"Most complete human genome assembly to date using single tech": Nature Biotech paper from consortium of nine centres use MinION to sequence human genome
Nature Biotechnology has today published a whole human genome assembly using the MinION nanopore DNA sequencer. The consortium of researchers, from nine different institutions, demonstrated the most complete human genome generated from a single sequencing technology to date.
As part of their assembly, the team were able to accurately estimate telomere lengths and resolve complex repeat regions. In particular, the study revealed new information about the major histocompatibility complex, which plays a crucial role in immunity. Ultra-long reads from nanopore technology allowed the entirety of this complex 4-Mb region to be phased and both alleles reconstructed.
Ultra-long reads were the critical step in obtaining this new level of completeness, and by generating 5x coverage of reads with an N50 > 100 kb and lengths reaching 882 kb, the consortium more than doubled their previous assembly contiguity to an NG50 of approximately 6.4 Mb.
The longest single read sequenced using nanopore technology is now in excess of 1.3Mb.
The authors note:
"[this] has resulted in the most complete human genome ever assembled with a single technology..."
“The increased single-molecule read length that we report here, obtained using a MinION nanopore sequencer, enabled us to analyse regions of the human genome that were previously intractable with state-of-the-art sequencing methods.”
Most notably, this milestone in human genomics reinforces the concept that although the human reference genome is thought to be complete, there are still gaps in the assembly that can only be bridged using ultra-long nanopore reads.
The breakthrough work of the consortium of researchers is being expanded by many in the field of human genomics. Other large-scale genome projects using Oxford Nanopore technology for de novo assembly are in progress, for example a 100-genome pilot project in Iceland and the imminent initiation of a Chinese human genome structural variation programme, which will start with 20 Chinese genomes and grow to ~1,000 samples in two years (NextOmics). Recent consensus accuracy results of 99.98% were shown on “de novo assembly of prokaryotic and large eukaryotic genomes with long nanopore reads” and on 8th February, Oxford Nanopore will provide a webcast update on its pathway to a sub-$1,000 nanopore genome.
Resources:
- Nature Biotech paper https://www.nature.com/articles/nbt.4060
- Press releases from the University of Nottingham, University of Birmingham.
- publications on human genetics/genomics using nanopore technology
- Consortium GitHub
- Nanopolish