Strategic collaboration between two organisations represents largest nanopore sequencing project to date, capitalising on recent developments bringing ultra-high yields with PromethION.
GrandOmics, a leading sequencing company in China, has announced a populational-scale project, dbSV100k, to understand the impact of structural variation on human disease. The project aims to sequence 20,000 human genomes in 2019, with a goal of 50,000 by the end of 2020 and total of 100,000 by the end of 2021. This uses high-throughput nanopore sequencing on the PromethION device and the project will explore viable opportunities for the development of clinical applications, with a view to ultimately providing clinical genetic diagnosis services in the future.
This research project aims to gain a complete understanding of genetic variations associated with human health and disease. Oxford Nanopore has entered into a Memorandum of Understanding with GrandOmics in support of their plan to build genome medicine services at an affordable price with high-quality that is accessible for anyone, anywhere.
The highest yields, with long reads
The performance of PromethION, the newest nanopore sequencing device, has now accelerated sufficiently to allow >7Tb on human samples using a complete set of 48 flow cells – the equivalent of 86Gb of real time sequencing data per hour, or ~1 human genome at 30X coverage.
PromethION, as with other nanopore sequencers, sequences the complete nucleic acid fragment and therefore provides very long reads – the current record is 2.3Mb in a single read and this represents the full fragment rather than multiple repeat passes of a smaller fragment. With real time data and modular flow cells, the performance of the technology has developed while flow cell costs have remained the same. Flow cells now deliver ultra-high yields, and the latest R10 nanopore has delivered Q50 (99.999% consensus accuracy) in a small genome in internal company experiments. R10 is now being trialled by GrandOmics.
GrandOmics: delivering high throughput nanopore genomics
To date, GrandOmics has sequenced more than a thousand human genome samples (G1k) and several hundreds of plants, animals, and microbial genomes using nanopore technology, servicing a network of over a thousand customers throughout the world. This has resulted in new discoveries in genome science and genomic medicine, in more than 50 publications for the last two years. This includes publications using nanopore technology, with more prospect papers in the near future.
This high-throughput infrastructure will be expanded to deliver dbSV-100K.
“GrandOmics’s mission is to provide innovative and precise genomics solutions for disease research and diagnosis. We have been running our PromethION devices to full capacity, and have developed our own bioinformatics pipelines to drive breakthrough projects to achieve new standards.” Said Mr. Depeng Wang, CEO of GrandOmics.
Dr. Gordon Sanghera, CEO of Oxford Nanopore said: “We are glad to form a strategic and ongoing collaboration with GrandOmics to support genomic medicine and personalized medicine for China. At Oxford Nanopore last week, the PromethION 48 has achieved 7.3Tb of data using a single set of 48 flow cells, and our development pathway offers higher future capacity. We are excited to see GrandOmics drive innovative solutions for offering accessible ‘de novo personal genomes’ to customers using high-throughput PromethION sequencing.”
“This is so far the largest high-throughput nanopore sequencing project in the world, and is the outcome of extensive effort between two parties in developing a strategic alliance for the last several months. This is achieved by a shared vision to create an opportunity to revolutionize genome medicine in the UK, China and the rest of the world.” Min S. Park, Director of GrandOmics Institute.
GrandOmics is a world-leading sequencing company in Beijing, China. It was one of the earliest to apply nanopore technology for commercial DNA sequencing in the world, and also the first in China and the second in the world to be certified to provide PromethION sequencing services using Nanopore technology.
GrandOmics provides comprehensive solutions for genome science and genomic medicine. The company aims to utilise advanced sequencing-based solutions for rare genetic diseases, complex diseases, microbial diseases, and cancer, by integrating nanopore long reads and optical mapping to detect and characterize complex mutations in clinical samples of patient genomes. GrandOmics has been establishing one of the world’s largest nanopore long-reads based structural variation databases (www.dbsv.com).
NextOmics, a subsidiary company of GrandOmics, has one of the most complete third-generation sequencing, optical and 3D mapping platforms. NextOmics delivers genome assemblies and analysis pipelines for animal, plant, microbial and human genomes, in research areas such as transcriptomics, metagenomics and epigenetics.