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Playing a long game

Monday, August 5, 2019

Michael Eisenstein | Nature Methods | 30 July 2019

This past February, Adam Phillippy of the National Human Genome Research Institute showed the genomics community something it had never seen before: a complete human chromosome. It’s no secret that the human genome sequence published in 2000 was merely a fragmented rough draft, and nearly 20 years later, the genome remains incomplete. Phillippy, Karen Miga of the University of California at Santa Cruz (UCSC), and their colleagues in the international Telomere-to-Telomere Consortium (T2T) now aim to rectify that—and the gapless X chromosome presented at this year’s Advances in Genome Biology and Technology (AGBT) meeting is a critical first step. 

That work was also a high-profile demonstration of the capabilities offered by nanopore sequencing, which can generate vast sequence reads spanning hundreds of thousands of bases—long enough to allow scientists to forge through the dense forests of repetitive sequence elements that have historically confounded assembly and analysis. “We’ve collectively had an interest in developing long reads to push into these ‘dark regions’ of the genome,” says Miten Jain, a genomics researcher at UCSC and collaborator in the T2T effort who receives funding from Oxford Nanopore Technologies (ONT) through his group leader Mark Akeson.

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