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How to sequence your DNA for <$2k

157 points by yichab0d

by teekert

5 subcomments

We are not “in the nanopore era of sequencing”. We are (still) firmly in the sequencing by synthesis era.
Yes it requires chopping the genome opening small(er) pieces (than with Nanopore sequencing) and then reconstructing the genome based on a reference (and this has its issues). But Nanopore sequencing is still far from perfect due to its high error rate. Any clinical sequencing is still done using sequencing by synthesis (at which Illumina has gotten very good over the past decade).
Nanopore devices are truly cool, small and comparatively cheap though, and you can compensate for the error rate by just sequence everything multiple times. I’m not too familiar with the economics of this approach though.
With sbs technology you could probably sequence your whole genome 30 times (a normal “coverage”) for below 1000€/$ with a reputable company. I’ve seen 180$, but not sure if I’d trust that.

by Aurornis

6 subcomments

Interesting concept, but between the broken hardware and the way they gave up before getting anything useful this article was rather disappointing:
> Another problem was our flow cell was malfunctioning from the start — only 623 out of 2048 pores were working.
Is this normal for the machine? Is there a better write up somewhere where they didn’t give up immediately after one attempt?

by ml_basics

1 subcomments

The graph at the beginning showing the cost of sequencing over time falling faster than Moore's law stops in 2015. Would love to see how things have progressed since then. Casually googling i only saw plots up to 2021 but looks to me like progress is now slower than Moore's law since ~2015. Maybe things will change when Nanopore gets more reliable

by dunk010

6 subcomments

Nebula and Dante will do this for like $300, and you can get 30x coverage at every base or even 100x coverage if you pay a little more. The $1000 genome was here more than a decade ago.

by jasongill

1 subcomments

Unfortunately, the "MinION Starter Kit" for $1000 appears to no longer be available; the link in the article to the kit goes to a 404 page, and the cheapest MinION device with flow cells is now $4950 USD

by arjie

0 subcomment

I used Nebula (seems to be rebranded and more expensive now) for my wife and me, and for my parents and brother, and it was pretty straightforward. I paid for the 'lifetime' plan but they removed it before we did it for anyone else and it was pretty reasonable. I downloaded the FASTQ files and stuck it in an R2 bucket for myself. Nebula cost about $250 and there's a monthly $50 or something plan that's compulsory but you can cancel it right away.
If you're curious about my genome, here are my VCF files https://my.pgp-hms.org/profile/hu81A8CC
If you want to indulge your curiosity some more:
```
     $ rg "20189511" /Users/george/tmp/genome/nebula_roshan_NG1AW8W7PU.mm2.sortdup.bqsr.hc.vcf
     3499829:chr13 20189511 rs104894396 C T 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.00;DB;DP=25;ExcessHet=3.0103;FS=4.008;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.11;ReadPosRankSum=0.666;SOR=0.160 GT:AD:DP:GQ:PL 0/1:15,10:25:99:281,0,436
```
Put that into an LLM or look it up here https://www.snpedia.com/index.php/Rs104894396 to find out which pathogenic mutation I am heterozygous for.
In practice, when my wife and I did carrier screening we didn't do it with Nebula, but carrier screening also confirmed that we had GJB2-related hearing loss genes in common. The embryos of our prospective children were also sequenced so that we could have a child without the condition.
Anyway, if you'd like a test file of a real human to play with, there's mine (from Nebula) for you to take a look at. If you use an LLM you can have some fun looking at this stuff (you can see I'm a man because there are chrY variants in there).
I also used Dante because I wanted to compare the results of their sequencing and variant calling. Unfortunately, they have a different way to tie the sequence back to the user (you take the code they have and keep it safe, nebula has you put the stuff in a labeled container so it's already mapped by them) and I was in a hurry with other stuff. They never responded to me with any assistance on the subject - not even to refuse the request to get the code for that address - so I have no idea how they work.
The nanopore stuff is very cool, but I heard (on Twitter) there were quality control issues with the devices. I'd love to try it some time later just to line it up with my daughter's genome.

by greazy

0 subcomment

The thermocycler replacement using an electric kettle is hilarious. Thats how old school dna amplification would happen before the invention of thermocyclers.
OP you'd get better results of you centrifuge your blood, extract the white blood cells and sequence those instead of whole blood. Thats a bit tricky with a lance and a tiny device though...

by kyriakos

1 subcomments

What is the practical use of having your dna sequenced?

by optionalsquid

2 subcomments

It's cool that nanopore technologies are getting this affordable, but keep in mind that these technologies (to my knowledge) still have very high error rates compared older sequencing techniques. Both in terms of individual nucleotides (A, C, G, and Ts) being misread, but also in terms of stretches of nucleotides being mistakenly added to or removed from the resulting sequences (indels).
So, yes, you can sequence your genome relatively cheaply using these technologies at home, but you won't be able to draw any conclusions from the results

by FL33TW00D

0 subcomment

Dante and Nebula have a bad reputation. ySeq has an 8 month wait list. This guys Nanopore sequencer doesn’t work.
It is quite hard to get yourself sequenced in EU in 2025.

0 subcomment

by IceHegel

1 subcomments

Who can do this with good data controls? I don't want to have to dig through the fine print of some Terms of Service page to figure out if a sequencing company is going to save a copy of my genetic code for possible future use.

by coppa

0 subcomment

Speaking of which I would advise : Svante Pääbo Neanderthal Man: In Search of Lost Genomes then even better imho The Naked Neanderthal by Ludovic Slimak. After these books I spent many hours listening to the full courses of Jean-Jacques Hublin, chaire Paléoanthropologie in college de France ( in french but probably translatable now with automatic features ?). This was an unexpected and wonderful path.

by nashashmi

3 subcomments

If I have my genome dna data, where can I get it analyzed? For ancestry? For health info? Etc. of course With privacy!

by shevy-java

0 subcomment

Wasn't the cost a few years ago below 1000 already?

by jaberjaber23

0 subcomment

Nanopore’s getting closer

by 7e

0 subcomment

Just wait for the Nebula Black Friday sale.

by pixelpoet

1 subcomments

> ‘Sequencing by synthesis’. instead of chopping up and separating each base pair through a gel lattice, we [cuts off]
k
> 200 µL of blood (about ⅕ of a ml)
"About"? Anyway, thanks for the clarification.