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BioArray Q&A: MARG s Knudtson on Compiling a Profile of the Microarray Field

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Two weeks ago the Microarray Research Group of the Association of Biomolecular Resource Facilities launched its 4th Annual Survey of Microarray Facilities. The 11-member group is requesting that microarray directors and facility personnel fill out the survey so it can come up with a profile of the field. The survey can be accessed at http://www.surveymonkey.com/s.asp?u= 74287542889. The deadline is Jan. 7, 2005, and analysis of the data will be presented at the ABRF 2005 meeting to be held on Feb. 5-8 in Savannah, Ga. In addition, the results will be posted on the ABRF website (http://www.abrf.org) shortly thereafter. As an added incentive, the group is entering each participant into a drawing to win an Apple iPod mini. This week, Kevin Knudtson, director of the University of Iowa’s DNA Facility and a former chair of MARG, took the time to answer some questions from BioArray News about the survey.

What is the goal of the survey?

The goal of the current survey and the past surveys is to determine a profile of a microarray facility. The first part of the survey, the general section, addresses the demographics, personnel, and types of services provided by a microarray facility. The remaining sections of the survey focus on specific technologies such as Affymetrix arrays, custom spotted arrays, protein arrays, bioinformatics, and future directions. After completing the gen-eral section, participants are asked to complete the appropriate remaining sections that apply to their experience or situation. The results of these surveys have been used by institutions as they plan for the adoption of microarray services and the hiring of personnel.

Who is eligible to fill out the survey?

Anyone may fill out the survey. However, if you look at the questions, they are aimed at the microarray service provider. Anyone who directs or works in a microarray facility would be the primary target. Two years ago we had about 70 respondents. Last year we had about 110 respondents. We’re trying to build the numbers. Obviously, the more respondents we can acquire, the more meaningful the data.

Tell us about the sections of the survey.

In the past we’ve had a general section, a spotted array section, and an Affymetrix section. Clearly the field has changed quite a bit, and we have expanded the section to include sections on bioinformatics, protein arrays, and future microarray technologies.

What kinds of questions are you asking, when it comes to bioinformatics, for example?

In the past surveys, our bioinformatics questions were vague and did not begin to address some of the specific issues faced by investigators as they analyze their data. In the present survey, MARG decided to dedicate an entire section to this important area to the microarray user. There are questions that address the types of data normalization used, analysis tools used, and the types of software used. The questions in the past have been general as to the type of software packages used. For example, we have asked whether you are using a commercially available software package such as GeneSpring or Spotfire or some of the other more recognized packages, or are you using freeware packages that you might get at TIGR, etc. Results of past surveys suggest that most facilities are using a combination of both commercially available software and freeware. Surprisingly, the past surveys have suggested that there does not seem to be a software package available that fits everybody’s needs. About one-third of the respondents indicated that they also needed an in-house solution to address some of their analysis needs. So, we are trying to get an idea of just how many people are able to get by with the commercial packages, or some of the freeware packages, or [whether] people have had to develop some things in-house to address all their issues.

Have you noticed any trends in doing this survey over the past few years?

The demographics of the survey respondents have changed as we are seeing a higher percentage of the total responses come from individuals outside the United States and Canada. There have been a few other trends that would probably not surprise very many people. The first survey, conducted in 1999-2000, indicated that most people were spotting cDNA or PCR products and not oligonucleotides. Clearly there’s been a shift to spotting oligos. Also, results from the Affymetrix sections of previous surveys suggest there has been a migration away from using Test arrays to assess sample quality.

Are personnel from academic or pharma/biotech labs more likely to fill out the survey?

In the past, we have had respondents from both academic and commercial settings, but most have come from academia. This is likely a reflection of the high number of ABRF members that work in an academic setting. Any microarray user or service provider, regardless of their lab setting, may fill out the survey. We would like to have both academic and commercial microarray labs fill out our survey as they each provide a unique perspective to the needs a microarray lab provides to its users.

Are you hoping to get more downstream users to fill out the survey?

We welcome anyone who is using microarrays, although the questions are primarily aimed at the microarray service provider.

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