The Human Genome Project took 13 years to complete at a cost of hundreds of millions of dollars. The device described below is available now, costs US$1,000.00 and can sequence an individual’s genome in roughly 3 days. Technological progress is so cool! What a time to be alive!

https://nanoporetech.com/products/minion

MinION is the only portable real-time device for DNA and RNA sequencing.

Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. The MinION streams data in real time so that analysis can be performed during the experiment and workflows are fully versatile.

The MinION weighs under 100 g and plugs into a PC or laptop using a high-speed USB 3.0 cable. No additional computing infrastructure is required. Not constrained to a laboratory environment, it has been used up a mountain, in a jungle, in the arctic and on the International Space Station.

The MinION is commercially available, simply by paying a starter-pack fee of $1,000. The MinION starter pack includes materials you need to run initial sequencing experiments, including a MinION device, flow cells and kits, as well as membership of the Nanopore Community.

https://www.nature.com/articles/nbt.4060

Discussion

We report sequencing and assembly of a human genome with 99.88% accuracy and an NG50 of 6.4 Mb using unamplified DNA and nanopore reads followed by short-read consensus improvement. At 30× coverage we have produced the most contiguous assembly of a human genome to date, using only a single sequencing technology and the Canu assembler23. Consistent with the view that the underlying ionic raw current contains additional information, signal-based polishing14 improved the assembly accuracy to 99.44%. Finally, we report that combining signal-based polishing and short-read (Illumina) correction26 gave an assembly accuracy of 99.96%, which is similar to metrics for other mammalian genomes9.

Wow. Looks too good to be true. Is it?

It’d have to beat liquid chromatography…

From link. Promises $2 per DNA barcode. Wow! High error rate (30 times overlap still gives a 0.2% error rate per base, which is large when you multiply it by 3 billion) but I can live with that.

“A MinION-based pipeline for fast and cost-effective DNA barcoding
25th January 2018

“DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory, is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION and demonstrate that one flowcell can generate barcodes for ~500 specimens despite high base-call error rates of MinION. The pipeline overcomes the errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. These barcodes are overall mismatch-free but retain indel errors that are concentrated in homopolymeric regions. We thus complement the barcode caller with an optional error correction pipeline that uses conserved amino-acid motifs from publicly available barcodes to correct the indel errors. The effectiveness of this pipeline is documented by analysing reads from three MinION runs that represent three different stages of MinION development. They generated data for (1) 511 specimens of a mixed Diptera sample, (2) 575 specimens of ants, and (3) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION barcodes for 490 specimens which were assessed against reference Sanger barcodes (N=471). Overall, the MinION barcodes have an accuracy of 99.3%-100% and the number of ambiguities ranges from <0.01-1.5% depending on which correction pipeline is used. We demonstrate that it requires only 2 hours of sequencing to gather all information that is needed for obtaining reliable barcodes for most specimens (>90%). We estimate that up to 1000 barcodes can be generated in one flowcell and that the cost of a MinION barcode can be <USD 2.<="" p="">

I suppose you can compare it to information storage we can fit a significant percentage of human knowledge on something the size of small fingernail today, it’s progression has been quite fast. I imagine in a decades time you could possibly do it almost instantly

More from conclusions of paper. By the way, I hadn’t realised that there is a biological sciences preprint server “ “ that is the eqivalent of the physics one at arXiv .

“Overall, we would argue that MinIONTM is already suitable for projects of small- to moderate scale (<1000 barcodes). For these, the method is attractive because it allows for the rapid turnaround of time-sensitive samples for which the barcode-to-sample association has to be maintained. This association is important for food authentication (Shokralla et al., 2015a), but similarly desirable for bioassessment and the identification of invasive species. For these purposes, it is important that a pipeline allows for the identification of unexpected pests and invasives for which the publically accessible barcode databases lack reference sequences”

This one. Worth a browse.

https://www.biorxiv.org

Cymek said:

I suppose you can compare it to information storage we can fit a significant percentage of human knowledge on something the size of small fingernail today, it’s progression has been quite fast. I imagine in a decades time you could possibly do it almost instantly

Gattaca.

mollwollfumble said:

This one. Worth a browse.

https://www.biorxiv.org

Thanks.

:)

mollwollfumble said:

More from conclusions of paper. By the way, I hadn’t realised that there is a biological sciences preprint server “ “ that is the eqivalent of the physics one at arXiv .

“Overall, we would argue that MinIONTM is already suitable for projects of small- to moderate scale (<1000 barcodes). For these, the method is attractive because it allows for the rapid turnaround of time-sensitive samples for which the barcode-to-sample association has to be maintained. This association is important for food authentication (Shokralla et al., 2015a), but similarly desirable for bioassessment and the identification of invasive species. For these purposes, it is important that a pipeline allows for the identification of unexpected pests and invasives for which the publically accessible barcode databases lack reference sequences”

Was wondering about the difference between “barcode”, DNA chip, and genome sequencing.

A “DNA chip” is used to identify common errors in genes, that’s the technology used by for example Ancestry in sequencing people’s DNA for under $100 plus postage.

A “barcode” is a short genetic marker, such as “The most commonly used barcode region for animals and protists is a segment of approximately 600 base pairs of the mitochondrial gene cytochrome oxidase I (COX1)”. How good is that at distinguishing between closely-related species?

There’s a world of difference between sequencing 600 base pairs and sequencing 3,000,000,000 base pairs for whole of genome sequencing. Yet this little device is claiming to be able to do both.

mollwollfumble said:

A “barcode” is a short genetic marker, such as “The most commonly used barcode region for animals and protists is a segment of approximately 600 base pairs of the mitochondrial gene cytochrome oxidase I (COX1)”. How good is that at distinguishing between closely-related species?

There’s a world of difference between sequencing 600 base pairs and sequencing 3,000,000,000 base pairs for whole of genome sequencing. Yet this little device is claiming to be able to do both.

The MinION seems to exist on an intermediate scale. With sample preparation using the $1700 “PCR Barcoding Kit 96” it is possible to sequence the barcodes of up to 96 different organisms in a single run, (for comparison, the kit for a single organism barcode is $300). The standard DNA length range ranges from 5,000 to 200,000 base pairs. 96 organisms at 600 base pairs each will easily fit in 200,000 base pairs.

To determine a complete human genome with 30 times coverage would require about 450,000 individual runs. Unless I misunderstand. There is one Nanopore device that will do 144,000 runs at once.

There is a portable sequencing device even smaller than MinION, still in the development stage, called SmidgION. It works with an iPhone as follows.

And the end game?

The “how it works” page.

This is brilliant, about ten years ago I heard a rumour that such a way of reading DNA was theoretically possible, but had far too high an error rate to be practical in the short term. I hadn’t heard a whisper about this since. But “Nanopore” has now got it working brilliantly.

https://nanoporetech.com/how-it-works

“DNA sequencing. A strand of DNA is passed through a nanopore. The current is changed as the bases G, A, T and C pass through the pore in different combinations.”

The nanopore

The sequencing. As each base passes through the nanopore it distorts the nanopore’s shape and this shape change is read out as a change in current. All this is thousands of times easier than, say shotgun methods or Sanger sequencing. It’s the exact same method as reading the magnetic signal on a cassette tape, but shrunk down in size a factor of nearly a billion..

How the DNA is read.

Peak Warming Man said:

And the end game?

In the short term. the end game is food purity, rapid blood tests for invading bacteria and viruses, identification of invasive species in the environment.

In the longer term, a hundred million new species, identification of biodiversity in soils and in the oceans, and better teaching of biology and biodiversity to high school students.

Absolutely win-win.

mollwollfumble said:

The “how it works” page.

This is brilliant, about ten years ago I heard a rumour that such a way of reading DNA was theoretically possible, but had far too high an error rate to be practical in the short term. I hadn’t heard a whisper about this since. But “Nanopore” has now got it working brilliantly.

https://nanoporetech.com/how-it-works

“DNA sequencing. A strand of DNA is passed through a nanopore. The current is changed as the bases G, A, T and C pass through the pore in different combinations.”

The nanopore

The sequencing. As each base passes through the nanopore it distorts the nanopore’s shape and this shape change is read out as a change in current. All this is thousands of times easier than, say shotgun methods or Sanger sequencing. It’s the exact same method as reading the magnetic signal on a cassette tape, but shrunk down in size a factor of nearly a billion..

How the DNA is read.

How interesting. Well done to the developers!

Michael V said:

mollwollfumble said:

The “how it works” page.

This is brilliant, about ten years ago I heard a rumour that such a way of reading DNA was theoretically possible, but had far too high an error rate to be practical in the short term. I hadn’t heard a whisper about this since. But “Nanopore” has now got it working brilliantly.

https://nanoporetech.com/how-it-works

“DNA sequencing. A strand of DNA is passed through a nanopore. The current is changed as the bases G, A, T and C pass through the pore in different combinations.”

The nanopore

The sequencing. As each base passes through the nanopore it distorts the nanopore’s shape and this shape change is read out as a change in current. All this is thousands of times easier than, say shotgun methods or Sanger sequencing. It’s the exact same method as reading the magnetic signal on a cassette tape, but shrunk down in size a factor of nearly a billion..

How the DNA is read.

How interesting. Well done to the developers!

Absolutely.

mollwollfumble said:

Peak Warming Man said:

And the end game?

In the short term. the end game is food purity, rapid blood tests for invading bacteria and viruses, identification of invasive species in the environment.

In the longer term, a hundred million new species, identification of biodiversity in soils and in the oceans, and better teaching of biology and biodiversity to high school students.

Absolutely win-win.

Great summary.

Another chip for the Star Trek body scanner.

Analysis tools for smartphones that can read that device would be cool.

Maybe even AI devices that can look for specific things that are known.

Can they use it as a security device?

I’d like to have one.

>>>Analysis tools for smartphones that can read that device would be cool.

Looks like they doing that already.

Tau.Neutrino said:

Another chip for the Star Trek body scanner.

Analysis tools for smartphones that can read that device would be cool.

Maybe even AI devices that can look for specific things that are known.

Can they use it as a security device?

I’d like to have one.

Ditto.

As a Star Trek body scanner, it even has a chance of working with alien genomes that don’t use DNA.