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James Hadfield on the John Innes Center s New Affymetrix LIMS Platform

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At A Glance

Name: James Hadfield

Title: Microarray Manager, Genome Laboratory, John Innes Center

Professional Experience: Microarray Manager, Genome Laboratory, John Innes Center, Norwich, UK; Lab Manager, University of Cambridge; Breast Cancer Research, Norfolk Norwich Hospital

Educational background: BS, 1995, molecular biology, University of East Anglia


James Hadfield is the microarray manager at the John Innes Center's Genome Laboratory in Norwich, UK, which is located in the Norwich Research Park adjacent to the University of East Anglia. He is also a member of the UK Academic Affymetrix Steering Committee.

Hadfield and his colleagues have been running Affymetrix microarray experiments for European researchers for five years. Through the process of receiving samples, running the experiments, performing the data analysis, and estimating costs to the researchers, they have developed a laboratory data-management system that not only can track the history of an experiment, but will tally the cost for the lab manager and researcher at the end.

As Hadfield sees it, the new LIMS is something that could be useful to other labs, and so the center recently decided to make the system available to other researchers through its website. To learn more about the new LIMS, and to get an update on microarray use in the United Kingdom, BioArray News rang Hadfield up last week for an interview.

How long has the center been in existence, and how long have you been working there?

I have been working in the genome laboratory for five years now. It has been in existence for five years.

How long have you been an authorized Affymetrix provider?

I think we have been authorized now for two years. We were a service provider before that for about three years.

And are you the only authorized provider in the United Kingdom?

Not right now; it has just changed actually. I think there's another service about to come online in the next six months.

So what is the user situation like in the UK? What kind of business do you do each year?

About 50 percent of our business is internal, within the Norwich Research Park. The other 50 percent of our business is primarily from the UK but also across Europe. And we are running around the 500-chip mark here, which is probably the standard level for these kinds of core labs and service providers. Certainly not for the core labs in the States, but I think it's about average for the core labs and service providers here in Europe. And that is growing relatively slowly. We are an academic facility, we are not a commercial company. So we provide all of our services on a not-for-profit, cost-recovery basis.

What kind of team do you have there?

In the genome laboratory altogether there are 12 of us, but they are spread across all of the services we offer. There are two people who run the microarray facility.

I noticed that you are also running Agilent arrays. When did you first start running this service?

We first ran the Agilent arrays about three and a half years ago. We're not really licensed as a service; we haven't negotiated with them to offer a fully fledged service. We have been running a few of those arrays in-house for different projects.

What are people using the Agilent arrays for?

We used the Agilent instead of the Affymetrix for some cross-species expression studies, so we put our different species onto the Arabidopsis array, [and] we've used Brassica. We went down the Affymetrix route five years ago basically because Affymetrix and Incyte were the only two companies that had Arabidopsis arrays. And then Agilent subsequently came out with something, but then again, we had a user community using the Affymetrix array already and for people who want to compare data between each other, a single platform made sense.

So what led you to develop the LIMS?

It was really the management of the projects — [managing] the actual individual samples within the project and merging the communication between myself, as the manager, and our customers. We needed to find a way to track what was being done, when it was being done, who did it, and, as we are developing it now, how much it all costs, so we can end up billing people.

So really it's a sample-tracking system, and it also allows people to submit their samples electronically rather than bringing over bits of paper, sticking them in lab books, and things maybe getting lost.

Did you get any kind of external help for putting this system together?

We had looked at a couple of commercial LIMS products and electronic lab book products, but we didn't find anything that fitted exactly what we wanted to do, or that was flexible enough to be able to change that. So in the end we went ahead and built our own system. And actually the bit that was built first [was] the sequencing LIMS, and on top of that we built the Affymetrix LIMS, and now we've released that as a standalone product itself for other Affy users.

Are there comparable systems offered by other core labs that you are aware of?

No. One of the reasons we had to develop our own and one of the reasons we made it available is [that] all of the microarray database systems that are out there at the moment seem to focus very much on when the data has been generated and then the downstream annotation and analysis of that data. And what we thought was lacking was from the sample and how that sample was put through the system to actually generate the data in the first place. And as a service provider that's primarily of more interest to us than what the company does with the data at the other end. So we wanted to make sure that the quality-control steps were all being tracked. That we had a record of who had passed something and who filed it, and why they made that call within the system. So it has modules for tracking the quality of the total RNA, the quality of the cRNA and such, so we can say whether a sample is good or bad.

Can you walk me through how it works?

It's a very simple system, it's all based on [standard industry programming], and it's relatively open source and easy to install web-based stuff. Users submit a sample over the web. They send us a sample physically as well. When we've got those samples we'll verify that they've come in — that starts the whole process off. And then, very simply, they can go to one web page and get a flow diagram of where their sample is in the processing stage through the Affymetrix gene expression processing worksite. So we'll check the quality of the RNA, we'll do the cDNA synthesis step, [and] the in vitro transcription step. We check the quality of the cRNA, which is kind of the final quality control before we run the Affymetrix arrays themselves.

And then when we finish running the Affymetrix arrays, the Affymetrix software generates report files, and our system does some analysis on those to allow us to pass or file the quality of the actual data before a user gets hold of it. And then the users can download their data electronically. It removes a whole lot of micromanagement, backwards and forwards, conversations about, 'How's it going?,' 'Whereabouts is it in the workflow?' — it saves a lot of time on a project basis.

How will you make it commercially available to other laboratories?

It's a relatively open-source piece of software. We are making it available to academic and commercial people. We are mainly interested obviously in the academic side of things. But we will speak to commercial companies if they want to use that software.

I have spoken to a few companies in the [US], and they have already developed, or are developing, their own in-house systems. This is an academic product. It's not a wonderful, click-on-execute-and-install-it, Windows operating system kind of product. It requires an academic sort of push to get it going. But it's available now. We have just got a licensing agreement from a lab in the States. Another two labs are looking at it at the moment. And we've got a couple people in the UK that are interested in using it. And they are just licensing it on a shareware basis. They get hold of it. They try it out to gauge if they like it, and they pass a small amount of money, and away we go. No restrictions.

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