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What is the most innovative thing you’ve done to keep array costs down?

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A. We make our own nylon membrane arrays. We can make a 17k element cDNA array for a unit cost (time and materials) of less than $10. We have made over 50,000 of them. This allows us to consider almost any size or type of array experiment.

Kevin Becker
Head, Gene Expression and Genomics Unit
National Institute on Aging, NIH

 

A. The most effective approach we have taken to minimizing array assay costs is to implement a stringent quality control test for sample RNA prior to labeling.

Chris Harrington
Manager, OHSU Affymetrix
Microarray Core
Oregon Health and Science University

 

A. I believe that it is important in microarray gene expression work to have internal standards available to all users that should allow a better comparison of results from one lab to another. Since I am using two-color arrays I would suggest using standards that could be bought from one or more companies. Indeed, this would be the same as what coagulation laboratories have in terms of specific standards for certain plasma constituents to assay patients plasma.

John McGregor
Thrombosis Research Institute

 

A. The most significant methods we’ve used in the last 18 months or so: 1. Couple comprehensive bioinformatics and analysis services with the technology services offered in the core. This has allowed a cost savings on software by keepings things centrally located. 2. Partnerships with other institutions in our state and nationally have allowed us to negotiate attractive bulk pricing from a number of vendors. 3. Ordering reagents and arrays on a yearly basis and generally placing the order at the end of the year or end of a sales quarter has allowed us to save a very significant amount of money. 4. Partnering with new companies in the evaluation of new products has allowed us to try new reagents and methods at a significant discount. 5. Using open source and publicly available software developed in the academic realm for much of our analysis needs. While the systems admin overhead can be high, the net savings is significant.

Shawn Levy, Director
Vanderbilt University Microarray Shared Resource

 

A. The most innovative way we’ve been able to cut costs in our lab is by automating standard procedures for labeling. This cuts costs in two ways: it reduces wasted reagents; and what it does is makes us more reproducible so fewer samples have to be reprocessed.

Andy Brooks, Director, Functional Genomics Center
University of Rochester Medical Center

 

A. The most important way is to try to automate things, to try to do things that save on manpower, and to try to multiplex things. My lab’s heavy into Affymetrix, and we have an older system — the fluidics system is literally an antique now, and it requires a technician to man it, essentially around the clock. The upgrade that came out a year ago allows you to walk away for two hours, so you can do something else at the same time without being concerned about extra personnel costs.

Chris Barker, Director, Genomics Core
Gladstone Institute of Cardiovascular Disease
University of California, San Francisco

 

Here’s the question for our June issue:

Integrated biology cuts across scientific and informatic disciplines. In your experience, what key skills or combinations will be most valuable to scientists in this field?

 

Blunt End is a forum for readers to share their experiences and advice. Don’t miss your chance to pass on your wisdom: Send your response to the upcoming question today to [email protected] Remember to be specific, and be sure to give us your full name and institution so we can give you credit for your suggestion.

 

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