[HN Gopher] How to sequence your DNA for <$2k
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How to sequence your DNA for <$2k
Author : yichab0d
Score : 62 points
Date : 2025-10-18 19:58 UTC (3 hours ago)
(HTM) web link (maxlangenkamp.substack.com)
(TXT) w3m dump (maxlangenkamp.substack.com)
| pixelpoet wrote:
| > 'Sequencing by synthesis'. instead of chopping up and
| separating each base pair through a gel lattice, we [cuts off]
|
| k
|
| > 200 uL of blood (about 1/5 of a ml)
|
| "About"? Anyway, thanks for the clarification.
| NuclearPM wrote:
| Maybe the "about" was supposed to cover the 200 uL as well.
| 7e wrote:
| Just wait for the Nebula Black Friday sale.
| dunk010 wrote:
| 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.
| sbassi wrote:
| yes, the difference here is that the $1000 tag is "at-scale
| price". You reach that price point by running multiple
| sequencing with a set of reactive.
| zaptheimpaler wrote:
| I wanted to try this, but I looked into Nebula a bit more.
|
| Nebula is facing a class action for apparently disclosing
| detailed genomic data to Meta, Microsoft & Google. The
| subreddit is also full of reports of people who never received
| their results years after sending their kits back. There are
| also concerns about the quality of sequencing and false
| positives in all DTC genomics testing. Given what happened with
| 23andme as well and all of this stuff, I'm wary of sending my
| genetic data to any private company.
| Aurornis wrote:
| > There are also concerns about the quality of sequencing and
| false positives in all DTC genomics testing.
|
| Even when the raw results are accurate there is a cottage
| industry of consultants and snake-oil sellers pushing bad
| science based on genetic testing results.
|
| Outside of a few rare mutations, most people find their
| genetic testing results underwhelming or hard to interpret.
| Many of the SNPs come with mild correlations like "1.3X more
| likely to get this rare condition" which is extremely
| alarming to people who don't understand that 1.3 times a very
| small number is still a very small number.
|
| The worst are the consultants and websites that take your
| files and claim to interpret everything about your life or
| illness based on a couple SNPs. Usually it's the famous MTHFR
| variants, most of which have no actual impact on your life
| because they're so common. Yet there are numerous Facebook
| groups and subreddits telling you to spend $100 on some
| automated website or consultant who will tell you that your
| MTHFR and COMT SNPs explain everything about you and your
| ills, along with which supplements you need to take (through
| their personal branded supplement web shop or affiliate
| links, of course).
| phyzome wrote:
| Yeah, the only way I would ever do DNA sequencing is
| anonymously...
| mquander wrote:
| I was interested to read this because some time ago I had my
| genome sequenced by Nebula. If you look at the lawsuit you
| can see that what Nebula did was use off-the-shelf third-
| party analytics products on their website, including
| recording analytics pings when users buy a kit, and pings
| when users use the Nebula website to browse Nebula's high-
| level analysis of their traits (leaking that the user has
| those traits to the analytics provider.)
|
| This behavior represents a contemptible lack of respect for
| users' privacy, but it's important to distinguish it from
| Nebula selling access to users' genomes.
|
| https://www.classaction.org/media/portillov-nebula-
| genomics-...
| zaptheimpaler wrote:
| That's a good clarification. I read through some of that
| link, and it does look relatively benign - Meta & Google
| pixels might see when you buy a kit but nothing more, but
| on page 21 they directly leaked genetic information to
| Microsoft via their Clarity tracker.
|
| I don't have any evidence they're selling anything but that
| lawsuit shows pretty sloppy behaviour for a company that
| should be thinking very deeply about privacy.
| freehorse wrote:
| Yeah but then basically somebody else gets ownership of your
| genetic data and gets the right to do anything with it in the
| context of their "legitimate interests". Not to mention to
| probability of that company getting hacked or sold, as it has
| already happened with some.
| subroutine wrote:
| Does Nebula or Dante provide BAM or just VCF?
| conradev wrote:
| Dante includes a BAM
| Metacelsus wrote:
| Both do. I got mine through Dante, my wife through Nebula.
| coppa wrote:
| Speaking of which I would advise : Svante Paabo 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 Paleoanthropologie in college de France ( in french but
| probably translatable now with automatic features ?). This was an
| unexpected and wonderful path.
| jasongill wrote:
| 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
| jolmg wrote:
| Article was posted 2 days ago...
| greazy wrote:
| The article author probably bought the starter kit a while
| ago. It might explain why the pore count was low. It's a
| biological product so it degrades over time.
| numpad0 wrote:
| These are by no means a new product. I think the early
| prototypes for these possibly predate the microUSB plug.
|
| The brochures always showed it next to a completely non-
| sterile laptop, but it never made sense. It's fundamentally a
| bio lab equipment, just small. You probably should be wiping
| the package with disinfectant, use DNA-cides as needed, or
| follow whatever bioscience people consider the basic common
| sense hygiene standards.
| Aurornis wrote:
| 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?
| sbassi wrote:
| it depends of the sample. usually you have at least 1200, with
| a guaranteed of at least 800, so maybe he could ask for a
| refund.
| homeless_engi wrote:
| Hi, believe it or not, I have actually done what the authors
| were attempting. I used saliva rather than blood as a source of
| DNA and extracted it using a Qiagen kit.
|
| My Nanopore flow cell had nearly every pore working from the
| start. So I would say that is not normal. Maybe it was stored
| incorrectly.
| IceHegel wrote:
| 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.
| greazy wrote:
| I sequences my genome about 10 year's ago using illumina
| platform for ~1200AUD. We used a university sequencing
| facility. They were happy to extract and sequence the dna using
| a shotgun approach. Depth was 5x and I think we achieved about
| 90% coverage. It was just for fun.
|
| The issue with this approach is that you'll receive raw data
| that needs to be processed. Even after processing you'll need
| to do further analysis to answer your questions. After all
| this, I'd be suspicious of the results and seek a medical
| councellor to discuss and perform further tests.
|
| I'd advise on thinking what questions you want answered.
| 'Sequencing your genome' sounds amazing but imo you're better
| off with seeking accredited tests with acrionable results.
| greazy wrote:
| 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...
| optionalsquid wrote:
| 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
| greazy wrote:
| With the recent R10 flow cells the error rate has improved. The
| basecalling models have also been steadily improving and
| therefore reducing the error rate.
|
| For assembling a bacterial genome the consensus error rate is
| as low or in some cases better than Illumina.
|
| Nanopore platform has its usecases that Illumina falls short
| on.
|
| > 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
|
| Agreed, any at home sequencing should not be used to draw any
| conclusions.
| Ovah wrote:
| That's a prevalent misconception even in the scientific
| community. Sure, each read has 1% incorrect bases (0.01). But
| each segment of DNA is read many times over. More or less
| 0.01^(many times) [?] 0 incorrect bases.
| optionalsquid wrote:
| The author got less than 1x coverage for their efforts. To
| get the kind of coverage required for reliable base-calls,
| you need significantly higher coverage, and therefore a
| significantly higher spend
| bonsai_spool wrote:
| > That's a prevalent misconception even in the scientific
| community. Sure, each read has 1% incorrect bases (0.01). But
| each segment of DNA is read many times over. More or less
| 0.01^(many times) [?] 0 incorrect bases.
|
| That's true in targeted sequencing, but when you try to
| sequence a whole genome, this is unlikely.
| nashashmi wrote:
| If I have my genome dna data, where can I get it analyzed? For
| ancestry? For health info? Etc. of course With privacy!
| isbvhodnvemrwvn wrote:
| Forget any use for ancestry with privacy guarantees. All you'll
| get is magic "ethnicity" percentages, kind of astrology of
| genealogy. For it to be useful in genealogy context you need to
| rely on matching and analyzing common ancestors, this will
| inherently lead to your data being shared in one way or another
| and possibly your identity being revealed.
| teekert wrote:
| 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 1000EUR/$ with a
| reputable company. I've seen 180$, but not sure if I'd trust
| that.
| Metacelsus wrote:
| >you can compensate for the error rate by just sequence
| everything multiple times.
|
| Usually, but sometimes the errors are correlated.
|
| Overall I agree, short read sequencing is a lot more cost
| effective. Doing an Illumina whole genome sequence for cell
| line quality control (at my startup) costs $260 in total.
| bonsai_spool wrote:
| > 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).
|
| There is no reason for Nanopore to supplant sequencing-by-
| synthesis for short reads - that's largely solved and getting
| cheaper all the while.
|
| The future clinical utility will be in medium- and large-scale
| variation. We don't understand this in the clinical setting
| nearly as well as we understand SNPs. So Nanopore is being used
| in the research setting and to diagnose individuals with very
| rare genetic disorders.
| jaberjaber23 wrote:
| Nanopore's getting closer
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