sequencing falling rapidly, sample preparation is becoming a bottleneck to surveying genetic variation across large populations or performing clinical diagnostics. Myllykangas et al. present an efficient approach for targeted sequencing in which genomic regions of interest are captured and sequenced inside a flow cell using a common oligonucleotide probe.

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.1996.html

Jason Buenrostro

[ECO]

Hey Jason! Welcome, great paper.

[JBuenrostro]

Thank you for the welcome and I'm glad you like the paper!

[protist]

Hey Jason,
A very interesting paper and congrats on an elegant strategy for enhanced use of the flowcell. Does it work out cheaper than standard capture methods?

[JBuenrostro]

Yea, its much cheaper actually. Its not easy to compare since we are comparing it to commercial products. But in theory the commercial product should be significantly cheaper because:
1.) You don't need specialized hybridization equipment (Microarray hybridization chamber/bead hyb instrument+magnet). Also you don't need the added enzymes/array/beads.
2.) Most importantly all the capture steps are automated on the sequencing platform, making it a set up and walk away protocol. Otherwise you have to pay someone to prep libraries using the commercial kits (takes ~6 days to prepare).

[lingfung.tang]

if i want to try this capture method, what should I do?

[JBuenrostro]

The paper has the xml capture scripts in the supplement and describes the structure of the oligos. A good place to start is to load the scripts onto your machine and test it out with an old flow cell and water.

Not sure what I can disclose but we've improved the system significantly since the paper. If you'd like to know more you should feel free to contact Hanlee.

[lingfung.tang]

thanks. may i know the max capture size of this method?

[JBuenrostro]

So far we haven't reached an upper limit. At this point only large companies like Agilent/Illumina/Nimblegen have the capability of synthesizing lots of oligos. Based on my experience, I think this system will be able to easily capture exomes.

[ECO]

Have you done it on a MiSeq yet?

[JBuenrostro]

Great question! We just got the MiSeq shipped this last week, this system is pretty closed so we'll have to tinker around with it.