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NIH, Genomics England Launch Large-Scale Human Genome Sequencing Studies Using Nanopore Technology

NEW YORK – Oxford Nanopore Technologies said earlier this week that the US National Institutes of Health and Genomics England have each launched a new sequencing project that will look at thousands of human genomes using the firm's PromethIon 48 instrument.

The NIH's Intramural Center for Alzheimer's and Related Dementias, or CARD, will use nanopore sequencing to look at 4,000 genomes, from patients with Alzheimer's disease, frontotemporal dementia, Lewy body dementia, and healthy controls.

"CARD's requirements were for a system that enables researchers to scale up with large projects. We determined that Nanopore's is one technology that fits our current needs," CARD Director Andrew Singleton said in an email. The project, as planned, is projected to take two years and cost approximately $4 million, he added.

Genomics England will use nanopore sequencing to analyze "thousands" of tumor genomes in a project that will evaluate the technology's potential to provide insights to cancer diagnostics, according to Oxford Nanopore. The study will seek to detect large genetic rearrangements and epigenetic modifications in cancer genomes.

The projects will use the PromethIon 48, an instrument that now enables high coverage of a whole human genome in a single flow cell, according to the company.

In December, Oxford Nanopore reported that internal studies have generated 10 Tb of data from a single PromethIon 48 instrument run of six different PCR-amplified human DNA samples, with median output per flow cell of 208 Gb and maximum output of 242 Gb.

These will be among the largest human genome studies using nanopore sequencing and could be a step towards the technology's use in clinical applications. The firm is developing a so-called "Q" line of regulated products.

Founded last year as a collaboration between the National Institute for Neurological Disorders and Stroke and the National Institute on Aging, CARD is pursuing basic, translational, and clinical research and will have a dedicated laboratory on the NIH campus in early 2022. Conducting long-read sequencing to better understand the genetic architecture of Alzheimer's disease and other dementias is a key project for the center and it plans to create a public database. Adam Phillippy, head of the genome informatics section of the National Human Genome Research Institute, and Benedict Paten, of the University of California, Santa Cruz Genomics Institute, are also involved in the long-read sequencing project.

The new CARD sequencing project will perform whole-genome sequencing using one PromethIon flow cell per sample, aiming for between 30X and 40X coverage with an N50 of approximately 30 kb, according to Singleton.

Genomics England's project will build on a pipeline for analyzing whole human genomes using PromethIon that developed as part of the response to the COVID-19 pandemic, according to Oxford Nanopore. Genomics England did not respond to a request for additional comment before deadline.