Genomics and next generation sequencing

ESR’s expertise in next generation sequencing provides more detailed genomic data than ever before. Along with the growth in genomics is the growth of bioinformatics; the science of collecting and analysing this complex biological data. ESR has expertise in genomics and bioinformatics, particularly in the areas of microbiology, human forensic science and some human non-communicable diseases. ESR’s genomic science encompasses metagenomics, RNA, epigenetics, microbiomics and others.

ESR uses the latest technology to provide its next generation sequencing capacity. These technological platforms combine speed with the ability to sequence across a wide range of applications. ESR also has expertise in the use and application of portable DNA sequencing. This provides real-time data analysis of sequences where the raw materials are in remote locations or where response time is critical.

ESR has genomics and bioinformatics expertise and capability which is applied to a range of ESR science: 

• Forensic biology, including DNA and mRNA expertise
• Analysis and advice on the behaviour of pathogenic bacteria and virus in biowaste, soil and water
• Identification of virus and bacteria
• Water microbiology testing and research
• Faecal source tracking
• Drinking water investigations
• Recreational water investigations and human health impacts
• Food forensic investigations to identify source in foodborne disease
• Molecular typing of foodborne pathogens
• Testing for microbial contamination and viruses such as norovirus, adenovirus and rotavirus

For more information - Philip.Carter@esr.cri.nz

COVID-19

ESR uses the latest technology to provide its next generation sequencing capacity and performs the national sequencing for all COVID-19 positive samples. We use a combination of platforms to obtain the most reliable genome data, these technologies are supplied by Illumina and Oxford Nanopore. To find our more contact Dr Joep De Ligt. 

The sequencing technology we use in conjunction with the laboratory automation allows for very rapid turnaround time and a good scalability, during the first wave there was a week in which over 200 genomes were sequenced. We can perform up to 12 urgent viral genomes, which means data is available the same day, this has been needed in some cases.

Innovative and disruptive technology

ESR is also utilising the MinION(external link) and coupling this with cutting-edge, portable, and affordable computing. We are exploring the capability(external link) of this innovative and disruptive technology across clinical and environmental use cases. This sees a portable and affordable (~$1500) compute infrastructure (based on the NVIDIA Jetson series of portable GPU [Graphics processing unit]) and powered by battery and solar (see image). This means that the minION sequencer can be deployed in ‘remote’ situations such as the: riverside/seaside; hospital bedside; primary health clinic; farmers field; meatworks, food production facility or potentially a crime scene. Therefore, the range of potential end-users is massive, and purely limited by ones imagination.