A new era of personalised medicine: or how I got myself sequenced for free
souradip.mookerj.ee
souradip.mookerj.ee
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 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!
"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.
https://bethematch.org/support-the-cause/donate-bone-marrow/...
> 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.
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.
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
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.)
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!
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.
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.
(To be clear here in europe medical records are held by healthcare services, but they are protected. They are not private property tho)
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.
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.
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.
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...
Ironically, this comes right after the line where his own website rendered the text between the asterisks as italic.
Not only that, but insurance will often cover services like GeneSight that do this specifically as a health service.
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.
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.
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's not exactly a message that will attract those interested more in helping people than free medical data about themselves.
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.
"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!
Because one can does not necessarily mean one should.
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 :)
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!"
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.)
* 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.
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.