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Joel Credle, Director of UC Berkeley DNA Analysis Center

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AT A GLANCE

 

BS in Biology, Radford University, Virginia, May 1998

 

Served as associate scientist at Eastern Virginia Medical School in Norfolk, Va., looking at transcriptional regulation of human genes in the context of CMV infection.

 

Hired to direct sequencing center at UC Berkeley in 2001. Opened microarray core facility in November 2001.

 

Scientific interests focus on genomic technology and how it can be used in research.

How did you get into the microarray field?

At Berkeley, when I joined the sequencing lab, they gave me a lump sum to start a core microarray facility. It gave me the opportunity to start from the ground up, to do the things the way we want to, from the samples and system, to controlling the prices we would charge customers on campus and outside. Bill Waxman at UCSD’s array facility was helpful in telling me of all of the pitfalls that would occur in starting the facility, and was very helpful in getting it up and running.

 

What type of system did you choose?

We chose Affymetrix because we feel that their technology and the internal controls they provide on the chip give us a good grasp on the [microarray] technology for the cheapest price and least amount of time compared with spotted and/or custom arrays. Affymetrix is also a very good company as far as support goes. They have instituted a monthly user group meeting on campus, where they bring in one of their PhD speakers to keep people up to date on the latest trends in technology and sample preparation. At the end, the Affymetrix speaker [usually] stays an hour or more afterwards to answer all of the questions people have.

 

Have you used the new Affymetrix U133 human arrays?

Yes. We think they are excellent. We find the expression levels of genes comparable and the results comparable. We have found a few researchers in ongoing processes who want to stay with U95 until the end of their experiment. But we have asked them, “Are you sure that when you think you are going to be done with the U95 that you will actually be done?” If not, it is better to switch now than start with the U133 later.

Another service that we’ve recently begun to offer is a small sample prep protocol, which Affymetrix is currently validating in-house, that deals with starting with less than five micrograms, down to 100 nanograms. People want to take small samples from paraffin embedded or laser capture microdissection samples. We have shown that it is comparable to doing the original protocol.

 

Are there any downsides to the Affymetrix system?

The one drawback is the fact that sample preparation is the most tedious part of the process. You have to order chemicals, reagents, and supplies from 20 to 30 different companies to do a sample preparation. I am waiting for someone to jump on the ball and say “We can sell you an all-in-one kit that has been validated, that’s one order number.”

 

Who at Berkeley is using microarrays, and about how many arrays do you go through a month?

The biology department members are the biggest users, but the new bioengineering department is also a big user. They are looking at expression of bone cells grown on different surfaces, to see what these surfaces do. Our facility is also available to people outside campus. We go through anywhere from 30 to 40 arrays per month.

 

Where do you get the money to run your facility?

We are almost an outside business. We don’t receive any external grant support. All of the money comes from a recharge of services we offer. But unlike a true business we can’t make a profit. We walk a fine line between getting in trouble for making a profit and getting in trouble for losing money.

 

How do you deal with data analysis?

There are three stages. First, I give users the latest version of the Affymetrix Data Mining Tool, and let them run with it for a week. After they get comfortable with it, we meet for one or two days for three or four hours a day and I show them how to do clustering, and tree analysis, instruct them on what they should use as a baseline, and the tunable parameters they can use to process the data. That gets them excited, to see the full potential of what we have.

 

What is the biggest challenge with microarray data?

The only challenge is that there’s so much of it. People [initially] expect they can fully analyze their data in a week to three weeks, then are looking at it for three to four months, and every time they look at it, there’s something new.

 

What are your future needs as far as microarray technology goes?

My future needs are to hire bioinformatics people specifically involved in the data analysis that can take the Affymetrix software and utilize as much as they can, and can also use third-party software such as GeneSpring that can be used for spotted or custom arrays.

 

Where do you think the microarray field and microarray technology are going?

I really see microarray labs being like the large automated sequencing machines. Sequencing is never going to be a dead science, but there is not really a need for these really large sequencing centers. Similarly, microarrays are going to be a more individual science where individual labs have microarray capabilities all up and down the halls of a science lab, once the prices come down. Instead of looking at the entire genome of the mouse or rat or human, people will have a personal microarray machine and look at a subset of genes. That’s cost-effective.

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