21 April 2020
The MRCG at LSHTM Genomics Core Facility has become the first and only service provider for the Oxford Nanopore Technology (ONT), GridION platform after attaining the standard requirements by ONT, following an intensive training of the Genomics team in 2019. The lab has recently demonstrated proficiency with the running of the GridION, a third-generation sequencing system, to support genetic and genomic research.
The ONT sequencing platform, MinION, a portable; and the GridION, a benchtop, low-cost device with real time analysis workflows make the technology attractive for in-field deployment, e.g. rapid screening, surveillance during outbreak of invasive viral and bacterial in remote regions of the developing countries. The Unit’s Genomics team employed the MinION platform for shotgun metagenomic sequencing and analysis of cultured isolates from 2 confirmed meningitis cases to be Streptococcus pneumoniae from a meningitis outbreak in Northern Nigeria.
The ONT sequencing devices can be used in field studies and outbreak situations, and supports long sequencing reads. This can support teams in diagnosis and monitoring. It can also help in preventing the sporadic outbreaks of some of the infectious diseases in Sub-Sahara Africa.
Dr Abdul Karim Sesay, Head of the Genomics Core Facility, commented “In 2014, I was able to formulate a metagenomics project at the Francis Crick Institute, Mill Hill Laboratory, London UK, and successfully bid and be included in the ONT MinION Access Program (MAP) in the early phase of the program. I am proud of my team at the MRCG at LSHTM which was established just over 2 years ago, to be the first lab to get a GriDION platform in Africa. The team led by Abdoulie Kanteh have demonstrated competence to successfully complete the qualification process to be the first and only ONT GRidION service provider in Africa.”
The Genomics core facility will offer the following areas of research:
• de novo Assembly – Combining Long- and Short-Read Sequencing
• Genome Re-Sequencing – SNV, INDELs, CNV and Structural Variation Analysis
• Transcriptome Analysis
• DNA Modifications
• Whole Genome Sequencing
• Amplicon sequencing
• Whole genome methylation sequencing
• cDNA sequencing
• Direct RNA sequencing