[Medicago] Plans for Medicago truncatula Goldengate Platform

medicago from net.bio.net via medicago%40net.bio.net (by medicago from net.bio.net)
Wed Nov 2 14:12:44 EST 2011

Medicago Colleagues:

Thank you for your responses to recent emails aimed at the development of Medicago truncatula Goldengate platforms. We heard from a reasonable number of labs indicating an overall interest in >25 arrays. Since that time, I've learned that feature density on standard Goldengate platforms can be increased twofold (3072 features) with minimal increase in pricing. Depending upon the final number of arrays that are ordered at the same time, the cost per array should be ~$11,000 (for 96 plant samples) including processing. When you think about it, that's quite amazing ---- essentially $0.04 per datapoint. It should also be possible to generate 1536 feature arrays, in which case the price should be ~$8300 ($0.06 per datapoint).

I should mention that the cost of $8,000-$11,000 per array is based on estimates that I've received from the Biomedical Genomics Center (BMGC) here at Minnesota. BMGC is a thoroughly up-to-date facility with hundreds of internal and external clients, a regular staff of 16, and a budget >$5 million. In other words, it is definitely capable of handling the Goldengate needs of the Medicago community. Nonetheless, different groups could order OPAs (SNP oligos) and have them analyzed in other facilities. In that case, costs would vary at different locations. Still, costs at Minnesota's BMGC are expected to be quite competitive. 

Please understand that because of the design and implementation process at Illumina, the cost per array is lower the more that we order at the same time. Also --- and this is important --- Illumina will probably synthesize only what we request in our group purchase order (plus a modest amount extra for insurance). This means if you decide at a later date to start using the Medicago Goldengates, they might not be available and/or might cost a great deal more to obtain. This is regrettable, but it appears to be  unavoidable.

Once we finalize the choice of SNPs and the total number of arrays that will be ordered, it will be necessary to coordinate funding and submit a unified order to Illumina in order to receive the most economical price quote. This is important to understand, as it will require a commitment of funds within the next few months, followed by subsequent availability to the arrays as soon as Illumina finishes production of the OPAs.

If you are interested in participating in the group purchase order to Illumina for Medicago Goldengates, can you please write back to confirm this and to provide the tentative number of 96-sample arrays that you are likely to order. Please re-send this information, even if you've sent an earlier email about the same subject. Note, this commitment to participate in the group purchase does not necessarily commit you to using the University of Minnesota BMGC, but as I wrote previously, the BMGC will provide a highly efficient and cost-effective option.

Finally, if your lab is committed to participating in the group purchase, can you send me the name and email of someone from your group (who could be you, of course) who is willing to work on the design and selection of SNPs that will eventually be included in the Goldengate platform.

We hope to have the arrays "designed" by the end of the November, and then organize the paperwork in December and January leading to a group purchase early in 2012. The OPAs should become available within a couple months after that time.

PLEASE write back to Roxanne Denny (denny004 from umn.edu) with your answers to these questions as soon as possible so we can get the process moving.


Nevin Dale Young
Distinguished McKnight University Professor
Office: 320 Cargill Building for Microbial and Plant Genomics
Mail: 495 Borlaug Hall
University of Minnesota
St. Paul, Minnesota USA 55108

Voice: 612-625-2225 / Fax: 612-625-9728
Email: neviny from umn.edu
URL:  http://umn.edu/home/neviny

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