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Bill and Melinda Gates Foundation: Metagenomic Next Generation Sequencing to Detect and Identify Pathogens

Deadline: December 5, 2018

In order to identify and treat existing and emergent infectious disease efficiently, clinicians and the global health community must have access to accurate and timely estimates of disease burden and distribution. Traditionally, summaries of these data have been manually reported by national health ministries from regional clinical data, aggregated from local health centers. Local institutions, however, face multiple challenges to accurately assess the emerging needs of their community with current toolsets. For example, most clinical tests are based on common or easily detectable pathogens previously identified, which can miss occult and/or emerging pathogens. In addition, curation of large-scale pathogen data across multiple locations/platforms is time consuming and expensive, preventing facile integration of individual patient-level diagnostic data into a larger pathogen landscape on the regional and national level.

Recent breakthroughs in pathogen sequencing technology – both at the hardware and software level – enable the combination of rapid deep sequencing of patient samples with subsequent sequence mapping to a custom, continuously updated reference database to provide near-real-time pathogen detection. Yet, these advancements alone have not been sufficient to provide metagenomic sequencing to patients in low- and middle-resource settings that could benefit the most, largely due to limitations in access or availability of the following essential components: a) expensive equipment/reagents, b) specialized biochemical training, c) accurate reference pathogen sequence databases, d) and advanced computational analytics.

Recognizing barriers for adoption of next-generation sequencing in global health, the Bill & Melinda Gates Foundation (BMGF) has partnered with the Chan Zuckerberg (CZ) Biohub and the CZ Initiative to enable patients in low- and middle-resource settings to benefit from cutting-edge pathogen detection and discovery. This partnership will provide highly specialized training in biosample preparation and sequencing to technical staff from awardee global health centers. Trainees will learn to use the open-source, open-access IDseq software developed by CZ-Biohub for the global health community to upload and analyze patient sequencing data. The BMGF-CZ-Biohub partnership will therefore aim to provide selected applicants the benefits of onsite next generation sequencing and rapid pathogen detection to better understand their local pathogen landscape. This initiative is specifically seeking projects that endeavor to build upon their initial locally-focused effort to contribute to future data-informed decision-making at the population level via data sharing and pathogen data comparison across sites.

Through this award, BMGF will support travel and accommodation of grantees for pilot analysis of samples from their home region during hands-on, intensive mentoring provided by the CZ-Biohub in San Francisco. This 2-week instructional period will include both biochemical sample preparation for sequencing and bioinformatic analysis using the IDseq software platform. Specifically, the hands-on training for bench scientists will include best practices and standards for sample processing, DNA & RNA extraction, library preparation, and data analysis on the Global IDseq software platform. Upon completion of training at CZ-Biohub, laboratory teams are expected to use the remaining GCE award primarily on the following items: 1) a sequencer suitable for the global health environment, 2) a dedicated sequencing technician, and 3) sequencing reagents for the duration of the award. The combination of intensive training with molecular, capital equipment, reagent, and personnel support is intended to maximize the potential for sustainable, prospective, onsite analysis of patient samples upon return to the home site. A list of compatible sequencers appropriate for global health use is listed here.

Amount: Phase I grants will be for $100,000 for a grant period of 18 months. Phase I projects that show promise will be eligible to apply for a follow-on grant of up to $1,000,000.

Eligibility: Anyone from any country and in any discipline, from student to tenured professor, and from any organization – colleges and universities, government laboratories, research institutions, nonprofit organizations, and for-profit companies can submit their ideas for the challenge.

Link: https://gcgh.grandchallenges.org/challenge/application-metagenomic-next-generation-sequencing-detect-and-identify-pathogens-round-22

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