Cancer Institute A national cancer institute
designated cancer center

Maybel Lam, a life sciences technician at the Stanford Functional Genomics Facility at the School of Medicine, works at a printer spotting small slides with samples of DNA sequences taken from thousands of known genes. The facility uses these slides, known as microarrays, to analyze gene expression in tissue samples as part of its support services for school clinicians and researchers.

The Stanford Functional Genomics Facility is an offshoot of research efforts by Pat Brown, MD, PhD, professor of biochemistry, and former genetics professor David Botstein, PhD, now at Princeton University. Brown and Botstein developed the techniques behind this type of spotted microarray when working on a cancer taxonomy project. Since its launch in 2001, the facility has produced 40,000 full genome microarrays, making it one of the largest academic producers of microarrays in the world.

The gene expression analysis employed by the facility measures the relative amount and type of messenger RNA (mRNA) in a biological sample. The mRNA molecules convert the “instructions” encoded by a gene into its corresponding protein. By identifying the mRNA molecules at work in a cell, researchers can infer which genes are active at any given time.
To run an analysis, a researcher first prepares a labeled cell extract from a sample. When the extract is incubated with a microarray, mRNAs from the sample stick to their corresponding DNA sequences on the slide, showing which genes are active and at what level.

This type of analysis is helping researchers understand the fundamental mechanisms behind growth and development as well as the underlying genetic causes of many diseases, says Michael Fero, PhD, facility director. It has been particularly useful for pinpointing differences between normal and cancerous cells as well as subtypes within certain cancers.
In the future, Fero says, clinicians will be able to use microarrays to more precisely diagnose a patient’s cancer and in turn customize an optimal treatment plan.


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