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!
"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.
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
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.)
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.
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.
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!
> 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.
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!"
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!
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.
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.
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.
[+] [-] ineedasername|4 years ago|reply
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.
[+] [-] souradip|4 years ago|reply
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!
[+] [-] iandanforth|4 years ago|reply
"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/...
[+] [-] shkkmo|4 years ago|reply
> 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.
[+] [-] renewiltord|4 years ago|reply
[+] [-] shepherdjerred|4 years ago|reply
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
[+] [-] et2o|4 years ago|reply
[+] [-] notahacker|4 years ago|reply
[+] [-] souradip|4 years ago|reply
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!
[+] [-] hellbannedguy|4 years ago|reply
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.)
[+] [-] kharak|4 years ago|reply
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.
[+] [-] esyir|4 years ago|reply
[+] [-] souradip|4 years ago|reply
[+] [-] amluto|4 years ago|reply
[+] [-] renewiltord|4 years ago|reply
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.
[+] [-] cblconfederate|4 years ago|reply
[+] [-] throwaway197812|4 years ago|reply
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.
[+] [-] hentrep|4 years ago|reply
[+] [-] croes|4 years ago|reply
[+] [-] cblconfederate|4 years ago|reply
[+] [-] souradip|4 years ago|reply
[+] [-] danellis|4 years ago|reply
Ironically, this comes right after the line where his own website rendered the text between the asterisks as italic.
[+] [-] _Microft|4 years ago|reply
[+] [-] blacksmith_tb|4 years ago|reply
[+] [-] chrisweekly|4 years ago|reply
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!"
[+] [-] ineedasername|4 years ago|reply
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.
[+] [-] souradip|4 years ago|reply
[+] [-] aj7|4 years ago|reply
[+] [-] dekhn|4 years ago|reply
[+] [-] renewiltord|4 years ago|reply
[+] [-] Zababa|4 years ago|reply
[+] [-] dekhn|4 years ago|reply
[+] [-] smegger001|4 years ago|reply
[+] [-] unknown|4 years ago|reply
[deleted]
[+] [-] tryonenow|4 years ago|reply
[+] [-] ImPostingOnHN|4 years ago|reply