As I mentioned in my previous post, nanopore sequencing using the MinION instrument is one of the hottest new sequencing techniques currently available. It has several benefits over the current generation of short-read sequencing instruments, including measuring epigenetic DNA modifications and ultra-long reads, which allows for improved coverage of difficult-to-sequence regions.
It does have a few drawbacks however, including the fact that it has a fairly low output, which mostly relegates it to sequencing microbial genomes. However, a recent paper by Jain et al. from UCSC  used the minuscule MinION instrument to sequence the human genome and compare it to the current reference genome.
There were several items of note in this paper, not the least of which is that this is the most contiguous human genome to date, getting us closer and closer to a telomere-to-telomere sequence. Additionally, they were able to close 12 gaps, each of which was more than 50 kb in length, significantly improving completion of the genome.
Amazingly, since nanopore sequencing does not utilize PCR amplification, epigenetic modifications are maintained and are actually measurable by the MinION. The instrument is capable of detecting 5-methylcytosine modifications, and this data showed good concordance with whole genome bisulfite sequencing performed in the past.
Furthermore, they were able to map several of their ultra-long reads with telomeric repeats to specific chromosomal regions. They were then identify the start of the telomeric repeats and calculate the length of the repeat sequence. Overall, they found evidence for repeat regions that span 2 – 11 kb.
Long and ultra-long reads are absolutely critical when it comes to annotating these highly repetitive regions. There are other sequencers, including the PacBio SMRT Sequel sequencing system, that allows for very long reads compared to the Illumina instruments. But Jain et al. were able to obtain reads that were up to a staggering 882 kb in length.
Jain et al. were able to effectively show that the MinION system is capable of being used to sequence something as complex as a human genome. Interestingly, they theorized that the MinION system may have no intrinsic limit to read length–meaning that this protocol can be improved even further by finding methods of purifying high molecular weight DNA without fragmentation. Additionally, MinION reads are still considerably less accurate than Illumina sequencing, so this aspect could be improved as well. Nonetheless, this is a truly astonishing accomplishment that indicates what the future of DNA sequencing holds in store.
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