The Technology Core is at the heart of the GCID, delivering the technical capabilities that will enable, empower and drive innovation for the cutting edge research areas in infectious disease and pathogenesis that are the focus of each of the component research projects. The Core will be established at the Broad Institute to provide three critical aspects of the overall GCID. First, it will provide the capabilities of a large-scale sequencing platform. In our state-of-the-art facility we will a) accept, QC, track and maintain a large library of samples, with currently over 950,000 samples in our collection;b) perform sample preparation and library construction for DNA sequencing of all production-scale samples required for this project;c) Carry out large scale DNA sequencing on our fleet of HiSeq machines. Total sequence data generation capacity is >50 Tb/month. Pacific Biosciences and Ion Torrent sequencing are also available. Second, it will provide analysis support via an expert team of bioinformatics analysts and computational scientists responsible for generating novel genome and transcriptome assemblies, high quality annotation, variant detection against existing references, expression profiling and sophisticated comparative analyses. These analyses will provide the basis for population and community-based investigations of virulence, transmission, and drug sensitivity of pathogens as well as their critical interactions with hosts and other microbes. Third, our deeply experienced technology development group will develop the new methodologies required to achieve the range of goals of the component research. These include innovative methods that extend current capabilities to more challenging samples, such as for preparing libraries from low quantity or low quality input RNA, from difficult sample types such as intracellular pathogens or from single or very small numbers of input cells. The Technology Core has an extensive record in delivering the power of genomics to infectious disease researchers, and is ideally prepared to apply both high-throughput and novel approaches to study the biology of microbial pathogens and their interactions with the hosts and vectors of disease.
The Technology Core provides laboratory and computational resources required for the GCID. Our state of the art large-scale sequencing platform carries out high throughput sample handling, library construction and DNA sequencing in a tightly managed manufacturing facility. A deeply experienced technology team is well suited to developing the required new methodologies. Finally, the expert computational team will perform assembly, annotation and analysis on the data delivered.
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| Sephton-Clark, Poppy C S; Muñoz, Jose F; Ballou, Elizabeth R et al. (2018) Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar. mSphere 3: |
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| Siddle, Katherine J; Eromon, Philomena; Barnes, Kayla G et al. (2018) Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018. N Engl J Med 379:1745-1753 |
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| Farrer, Rhys A; Ford, Christopher B; Rhodes, Johanna et al. (2018) Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways. mSphere 3: |
| Myhrvold, Cameron; Freije, Catherine A; Gootenberg, Jonathan S et al. (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444-448 |
| Cuomo, Christina A; Rhodes, Johanna; Desjardins, Christopher A (2018) Advances in Cryptococcus genomics: insights into the evolution of pathogenesis. Mem Inst Oswaldo Cruz 113:e170473 |
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