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PGC Mindanao receives sub-grant funding from the Bill and Melinda Gates Foundation Through Public Health Alliance for Genomics Epidemiology (PHA4GE)

Bioinformatics training in PGC Mindanao

DAVAO CITY, PHILIPPINES – Philippine Genome Center (PGC) Mindanao was one of the awardees in 2022 of the sub-grant funding from the Bill and Melinda Gates Foundation through the Public Health Alliance for Genomic Epidemiology (PHA4GE). The grant enables PGC Mindanao to implement standardized bioinformatics practices, pipelines, and data structures in SARS-CoV-2. 

 “The 2021 call for sub-grants funds will go to support our aim to promote sustainable developments in bioinformatics in support of public health,” said Dr. Alan Christofels, Director of South African National Bioinformatics Institute.

Mr. Alan Christofels, Director of South African National Bioinformatics Institute, discussing PHA4GE objectives and different working groups during the PHA4GE awardees orientation held last 16 May 2022 via the Zoom platform.

The sub-grants from PHA4GE were awarded to support projects that aim for the development of an open and interoperable public health bioinformatics software, development and usage of standardized bioinformatics tools and infrastructure, implementation of standards developed by PHA4GE, maintenance of bioinformatic software or infrastructure, capacity development in bioinformatics, and other related activities to bioinformatics. 

“This grant will help strengthen our capabilities for bioinformatics research”, said former PGC Mindanao Director and now University of the Philippines (UP) Mindanao Chancellor, Dr. Lyre Anni E. Murao. “We build stronger research engagements, one step at a time.” 

Initially proposed by Dr. Murao, the project will now have its new principal investigator, Dr. Ritchie Mae T. Gamot, who is also a technical expert in the Bioinformatics Division of PGC Mindanao. She is joined by PGC Mindanao Bioinformatics Division Research Staff, Mr. Paul Lorenzo A. Gaite, MSc., and PGC Mindanao Administrative Support Staff, Ms. Marian S. Luayon. The entire project is expected to be completed within 5 months, from May to September 2022. 

Through the grant, PGC Mindanao will implement the project under Theme 2 (SARS-CoV-2 sequencing laboratories in low- to middle-income countries in Africa and Asia), with provisions for hiring technical experts and building computing infrastructures, such as structured LAN cabling for internet connectivity and additional storage and memory devices, to support bioinformatics analysis in the center. 

Partnership with BugSeq

To assist in the implementation of the PHA4GE project, PGC Mindanao has sought collaboration with BugSeq for the project data analysis and management of samples received from partner sub-national laboratories.

BugSeq is a fully-automated bioinformatics platform for microbiology laboratories (www.bugseq.com). It has several analysis tools that deliver data analytics and the expertise to convert sequencing data into actionable results. 

Meeting of PGC Mindanao Project Staff members, Dr RMT Gamot and Mr Paul Gaite, with BugSeq Co-founder and Chief Executive Officer, Dr. Sam Chorlton and BugSeq Co-founder Mr. Josh Chorlton (not pictured)

BugSeq will provide data analysis, including quality control, consensus sequence generation, variant calling and identification, and automated report generation for the project. It will also guide PGC Mindanao in the data submission to online sequence databases. Parallel to this, PGC Mindanao will conduct its own bioinformatics analysis on the same set of samples and compare it against BugSeq’s results to allow for consistency and verification. 

As part of the goals of PHA4GE to enable standard data collection, storage, sharing, and submission to databases, it has developed and provided a contextual data specification package (e.g. submission template and scripts). PGC Mindanao will primarily use this package to facilitate the upload of consensus sequences and corresponding contextual data to databases within the International Nucleotide Sequence Database Collaboration (INSDC). PGC Mindanao will also create documentation for the entire project, which will be published in Protocols.io.

With the collaboration with BugSeq and the sub-grant provided by the PHA4GE, the immense potential of research and development in the southern part of the country, in Mindanao, could be facilitated using an improved and developed bioinformatics infrastructure. Ritchie Mae T. Gamot and Paul Lorenzo Gaite

About the PHA4GE Sub-grant

PHA4GE is a global consortium founded on principles of fairness, openness, and transparency. In 2021, PHA4GE announced a call for sub-grants funded by the Bill and Melinda Gates Foundation, with the aim to promote sustainable development in bioinformatics in support of public health. Know more about PH4GE: https://pha4ge.org/

About the Bill and Melinda Gates Foundation

The Bill & Melinda Gates Foundation (BMGF) is an American private foundation founded by Bill Gates and Melinda French Gates in 2000. The primary goals of the foundation include enhancing healthcare, reducing extreme poverty across the world, and expanding educational opportunities and access to information technology. Since its establishment, the foundation has assisted and supported developments in the areas of social, health, and education. In 2020, it was reported to be the second largest charitable foundation in the world.

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