Researchers have sequenced and assembled the full genome of a living organism using a genome sequencer that can fit in the palm of your hand.
The Nanopore device, dubbed MinION, was used to sequence the genome of the bacteria Escherichia Coli. Its success could lead to the ability to perform sequencing on more complex organisms, and eventually even humans, the Ontario Institute for Cancer Research reported.
"The amazing thing about this device is that it is many times smaller than a normal sequencer - you just attach it to a laptop using a USB cable," said Jared Simpson, Principal Investigator at the Ontario Institute for Cancer Research and a lead author on the study. "And while our work is a demonstration of the capabilities of the technology, the most significant advance is in the methods. We were able to mathematically model nanopore sequencing and develop ways to reconstruct complete genomes off this tiny sequencer."
Today's sequencing technology can either generate huge amounts of data or read long stretches of the genome, but this new device could potentially do both at the same time.
"Long reads are necessary to assemble the most repetitive parts of genomes but we need a lot of reads if we want to sequence human genomes. The small size of the MinION suggests there is room to scale up and sequence larger and more complex samples," Simpson said.
The new method could also improve the accuracy of the genome reads, creating a more accurate final sequence. The method is composed of three stage: overlaps between reads are detected and corrected through a multiple alignment process; the corrected reads are assembled using the Celera assembler; and finally the assembly is refined using a probabilistic model of the electric signals generated when DNA moves through the nanopores.
"This work has incredible potential," said Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research. "Scaled up, this technology could one day be used to sequence [tumor] genomes. The device's portable nature would allow for sequencing to become far more accessible, bringing the option of more personalized diagnosis and treatment to more patients."
The findings were published in a recent edition of the journal Nature Methods.
