Clinical Metagenomics

We are creating new tools to diagnose infections in humans utilizing next generation DNA sequencing combined with ultra-fast algorithms. Due to the increased yield and ever decreasing costs of DNA sequencing we are now able to inexpensively and efficiently find nucleic acids from microbes within normally sterile human bio-fluids. We envision a $50 global assay for infectious agents using this technology and we have concerted efforts to decrease the time to result. Graduate students include: Kizee Etienne (fungal project), Angela Pena (viral project) and Julliana Soto (bacterial project). MSc student include Pete Audano (creator of K-analyze), Cai Huang (algorithm development), Shengyun Peng (k- mer pipeline) and Vivek Sagar (creator of Clinical Metagenomics Analysis Pipeline – CMAP). This work is in part funded by a generous Georgia Tech seed grant to our group and Prof. King Jordan (Biology, Georgia Tech).

Human Genetics

Our laboratory is building an automated pipeline to analyze whole genome datasets in the context defining the causative mutation underlying Mendelian diseases. Recent work on a Mucopolysaccharidosis patient from Colombia revealed a complex disorder intermediate between Sanfilippo and Hunter Syndromes. We believe that whole genome sequencing will become the standard diagnostic method for Mendelian disorders and by automating this pipeline we will be able to enable a better understanding of the complex nature of the primary Mendelian mutation as well as important genetic modifiers that can lead to differential clinical presentation. Amit Rupani and Kelsey Rogowski have been leading these efforts.

We are also continuing our work on understanding the genetic basis of susceptibility to infectious diseases, including work on Buruli ulcer in Ghana. Our main collaborator is Prof. Julius Fobil at the University of Ghana.

Systems Biology

Nanovesicular exosomes are relatively understudied conveyers of action-at-a- distance signaling within higher organisms. Swetha Srinivasan is carrying out a systems biology approach to understand the role of these vesicles during the immune response, especially focused on the role of Toll like receptor (TLR) modulation of exosome composition and effector function. Pam Head, Jillian Le and Michelle Su are undergraduate students who are contributing to various aspects the research into the basic biology of exosomes. Andrew Sammond and Sean Lucking are undergraduates who are investigating real time capture and visualization of exosomes. This work is funded by a generous Georgia Tech seed grant to our group in collaboration with Prof. Brandon Dixon (Mechanical Engineering , Georgia Tech).

Therapeutic decision analytics for cancer based upon DNA mutations and RNA expression profiles will become the standard of care for cancer patients. Working with Professor John McDonald’s laboratory (Georgia Tech), we are building a computational pipeline to match mutations within a panel of cancer-linked genes with optimal therapeutic strategy. Vivek Sagar and Benjamin Metcalf are leading these studies within the laboratory. This work is funded by a generous grant from the Cancer Treatment Centers of America.

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