Associate Professor, Department of Molecular and Human Genetics
Associate Professor, Program in Integrative Molecular and Biomedical Sciences
Assistant Director, Future Technologies, Human Genome Sequencing Center
B.S., University of California, Davis, 1984
Ph.D., Baylor College of Medicine, 1996
My laboratory is involved in next-generation sequencing (NGS) technology development, which stands to change the way we think about scientific approaches in basic, applied, and clinical research. The broadest application for NGS technologies is medical resequencing of human genomes, which could unravel genetic causes of common disease and cancer, assist doctors in prescribing personalized medicine, and provide predictive indicators of disease prior to onset opening the door for preventive therapies. Diabetes mellitus is a complex disease with genetic and environmental components contributing to its onset, progression, and severity. In collaboration with Dr. Ashok Balasubramanyam (Department of Medicine; Division of Diabetes, Endocrinology and Metabolism at BCM), we have begun candidate gene sequencing using the Sanger method, with plans to expand our efforts using NGS methods, of diabetic patients prone to ketosis, called ketosis-prone diabetes, in the near future.
Of the numerous next generation sequencing strategies under development, my group has focused on the cyclic reversible termination (CRT) method. CRT is comprised of a three-step process of incorporating modified nucleotides, fluorescence imaging, and cleavage, after which the cycle begins again. CRT reactions are performed in a high-density format using single DNA molecule or clonally-amplified templates, eliminating the requirement for gel electrophoresis while significantly increasing sequence throughput. The foundation of this approach is the reversible terminator, its chemical and biological properties of which directly impact the performance of the sequencing technology. Scientists at LaserGen, Inc. have discovered a novel paradigm in reversible terminator chemistry, the attachment of a photocleavable, 2-nitrobenzyl group to the nucleobase of dNTPs, which, upon incorporation, terminates DNA synthesis. The 3'-OH group of the RT remains unblocked, providing favorable incorporation and termination properties for several commercially available DNA polymerases, while maintaining good nucleotide selectivity against mismatch incorporations. Upon removal of the 2-nitrobenzyl group with UV light, the natural nucleotide is restored without molecular scarring. We are now at the stage of technology development to begin integration of the CRT chemistry to an instrumentation platform.
My laboratory, in collaboration with Dr. David Hillis at the University of Texas in Austin, has pioneered approaches for appropriate uses of phylogenetic methods in HIV forensic cases. For example, phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically-related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. In our 2010 PNAS paper, we presented methods and results from two criminal cases, State of Washington vs. Anthony Eugene Whitfield and State of Texas vs. Philippe Padieu, which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., the index case), whose identity was revealed at trial to be that of the defendant.