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UT s Shelly Gunn Spreads the Gospel of Genome Scanning

Shelly Gunn
Clinical Pathology Resident
University of Texas Health Science Center at San Antonio

Name: Shelly Gunn

Title: Clinical Pathology Resident, University of Texas Health Science Center at San Antonio

Professional Background: 2003-present, clinical pathology resident, UTHSCSA; 2002-2003, adjunct instructor, Department of Pediatrics, UTHSCSA; 2002-2003, adjunct instructor, Department of Cellular and Structural Biology, UTHSCSA.

Education: 2002 — PhD, genetics, UTHSCSA Graduate School of Biomedical Sciences; 2002 — MD, UTHSCSA Medical School

Boston — Something is brewing in the world of array comparative genomic hybridization. What was once just one tool discussed alongside others at array-related conferences has now graduated to having its own meeting tracks, such as the Array CGH Microarray session at Cambridge Healthtech's GOT Summit, held here last week.

One of the speakers that helped kick off the event was Shelly Gunn, a clinical pathology resident at the University of Texas Health Science Center at San Antonio who is in the process of setting up her own genomics lab to offer array CGH as a service.

During her talk, Gunn discussed the new lab, the strengths and weaknesses of array CGH, and why she has dubbed array CGH "genome scanning" to give it a clinician-friendly handle. BioArray News interviewed Gunn following her talk.

Can you give me a little background on how you got into array CGH?

I was first introduced to array CGH in the spring of 2002 while I was finishing a combined MD-PhD degree program at the University of Texas Health Science Center at San Antonio. My dissertation project involved the molecular characterization of 50 pediatric patients with a specific CNS abnormality and normal chromosomes by traditional G-banding analysis.

We had a hypothesis that there was a sub-microscopic gene deletion of the myelin basic protein gene on chromosome 18, but we had only found a couple of patients who supported our hypothesis. One of them was particularly perplexing. He had normal chromosomes by G-band, but a large deletion by fluorescence in situ hybridization, and we couldn't resolve that.

So we ran an array on this patient and it completely answered all of our questions, and also gave him a diagnosis. The array CGH confirmed the deletion of 18q seen by FISH and revealed gain of material on 4q which had translocated to 18q. There have been several subsequent patients who have shown that same translocation by both FISH and array CGH. It was through studying these patients that I decided that instead of continuing in basic research, I would pursue a residency in clinical pathology because I believe that array CGH will enter the clinical arena through the door of clinical pathology, also known as laboratory medicine. I am just finishing that right now, and this summer I will join the faculty of the Department of Pathology and help run a clinical genomics lab.

What kind of resources will your lab have?

The Department of Pathology is going to support it in part based on our potential success and our department chairman is committed to advancing clinical genomic analysis of patient samples. My co-director, Ryan Robetorye, and I also have grant money that has been awarded. Both research and clinical samples will be analyzed in our lab.

What tools will you be using?

I am going to be using mainly the CombiMatrix Molecular Diagnostics array platform for two reasons: One is that they have the constitutional array, which is up and running and ready to go and I have been using it to work with tumor samples, so it's a good array to start with. Another reason I am choosing that platform is because it is user-friendly; you can open your data in a Microsoft Word program. You obviously need special software to read what comes through the scanner, but you can share the data with clinicians and researchers and it's easily interpretable.

Where have the samples you currently work with been coming from?

I have had three different projects. I have been running multiple myeloma samples as part of a San Antonio Cancer Institute-funded study, and our samples come to us from the Myeloma Clinics at the VA and University Hospital in San Antonio. The congenital samples are just sent to me now on a regular basis. People read a paper and then they send me samples and ask for an analysis. So we have received samples from as far away as the UK; I feel like my own reference lab right now. And then the third project is just to answer questions that we have about how the arrays are run, what are they going to tell us about patients, et cetera. There is an approved protocol for samples that are being discarded in pathology. You can use them to try new tests, and as long as you don't use [them] for the clinical chart and as long as there is no patient's name on the sample, it's OK.

How do you plan to handle any regulatory issues in your lab?

It's just like when FISH started, it wasn't approved by the US Food and Drug Administration. But the College of American Pathologists and different regulatory boards have criteria for setting up a test in your lab using experimental reagents.

So you put a disclaimer on it that says that it's for research use only and it is not an FDA-approved test, and that information can be given to the physician in whatever way he or she sees fit. So it's all under that.

But we are not there yet. We are still figuring out how to use this in clinical research.

You mentioned during your talk that you are calling it a 'genome scan' instead of an array CGH test. Can you tell me a little about that?

That's for my clinician colleagues. Because if you talk about an array-based comparative genomic hybridization test as a clinical test, they look at you like, 'What are you talking about?' But if you say you want to do a genome scan, they are all ears. They want to know more about it. And that's really what it is. It's a survey of the entire genome. It makes it a very orderable test.

You said that you are more comfortable with using array CGH to answer congenital questions rather than working with cancers, especially malignant tumors. Can you explain why?

Well, I've done more congenital work. But another problem with a tumor is that you are going to need to get a pure sample, whereas with congenital you just take a blood sample and every cell is going to have the genome of interest.

Malignancies are a big challenge, in both hematological tumors and solid tumors because you really have to separate the tumor cells away from the normal cells before you can extract DNA.

You said that your new lab will work with both UT's cytogenetics lab and its molecular diagnostics lab. Of the two, has one shown more interest?

Cytogenetics definitely — this is such a direct progression from G-banding. The cytogeneticists, at least at the center where I work, want this technology as an adjunct to the genome scanning already being done by G-banded karyotyping.

We will always need G-banded karyotypes and FISH because array CGH can only show you genomic imbalances, for example, gains and losses of DNA. If you want to know where that material is located in the genome you need to use karyotyping or FISH. For example, our congenital patients with unbalanced t(4;18) show gain of approximately 4 Mb on 4q, but we have to use FISH to localize the gain of material to chromosome 18q.

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