Genome Analysis Core
Daniel Douek, M.D., Ph.D.
Major Areas of Research
- Unbiased bulk 5’RACE for TCR and Ig sequencing
- Bulk RNA sequencing for whole transcriptome analysis
- Molecular baiting for targeted genomic sequencing
- Whole genome sequencing
- Microbiome analysis by nucleic acid fragment sequencing
- Virus discovery by shotgun sequencing from human, animal and environmental samples
- Single cell RNA-seq, Ig-seq and TCR-seq by SMARTseq
- Single cell RNA-seq, Ig-seq and TCR-seq by 10x Genomics incorporating hash-tags, CITE-seq, ATAC-seq
- Virus sequencing for HIV, SIV, SARS-CoV-2 including:
- Short amplicons for phylogenetic analysis
- Shotgun sequencing for characterization of virus stocks
- Ig and TCR target epitopes
- Single genome analysis
- Full length HIV genomes
The Genome Analysis Core (TGAC), within the Human Immunology Section fulfills many of the specialist sequencing needs of the Vaccine Research Center. The VRC is designing, producing and testing candidate immunogens aimed at eliciting neutralizing antibodies against a number of human pathogens including HIV, Malaria, Influenza, RSV and SARS-CoV-2. At the core of this effort lies the requirement to elicit antibodies that use particular IgH and IgL chain gene pairs. For evaluation of vaccine candidates, the evolution of such antibodies, and thus the effectiveness of the vaccine, needs to be monitored using a variety of molecular techniques that culminate in single-cell NGS of pathogen-specific B cell Ig genes. In addition, passive antibody applications necessarily depend on the identification and sequencing of neutralizing pathogen-specific antibodies in infected and/or convalescent people. Similarly, vaccines being developed by the VRC that aim to elicit T cell immunity, such as those against TB, malaria and cancer, require analysis at the level of TCR sequences. To complement these studies of immune adaptive receptor use, the VRC also investigates host genomic associations with vaccine responses and disease progression, the microbiome, pathogen sequence diversity within and among infected people, and host cellular reservoirs of pathogens. To achieve these goals the TGAC has developed a broad portfolio of next-generation sequencing methodologies. These assays are performed on samples from multiple species including humans, NHP and various rodents.
M.D., University of Oxford
Ph.D., University of London
Daniel Douek, M.D., Ph.D., is the Chief of the Genome Analysis Core (GAC). The GAC was established to develop and perform innovative sequencing techniques specifically targeted at immune respertoire analysis. These sequencing technologies are also being used to evaluate candidates for other vaccines, such as influenza and respiratory syncyticial virus, including those undertaken with VRC intra- and extramural collaborators.
Daniel Douek, M.D., Ph.D., is also the Chief of the Human Immunology Section (HIS). HIS studies the processes that determine the course of human diseases in which the immune system plays a central role in their pathogenesis and outcome. Our overriding philosophy is to address questions of human disease directly in humans.