Overview of Research Labs in the Genomics Center:

Our research laboratory has all the tools needed for genetic studies of complex disease. These labs occupy 18,400 square feet of a newly renovated research building at WFUSM and include dedicated equipment and space for high throughput experiments in molecular biology, genotyping, sequencing, functional genomics, cell biology, and mediator analysis.

Yearly lab statistics:

• We genotype more than 1.5 million SNPs per year.
• Perform more than 95 thousand sequencing reactions per year.

Detailed laboratory description:

The Center's laboratories are well equipped with state of the art equipment necessary to perform current molecular genetic procedures including genome scanning, DNA sequencing, high-throughput SNP genotyping, and gene expression studies. Equipment includes one ABI 3730XL and one ABI 3700 DNA analyzers, a Li-Cor automated sequencer, a 7700 sequence detection system (for Taqman® assays), an AutoPure LS DNA isolation robot for isolation of DNA from large volumes of whole blood (Gentra Systems, inc.), a Luminex100 (Luminex, Inc.) for protein measurements, two Beckman automated robotic workstations (a Biomek 2000 and a Biomek FX), a ScanArray 5000 microarray scanner (Packard BioChip Technologies), a Qiabot 9600 robotic workstation (Qiagen), a DNA shearer (Gene Machines, Inc.), an electroporator, two shaker incubators, 14 thermocyclers, -70° (3) and -20° (3) freezers for sample storage, 4 refrigerated (Sorval) table top centrifuges, a high-speed and ultra-centrifuge (Beckman), a UV spectrophotometer (Beckman), a 96-well spectrophotometer (Molecular Dynamics), a gel imaging system (Alpha Innotech), microcentrifuges, multichannel pipetters, biologic safety cabinet and fume hoods, and CO2 controlled incubators. For SNP genotyping, we currently use the MassARRAY SNP genotyping system (Sequenom, Inc.). The MassARRAY is a combination of various automated workstations, in addition to a mass spectrometer, that utilizes a primer extension assay for high-throughput allelic discrimination. Using single-plex reactions (1 SNP per DNA sample), this system is capable of analyzing ~8,000 SNPs per day. By adding multiplexing capabilities, the throughput may be increased to ~40,000 SNPs per day. In addition, this system automatically designs SNP assays and scores the alleles, further increasing the efficiency. A BioRad FX imager (combination fluorimager and phosphoimager) was recently purchased for autoradiography and fluorometry. In addition, a BioRad Versadoc imaging station is being installed in the lab for agarose gels imagery and chemiluminescence.

Genetic analyses are performed on a SUN Enterprise 450 which has the capacity for the calculation and storage of genetic epidemiologic data with high throughput performance. It has four 400 MHz/4-MB UltraSPARC-IITM processors (CPU), a 1.6-GB/sec UPA interconnect, and a 1GB/sec PCI I/O subsystem as well as 4-GB of main memory, and a 218-GB of fast hot-swap UltraSCSI internal hard drive. In addition, there are three Sun workstations and 15 high speed PC's used for data management and computational analysis. In October, 2002, the Center ordered a Sun Fire V880 Server 8, which will markedly increase our computing power. This server has twelve 750 MHZ CPU, 32 GB memory, and 432 GB hard drives.

Laboratory productivity in the last three years:

Following the creation of the genomics lab three years ago, we have evaluated over 30 genes in disease susceptibility and published ~30 peer-reviewed research papers. Many of these are in prestigious journals including Nature Genetics, The New England Journal of Medicine, The Journal of the National Cancer Institute, Cancer Research, and The American Journal of Human Genetics.