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A new era of personalised medicine: or how I got myself sequenced for free (mookerj.ee)
90 points by souradip 35 days ago | hide | past | favorite | 72 comments

An importing distinction: The author did not get himself sequenced. He had genotyping.

Genotyping basically picks out a few specific data points. Sequencing reads an entire piece or entire genome completely.

From a health perspective, genotyping pulls data points that we already know can be markers for something significant. Sequencing gets a lot more data, and would sort of be "future proof" against the need to do further testing if new markers were identified you can just look at the data already gathered. Otherwise you'd need to get Genotyping done again.

This is very true, and genotyping just the HLA/KIR loci won't tell you much about all the other genes that are important for health. However, the HLA typing is at least a start (and a free byproduct of signing up to donate stem cells) to introduce you to the rabbit hole of personal genomics! :)

This is also slightly different to the (linkage-disequilibrium-based) SNP arraying done by other genotyping places, since the HLA locus is fairly widely researched in its associations with infection and (auto)immunity!

Oh absolutely... It's a lot more expensive for sequencing, so there's no reason not to take a cheap option that at least gets you checked against known issues.

"You may be aware of bone marrow, or stem cell transplants. These are life-saving for the people who need them, especially after a blood cancer. You can sign up for free at charities such as Anthony Nolan or DKMS in the UK."

"And it was a win-win scenario - they get to call upon me if someone needs my stem cells (a painless procedure that's no more complicated than donating blood)!"

Maybe I'm confused but this person doesn't seem to know what is involved with donating bone marrow. It is a serious surgical procedure done under anesthesia.


The there are two procedures, the stem cell procedure is acurately described according to the link you posted.

> How are bone marrow and peripheral blood stem cell (PBSC) donation different?

> Donating bone marrow is a surgical procedure done under general or regional anesthesia in a hospital. While a donor receives anesthesia, doctors use needles to withdraw liquid marrow from the back of the pelvic bone.

> PBSC donation is a non-surgical procedure done in an outpatient clinic. PBSC donors receive daily injections of a drug called filgrastim for five days, to increase the number of blood-forming cells in the bloodstream. Then, through a process called apheresis, a donor's blood is removed through a needle in one arm and passed through a machine that separates out the blood-forming cells. The remaining blood is returned to the donor through the other arm.

As someone who's donated via PBSC it's a whole lot more than a regular blood donation. Two batteries of tests, the drugs are no joke, and the donation session is more or less a whole day affair - or two days if you're unlucky and they don't harvest enough cells the first day (I was unlucky).

I don't have any regrets doing it - the impost on me was fairly trivial compared to the difference it can make for the recipient, but it's not a thing to be taken lightly.

Ahh that's what's going on, the first sentence conflates the two and the second sentence doesn't specify PBSC.

Easy mistake to make since the first part lists two different things. However, the listed orgs are both blood stem cell donation charities.

It's a minor surgery, and you can also donate without surgery via apheresis.

In the case of surgery you're put under and they dig around in your hip bones. You feel sore for a couple of days and then continue life as normal. It's safe aside from the normal risks that comes with any surgery. Source: I donated bone marrow

Not that serious

I'm all in favour of signing up as a marrow donor (I'm registered with DKNS myself) but burdening charities with administrative tasks to save yourself money feels a bit... cheap, and you get a lot more for paying for a full genome sequencing or even a 23andme report.

I should probably say that my primary reason for signing up to a stem cell donor registry is to actually be a donor! This data is generated as a byproduct of signing up and is also quite interesting on a personal level.

I was thinking that framing it in a way to also find out interesting things about yourself might be a good way to encourage people who might not have thought about it to sign up for the first time, and this would be far more cost-effective than a traditional in-person donor recruitment drive, but let me know what you think!

I don't know anything about those two charities. In the USA, 501c3's are in many cases just businesses. Meaning--they aren't sacred benevolent entities.

Waystar used to off a free look at a nonprofits 1040's. I believe their are other that offer a free look at this public information.

So many nonprofits are ridiculously overfunded. So many only pay a livable salary to the key founders, usually an husband and wife team.

One day, I want to put together a list of good nonprofits.

I once heard St. Jude Children's hospital has enough funding to last for 20 years, including costs of new technology; if donations were cut off today.

My point is be savvy with donations. There are very good charities out there.

(True story. National parks have one spot in the park available for first admendment speech. In Muir Woods National Monument it was a couple of parking spots. For years this guy used to hand out flyers to tourists who just got off buses.

He had some nonprofit that proposed to save Redwood trees. I looked up the nonprofit, and couldn't find it. Every night he would show up to the local watering hole with a 3" stack of money he woukd count out. I imagine he was making 2-3k a day. Why am I enclosing this? Because I'm tired of charities taking advantage of certain people.)

GiveWell and Charity Navigator are well-known and trusted organizations that provide this service.

https://www.givewell.org/ https://www.charitynavigator.org/

I personally feel that this embodies the hacker spirit perfectly. Has this service been intended to allow the donor access to his sequencing data? No. Can someone use the systems in place to get this info anyway? Yes, as it shows.

The other comments mind the burden to the charities. I personally cannot agree here. After all, this is the donors data. One might even think, that proactively sharing data could increase the number of donors.

Sure it does, in exactly the same way running crypto on Ci does too.

Much appreciated, I'm glad you agree! :)

I feel like GDPR-ing a bone marrow registry to obtain one's data is rude. I got my HLA data from the registry by asking politely.

GDPR SARs are just a standardized form for a data subject to have access to data on herself.

It is, in my opinion, far politer to use a form letter Subject Access Request that can be dealt with using a standard process rather than a custom interaction.

I see it as just picking things off a menu. Far less trouble than describing to your waitress that you’re looking for a ground beef patty, grilled with cheese, with onions, tomatoes, and lettuce added and placed between two buns.

Just say cheeseburger. You know cheeseburger. They know cheeseburger. Everyone is better off.

There's no reason why we don't have sequencing for everyone at this point. Just imagining the opportunities we are missing here because of a) the US inane insurance system and b) the irrational technophobia of EU. It's 2021 and we 're not allowed to use our SNPs to prevent illness

There's no reason why we don't have sequencing for everyone at this point.

There are at least two reasons: it's still expensive, and we still don't really know what to do with it.

The "$1000 genome" is a bit of a myth, or rather PR hype from Illumina. Sure, they proved it could be done if you juke the numbers the right way. But I believe a clinical-grade whole-genome sequence still costs several times that much (see https://bmchealthservres.biomedcentral.com/articles/10.1186/...). Even at $1000/genome, sequencing the entire US population would still be $330 billion, for unclear benefit.

I'd love to be corrected, but the science just isn't there to show us what to do with WGS data except in limited applications like cancer or "rare diseases". It's a bit of a chicken-and-egg problem in that sense, and it's being worked on. There are pharma companies and public consortia sequencing hundreds of thousands of genomes, and mining them alongside medical records and other phenotypic data. So the value may come eventually, but it will probably be less about preventing illness so much as curing disease in a much more targeted way. And even then, you won't need to have your whole genome sequenced just to know if you should take drug A or drug B -- a cheap targeted test will suffice.

Not quite, that paper is pretty misleading if you're using it as a rock solid rejection of the $1000 genome.

First, context: These are small scale clinical/experimental settings which clearly do not take advantage of economies of scale. Labor costs are thus greatly magnified. This effect is also obscured by their costing breakdown, which often does not separate reagent cost from labor.

Unless I'm misreading this, the pricing that they define often includes 2 sets of sequencing runs, one for the baseline and one for the tumor samples. That puts the existing price at about 4000 USD for 2 samples or a 2000 USD/sample cost.

The expansive definition of "sequencing cost" to envelope downstream analysis and storage here is also a mistake IMO. I would rather narrow down on specifically the cost to get the raw sequence data out, excluding clinical and bioinformatics analysis. This would include (reasonable) sample extraction, library preparation, and the actual sequencing process itself.

There are definitely significant cost barriers to sequencing, but we shouldn't discount savings that come with scale.

Of course, all this math goes out the window if we were to look at exome sequencing instead which while less complete, still gives a large amount of information at a fraction of the cost.

You make good points, but I think my overall point stands: Even a $1000 genome does not provide $1000 worth of value to a healthy individual today. So there is no point in trying to make WGS broadly available, nor is there any justification for insurance companies to cover it. It would be nothing more than a form of luxury "scientific entertainment" a la 23andMe.

Also, I would challenge your suggestion that "The expansive definition of 'sequencing cost' to envelope downstream analysis and storage here is also a mistake." I would argue that it's the opposite: delivering valid and useful sequencing results to a broad population would require even more resources directed toward analyzing the results and also interpreting them for the patients.

Is data privacy not a valid reason?

A lot of people would be willing for sequences to exist if they were treated like the medical records they are, and not as a startup's fungible data asset.

Are people's medical records private?


Then DNA can be private too

(To be clear here in europe medical records are held by healthcare services, but they are protected. They are not private property tho)

Once a genetic condition is found, your insurance company will exclude certain treatments or skyrocket your premiums.

In the US. Can't they legislate against that? Are we going to be stuck forever in the year 2000 because of such fears?

They can, but they won't. It's always about maximizing profit while reducing the costs. Everything they have can be used against you.

dont do this. you can sequence yourself from Dante labs (an italian company IIRC) which will give you all the data of 30x sequencing including the raw reads for like $200. The problem is -- i don't know what to do with the data as i havent had the time to do anything.

You can sequence yourself properly (and it's more information that way), but this way you can get called upon to donate if you're a match for someone somewhere in the world!

shouldn't you be able to match yourself (at least partially) by uploading your data somewhere?

Ideally, non profit organizations around tissue sourcing provide a mechanism to ingest raw genotyping data [1] from providers through an auth flow for those who have previously been sequenced or don’t want to burden the charity (if a donor can afford it) with the sequencing cost.

If one could “one click” share their genotyping from from a sequencing provider, I imagine you’d see an uptick in coverage for donor sourcing across the populace. The data is already out there.

[1] https://customercare.23andme.com/hc/en-us/articles/212196868...

> NB: Some journal websites find it difficult to display the asterisk and so they replace it with a w - so HLA-Cw04 and HLA-C*04 both mean the same thing.

Ironically, this comes right after the line where his own website rendered the text between the asterisks as italic.

Let me be blunt, costing charities time and money that they could use for their actual mission of helping people to find a life-saving match with a donor is a real shitty move. This is freeloading at its finest.

I wonder if charities couldn't offer it as an incentive to attract more potential donors? Agree to participate, and we'll give you your sequence upfront, no data-release-requests needed? Obviously some people are trying hard not to be sequenced for any reason (because of privacy concerns apparently) but plenty of other people are interested in heredity, or health implications.

I'm assuming the charities get a better rate, but typical home kits cost about $200... Not cheap to give out for free even if they get a 75% bulk discount. They're also not likely to get money from people like this who were deliberately working the system to avoid paying.

Not only that, but insurance will often cover services like GeneSight that do this specifically as a health service.

If you don’t ask them for the info, they still pay the same rate. You’re only asking them for data they already have on you. And you’re still on the donor list.

The difference between you and someone who doesn’t request is minuscule. An automated process sends someone a PDF. The world isn’t going to collapse under that weight.

Sure, though here in the US I would bet most insurers would require a physician to order the test for it to be covered? Which presumably would happen only if they thought it'd be useful for diagnosing something, rather than that you were curious (esp. if your curiosity was about your heritage and not something clearly medical).

Yep, a physician has to order the test, but considering they are extremely useful in preventative medicine most people I know that have had it done didn't have any issue getting a doctor to order one.

That's pretty harsh, and makes an ungrounded assumption that turns out to be not just uncharitable, but false.

The OP commented in a different thread around the same time as your rant:

> "I should probably say that my primary reason for signing up to a stem cell donor registry is to actually be a donor! This data is generated as a byproduct of signing up and is also quite interesting on a personal level.

I was thinking that framing it in a way to also find out interesting things about yourself might be a good way to encourage people who might not have thought about it to sign up for the first time, and this would be far more cost-effective than a traditional in-person donor recruitment drive, but let me know what you think!"

Yeah, kind of like "how I got my food for free" and the punchline is you went to a local food bank.

If you're really that interested it getting it done for the sake of curiosity the you can pay a variety of services about $200 for it.

Er, no. OP, in another thread:

"I should probably say that my primary reason for signing up to a stem cell donor registry is to actually be a donor! This data is generated as a byproduct of signing up and is also quite interesting on a personal level. I was thinking that framing it in a way to also find out interesting things about yourself might be a good way to encourage people who might not have thought about it to sign up for the first time, and this would be far more cost-effective than a traditional in-person donor recruitment drive, but let me know what you think!

Maybe he should have put that front & center in his blog post. Instead, the tone of most of it was "Hey I worked the system to get this cool free thing!"

I like to think that using this analogy, here you're going to the food bank and donating food (or your stem cells) while getting data on how many people liked it in return.

I've seen too many kids with blood cancer who couldn't get a match, so please do consider signing up to your local charity :)

That assumes this person is willing to donate-- from their statement on the organization I think they probably are, but the tone of the article beside their description of the organization seems to be "Yeah DKMS is good but look here's a cool loophole to get free stuff!".

That's not exactly a message that will attract those interested more in helping people than free medical data about themselves.

The person you're replying to is the author of the article

That does not change anything about my comment. As I said in it, it did seem they were probably willing to donate if called upon. The real problem is what I said about the overall tone in my comment above.

Heck, just look at the title of the post. It was not "Helping to Save Lives can Get You Free Genotyping!"

No, instead it was just about how he got free genotyping, which just reinforced my impression of where the tone of the post's real focus was-- the free data, not helping people.

I will fully give the author the benefit of the doubt that it was not their intention to set that tone. But that was nonetheless the tone I saw, and clearly others did as well.

Hiya, author here! I wrote the article to mostly encourage others to sign up to these charities to help accomplish their mission, the data generated as a by-product is just a cool side-effect!

It’d be fine if the charity made it an option to donate an additional amount if you wanted your sequence provided to you, to cover their cost to fulfill the request (negating the need to fulfill a GDPR request). Otherwise, it’s just poor form and not to be emulated.

Because one can does not necessarily mean one should.

I do, and I donate to these charities because it's a cause quite close to my heart.

At present it's clearly not scalable to be sending GDPR requests one person at a time. I think perhaps if this kind of incentive brings more people to sign up than traditional donor recruitment drives (which is often much more than handling a request for data!) then these charities will provide easier, more scalable ways to access this data :)

I wouldn’t get sequenced in America with the fascists so close to control.

I had my genome sequenced and it's uploaded to the web with my name attached. Can you articulate a specific concern?

That’s easy. A government decides to collude with healthcare-for-profit. So they allow any provider to demand your genetic sequence. As things are discovered, they price your healthcare accordingly, economically disadvantaging you based on your genes.

I actually regretted donating because of this very reason. If I’d thought about it I wouldn’t have. But the bethematch.org marketing material really tugged at the heartstrings. Never again, though.

Out of curiosity, why 'never again'?

If your concern is that your genetic information is no longer entirely private, wouldn't continuing to act as a donor cause no /further/ harm? (They aren't getting anything they don't already have I guess.)

Ah, for a couple of reasons:

* They need perfect information retention for refreshing to be useless. I don't think they have that.

* I didn't intend to refer only to them. Not going to donate ever again. That's just an information proliferation thing.

It's sort of like how I know that my SSN is out there because of Equifax, but I still don't post it on gas station bathrooms with other info.

Fun fact: getting a DNA sequencing is illegal in France and is punishable by a 3750€ fine. I find this frustrating that I can't legally access my own DNA.

You mean DTC DNA tests are illegal. DNA sequencing of humans is not. https://www.fiercebiotech.com/it/france-plans-745m-investmen... and I didn't have to look hard to find papers published by French authors in French journals that show they are sequencing humans in France.

You're right, that's what I meant. I didn't know the term "DTC" and should have explained the situation better.

Can the average person do it? Usually that is a sufficient bar for illegal in common parlance.

I don't see any reason why an individual couldn't purchase their own whole genome sequence in France if only DTC is illegal.

What does DTC mean in this context? I had assumed it meant "direct to consumer".

Why would they make that a law? Please say there are medical/research exemptions at least?

The ban is apparently to prevent access to paternity testing. Medical/scientific/judicial purposes are exempted.

afaik it was to prevent paternity tests

What???? Why would France not want paternity tests? Did they just watch 'Maury' to much and descide to nope out on this or something?

Because it, naively perhaps, seems to me like paternity test are a good thing on a societal level. Makes it easy to hold deadbeat fathers accountable. Proof of paternity can be used to for single mothers to demand child support. and in cases divorce due to infidelity can be prevent men from having to pay for other mens children.

I think it's a backwards logic of how paternity tests mean you "don't believe women" and thus are oppressing them. Completely ignoring the plight of men paying for children which aren't even their own.

It's hard for me to believe that there is still no way to get your genes sequenced anonymously. There has to be a big enough market for a startup to do so without storing and selling "anonymised" data, right? Is it really that expensive with modern tech to sequence a person's genes and compare against an existing database? I'd pay a good deal extra to 23&me if they'd be willing to take my sample without identifying information and return my results via an [throwaway] email address.

You can provide fake info to 23andme.

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