Forum: Suggestion For A Good Genome Center
3
gravatar for Pals
5.3 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

I am looking for a genome center (preferably in Europe) to sequence mRNA and miRNA from >30 samples as well as SNP-genotyping. I would really appreciate if someone recommends me based on his knowledge and experience (price, turn-around time). We have been waiting nearly 6 months for first round of sequencing from one of the local genome centres - and really disappointed by their service. Therefore, we are looking for an alternative.

Thanks!

forum • 1.5k views
ADD COMMENTlink modified 5.3 years ago by Malachi Griffith16k • written 5.3 years ago by Pals1.3k
5
gravatar for Alastair Kerr
5.3 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

I have had experience with many genome centres in Europe/USA/China. All have had turn around time issues, or serious communication issues at some point and I do not want to post a lasting recommendation or criticism for fear that it would no longer be relevant.

Some advice though:

  • pay for the provider to make libraries as these generally come with a data quality guarantee.
  • make sure you know who is responsible for dealing with rRNA depletion in your samples (you or the company)
  • make sure you are fully aware of what data you get back and what processing has been done to that data. Companies such as BGI that use proprietary linkers/adapters may remove them before giving you the raw data to protect their IP. If this is done aggressively, e.g. returning only that which maps to the genome, you may miss interesting data such as 3' RNA editing events.
  • do your homework for what sequencing depth you need in your samples

Basically when ordering make sure the provider is contractually obliged to provide all the things that are important to you

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Alastair Kerr5.2k

Thank you very much for your advice! I will definitely consider these.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Pals1.3k
3
gravatar for Niallhaslam
5.3 years ago by
Niallhaslam2.2k
Dublin
Niallhaslam2.2k wrote:

Given this is biostars, most of us are I would assume working on the data analysis side rather than data generation so I'm not speaking from personal experience. But I've heard good things about BGI. They now have an centre in Europe, but I know people have been able to FedEx stuff to them in China without problems.

http://www.genomics.cn/en/navigation/show_navigation?nid=4176

ADD COMMENTlink written 5.3 years ago by Niallhaslam2.2k

Thanks. In fact, my colleague is working with whole genome data sequenced in BGI China. However, he is not really satisfied with their primary analysis especially the choice of their tools. I will contact BGI considering advice from Alastair.

ADD REPLYlink written 5.3 years ago by Pals1.3k
2
gravatar for Malachi Griffith
5.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith16k wrote:

A list of genome centers was created here: List of Genome Sequencing Centers/Institutes

You may find that for many of these, a project consisting of ~30 samples is a bit small. If the center has unused capacity they may be willing to take on a project of this size though. Particularly if there is an understanding that raw data will be delivered without an expectation of ongoing analysis support.

ADD COMMENTlink written 5.3 years ago by Malachi Griffith16k
2

From top reply: http://omicsmaps.com/ : link seems to be reasonably up to date.

ADD REPLYlink written 5.3 years ago by Alastair Kerr5.2k
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