Automating Process from Biological Sample Handling to Sequencing Results Display

[vs92]

Hello everyone,

I am in the process of deciding what state-of-the-art equipment to buy to setup a new genomics lab, so that I can automate as much of the process of 16s rDNA based bacterial community profiling (for human microbiome studies on samples such as stool and saliva). As I understand, some of the steps involved are:

1. Automating sample addition into DNA extraction kit

2. DNA extraction (right now I am using a Kit, but I'd like to know if there is any machine/equipment that will do this automatically)

3. Amplifying extracted DNA (e.g. PCR machines)

4. Post-PCR purification of amplified DNA and feeding into sequencing machine (e.g. Illumina MiSeq) which will provide all the target 16s rDNA sequences in a centralized server/cloud for subsequent bioinformatics analysis

Any advice on the industry best machines/instruments for each of the above steps (and any additional/intermediate steps I may have missed) would be very helpful. Thanks!

[adaptivegenome]

This can all be done with automated robotics from Qiagen, Beckman, and others.

[vs92]

Thanks, a more specific list (or pipeline) of instruments would be very helpful.

[adaptivegenome]

Thanks, a more specific list (or pipeline) of instruments would be very helpful.

QiaCube automates most Qiagen kits:

http://www.qiagen.com/products/bytechnology/automation/default_qiacube.aspx

For more flexibility, there are customizable systems from Beckman, specifically they are the Biomek workstation and the Biomek FX.

I'm sure there are lots more but these are my favorite.

[Ber7702]

Hi vs92.
For post amplification cleanup Beckman Coulter has prewritten methods for the AMPure XP kits for both the Biomek NXp and and the Biomek FXp. For simple amplicon cleanup, the Biomek NXp will do the job nicely, capable of cleaning up 96 samples in around 20 minutes and 4x96 in around 35-40 minutes. The methods provide simple GUIs with dropdown menus.

If you are looking to do complete library construction for the MiSEQ, then we would recommend the Biomek FXp. With the larger deck capacity, you can perform 96 library constructions with per-well size selection in around 5-6 hours.

Visit our website or get in touch with your local rep for more information.

Best wishes