[HN Gopher] A new era of personalised medicine: or how I got mys...
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A new era of personalised medicine: or how I got myself sequenced
for free
Author : souradip
Score : 49 points
Date : 2021-05-13 20:26 UTC (2 hours ago)
(HTM) web link (souradip.mookerj.ee)
(TXT) w3m dump (souradip.mookerj.ee)
| kharak wrote:
| 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.
| ineedasername wrote:
| 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.
| souradip wrote:
| 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!
| Zababa wrote:
| Fun fact: getting a DNA sequencing is illegal in France and is
| punishable by a 3750EUR fine. I find this frustrating that I
| can't legally access my _own_ DNA.
| smegger001 wrote:
| Why would they make that a law? Please say there are
| medical/research exemptions at least?
| notahacker wrote:
| 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.
| hellbannedguy wrote:
| 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.)
| souradip wrote:
| 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!
| [deleted]
| cblconfederate wrote:
| 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.
| souradip wrote:
| 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!
| cblconfederate wrote:
| shouldn't you be able to match yourself (at least partially)
| by uploading your data somewhere?
| toomuchtodo wrote:
| Ideally, charities provide a mechanism to ingest genotyping
| data 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 my genotyping from 23andme
| (and any of their other customers could as well), I imagine
| you'd see an uptake in coverage of the populace. The data
| is already out there.
| redis_mlc wrote:
| > you can get called upon to donate
|
| Dude, calm down.
|
| Donating bone marrow is probably ok, but note that before
| donating a kidney, understand that can affect your health and
| life expectancy. That was not told to past donors, but it's a
| thing. (As you get older, your organ function decreases from
| 100% (or 200%) to less than 100%, so losing a kidney affects
| older people.
|
| In China, people in banned religions are "volunteered" for
| double-lung and heart transplants, so it also matters what
| country you're in. Their transplant science is based on 28
| year-olds, so if you're several years younger or older, you
| should be good unless you have a rare typing.
| _Microft wrote:
| 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.
| ineedasername wrote:
| 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.
| souradip wrote:
| 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
| :)
| souradip wrote:
| 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!
| toomuchtodo wrote:
| 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.
| souradip wrote:
| 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 :)
| [deleted]
| blacksmith_tb wrote:
| 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.
| ineedasername wrote:
| 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.
| blacksmith_tb wrote:
| 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).
| toomuchtodo wrote:
| While I'm unsure if insurance will cover sequencing of
| the general public, the medical portion is covered as an
| eligible FSA/HSA expense. We paid for our 23andme
| genotyping with an FSA card, and 23andme provides a
| letter and receipt from their website for reimbursement
| if necessary.
| amluto wrote:
| 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.
| renewiltord wrote:
| 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.
| iandanforth wrote:
| "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.
|
| https://bethematch.org/support-the-cause/donate-bone-marrow/...
| shkkmo wrote:
| 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.
| iandanforth wrote:
| Ahh that's what's going on, the first sentence conflates the
| two and the second sentence doesn't specify PBSC.
| [deleted]
| renewiltord wrote:
| Easy mistake to make since the first part lists two different
| things. However, the listed orgs are both blood stem cell
| donation charities.
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(page generated 2021-05-13 23:00 UTC)