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Lisa White, Director, Baylor College of Medicine Microarray Core

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At A Glance

PhD in molecular genetics, University of Houston.

Postdoctoral research at University of Maryland Center for Agricultural Biotechnology developing gene transfer technology for non-Drosophila insects including flies and screw worms.

Research scientist at Houston-based Identigene, a human DNA identification company.

Accepted directorship of Baylor Microarray Core in September 2001.

Interests include travel, gardening, and landscaping.

QHow did Baylor go about setting up its microarray facility?

AIn 1995, Baylor received a NIST ATP grant to develop microarray technology, along with Duke, Identigene and AP Biotech. This core facility grew out from that consortium. We started out doing mini-sequencing on chips which consisted of arrayed primer extension, or APEX. As a scientist at Identigene, I became involved in this work in 1998. Then in 1999, Baylor established this facility as an official core, and we started spotting arrays for researchers.

QWhen you were setting up the facility, how did you choose which platform to use, i.e., Affymetrix: vs. spotted arrays?

AWhen we started working with arrays there weren’t Affymetrix arrays. So we started spotting arrays. We developed our own slide attachment chemistry as well. The previous director of the lab developed a laser detector, so we were doing this type of detection through our affiliation with AP Biotech. Then AP Biotech purchased Molecular Dynamics, so we ended up doing confocal laser scanning for slides. This works fairly well and there is some unhappiness with the strength and the way some of the older scanners hammer the fluor [labels] for the arrays.

QWhat kind of arraying equipment do you use?

AWe initially had started with a capillary spotter developed by our previous director. It wasn’t miniature enough so then we began using a Pat Brown-ish model. Then we bought our own arraying robots from GeneMachines and Cartesian.

QI understand the core facility, and other Baylor College of Medicine facilities recently faced a major challenge from nature, in the form of a flood. How did you cope with this?

AIn June, Tropical Storm Allison hit the medical center, and our building was hit very badly. The basement and sub-basement were both completely flooded. Our throughput really came to a stop. We lost power, and because the freezers died we lost reagents and clone sets. The machines were fine. Since then we have come back, and now have the capability of doing 100 9,000-spot arrays per day.

QWhat types of experiments do the researchers who use your labs primarily conduct with arrays?

AThe majority of the arrays that we are producing are for gene expression studies in mouse and human. We are also doing SNPs for heart disease and are doing some BAC arrays. We also have an 8,000-spot chip for Dictyostelium or slime mold. That clone set was developed here. The researchers in the Dictyostelium group print every week. They’ve probably done two thousand chips. We also have a custom retina array for humans, and have the human cDNA IMAGE clone set from Incyte. This is still being amplified, since there are 40,000 of these cDNAs.

QWhat has been the biggest challenge in working with microarrays, and how have you addressed it?

AThe biggest challenge, especially for a small core facility, is making sure you implement your quality controls in all of the steps of the arraying process. Producing and manufacturing arrays is probably the most tiresome and cumbersome part of it, which includes making sure that you get consistent arrays batch after batch. Because we functionalize our own glass, we have quality control steps in that area, and also we do visual inspection of the array after it has been printed. We hybridize it with something that hybridizes to everything on the array, so we can get a good idea of the spots that have DNA and the ones that have DNA and the ones that don’t.

QFinally, what improvements or changes would you most like to see in the microarray sector in the coming year or so?

AThere has been some disagreement on the annotation for the mouse GEM clone set from Research Genetics, for example, and I would like to see better annotation of the clones and ESTs that are available, especially those commercially available.

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