The Stanford Genome Technology Center (SGTC), formerly the Stanford DNA Sequencing and Technology Center, has been funded since 1993 by the National Human Genome Research Institute (NHGRI; and its predecessor) of the U.S.A. National Institutes of Health (NIH). SGTC is headed by Director Ronald W. Davis, PhD, Professor of Biochemistry and Genetics and Co-Director Lars Steinmetz, PhD, Professor of Genetics.
The SGTC was originally funded with two primary missions:
- To design and build instrumentation and to invent novel technologies to increase the throughput and decrease the cost of large-scale DNA sequencing and genomic analyses.
- To participate in the international consortium sequencing the genome of the model eukaryote, baker's yeast: Saccharomyces cerevisiae.
Meeting our goals
The Stanford Genome Technology Center has been successful in developing technologies for biology and medicine.
- Our automated systems for the Human Genome Project have contributed to enormous cost reduction.
- In 1993, we developed a new form of oligonucleotide synthesizer that reduced synthesis cost by 20-fold. Reduction in the cost of oligonucleotide synthesis made molecular biology research, genomic analysis, and DNA sequencing less expensive and more broadly accessible.
- In the 1990s SGTC began a collaboration with Affymetrix. This joint effort resulted in today's DNA microarrays, producing high-quality multiplexed data with ever more clinical uses, while dramatically reducing the cost of aquiring biologically and medically relevant data.
SGTC developed standard operating procedures pertaining to gene expression using Affymetrix U133 Plus 2.0 Arrays and we released a video training series showing step-by-step instructions on our web site at http://www-sequence.stanford.edu/glue/video.html.
- In the late 1990s we focused on developing Molecular Bar Codes and Molecular Inversion Probes (MIPs), a novel method for high-throughput genome-wide detection of single nucleotide polymorphisms and gene copy number.
- SGTC developed new tools for blood collection and analysis for clinical studies that have greatly reduced cost while providing greater data quality.
- Other, more recent innovations include chemogenomics applications of Molecular Bar Codes and proximity ligation. SGTC was successful in conducting a 40-plex assay of cancer markers on clinical samples. The technology has been fully commercialized.
- SGTC has been developing novel biosensor technologies. Diverse technologies using molecular probes, bioluminescence, beads or electrical detectors are finding applications for detecting TB, avian influenza, HPV and Pseudomonas aeruginosa. Collaborations with CDC (Center for Disease Control), UCSF (University of California San Francisco), and others have provided valuable clinical perspective, and helped to develop broad expertise and understanding in the field of molecular diagnostics.
- We developed technologies that led to clinically relevant insights for trauma and burn patients (see Inflammation and Host Response to Injury].
- The Yeast Deletion Library and the SGTC chemogenomics platform have found applications providing new insights into the genotype-phenotye relationship on a genome-wide scale. The combination of technologies illuminates for the first time the fitness characteristics of the entire genome in varied environmental backgrounds. The startling discovery that most of the yeast genome is associated with fitness changes has a bearing on evolution and functional genomics. Results from studies based on this technology are visible at the "yeast fitness database".
- We successfully sequenced the genome of Saccharomyces cerevisiae strain YJM789.
- The Atopobium vaginae genome and the Gardnerella vaginalis genome have been shotgun sequenced to three-to-five-fold genome coverage. The shotgun reads have been assembled into contigs and made available on our web site. Both projects have been undertaken to provide support for studies of the role that A. vaginae and G. vaginalis play in the health of the human female urogenital tract.
The SGTC has received numerous patents for the instrumentation and the software that we have developed. The instrumentation, robotics, and software that we have invented and/or developed have been transferred from Stanford University to the commercial sector by the Stanford University Office of Technology Licensing. Such instrumentation often carries the SUTECH® logo, which was developed in conjunction with the Stanford University Office of Technology Licensing. As a direct result of these activities, the SGTC is an ongoing major contributor to a whole new industry, that of commercial genomics. Current activities toward the first goal is described in detail on the SGTC Technology Development Group pages. SGTC has spun-off several companies and has numerous ongoing collaborations.
The genome sequence of S288c was completed by the international collaboration, released to GenBank, and published in 1996. The SGTC contributed 872 kb of fully finished DNA sequence: all of chromosome V, a substantial portion of chromosome IV, and a tiny portion of chromosome XVI. Further information about the S288c genome can be obtained by accessing the Genome Database. Since the successful completion of the genome sequence, the SGTC has completed, and published, two bacterial genome sequences, those of Chlamydia trachomatis and The SGTC has been a major participant in the international Malaria (Plasmodium falciparum) Genome Project and the (model plant) Genome Project. Both of these genome sequences have been published in the journal . We also participated (in a small way) to the Human Genome Project. The diploid genome sequence of has been published in 2004 (PNAS | May 11, 2004 | vol. 101 | no. 19 | 7329-7334) and Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans was published in 2005 (Science 25 February 2005: Vol.307. no.5713, pp.1321-1324). Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces S. cerevisiae C. pneumoniae.Plasmodium falciparumArabidopsis thaliana NatureCandida albicans the genome of the
The success of our efforts has been driven by the ability of the SGTC to attract an interdisciplinary team of physicists, computer scientists, engineers, chemists, and mathematicians to work alongside biologists, biochemists, and physicians for the purpose of employing genomics approaches to attack fundamental problems in biology and medicine. This interdisciplinary approach gives the SGTC a unique ability to identify future technology needs and to develop and implement those technologies.
With NIH-funded large-scale DNA sequencing now consolidated at a few very large centers, we are concentrating on developing new technologies for functional genomics, particularly for complex genomes such as human. In 2000, we changed the name of our center to the SGTC to reflect a shift in our focus.