Hello from Thomas

[tlitman]

Hi all,

My name is I'm Thomas Litman; I run the microRNA biomarker discovery department at Exiqon, Denmark.

We are looking for new and interesting miRNA biomarkers for cancer diagnostics, and so far, we have applied 454 and Solexa/Illumina technology for this (outsourced to service providers).

Now, together with our collaborators at University of Copenhagen (professor Anders Krogh) and the State University Hospital (Finn Cilius Nielsen and Gedske Daugaard) we have received a grant to purchase next generation sequencing equipment. Initially, we were planning to go for the SOLiD system, because - on paper - it had the best specifications compared to 454 and Solexa. However, we have had problems obtaining a test run with our synthetic miRNA pool on the SOLiD system, so I wonder if the technology is ready yet, and whether there are other - and better - alternatives?

What do you think?

Should we instead go for the Polonator?

Or perhaps even Helicos?

Any thoughts are more than welcome.

BTW, soon we will be looking for talented Ph.D.s / post docs to help with the data analysis ... just in case you know anybody interested

Best regards

- Thomas
([email protected])

[Chipper]

Hi,

I wouldn't hesitate to go for SOLiD from a sequence quality and throughput point of view. For the other machines I guess you will have to wait for more data to come out to be able to judge them. What sort of sequence depth do you need for your samples?

[tlitman]

SOliD or Solexa?

Thanks for the reply Chipper,

So far, I have been happy with the depth of the 454 system (ca. 300K sequences), and the even higher of Solexa (ca. 4M seqs), so I don't think that I need more than this for now.

With respect to data quality, I wonder why the service provider GATC in Germany have decided to give up on the SOLiD system, and instead go for another Illumina/Solexa machine?

Perhaps the specs of the SOLiD system are so good mainly because of the algorithm (the color space decoding), rather than the actual chemistry used?

- Thomas

[Chipper]

Hi,

no, the color space "magic" is not in the algorithm but is an intrinsic part of the chemistry used. But of course there are errors also with the SOLiD but in the aligned reads you will likely se ~0.1% compared to ~1% for the Solexa.

Dont know about GATC, but If they have one Solexa already I guess it makes sense to get another, the data handling and labwork will be much more efficient then.

But why not try to get a sample run on the Helicos, they should be eager to get customers I guess...