Live data from Hacker News

A new era of personalised medicine: or how I got myself sequenced for free

souradip.mookerj.ee

61–70 of 79 posts

Re: A new era of personalised medicine: or how I got myself sequenced for free

#61

"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…

Not that serious

Re: A new era of personalised medicine: or how I got myself sequenced for free

#62
> 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.

Re: A new era of personalised medicine: or how I got myself sequenced for free

#63

Earlier quoted context omitted.

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 t…

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!"

Re: A new era of personalised medicine: or how I got myself sequenced for free

#64

Earlier quoted context omitted.

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.

Re: A new era of personalised medicine: or how I got myself sequenced for free

#65
post #35

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

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.)

Re: A new era of personalised medicine: or how I got myself sequenced for free

#66

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.

Re: A new era of personalised medicine: or how I got myself sequenced for free

#67

Earlier quoted context omitted.

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.

Re: A new era of personalised medicine: or how I got myself sequenced for free

#68
post #9

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 t…

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

Re: A new era of personalised medicine: or how I got myself sequenced for free

#69

"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…

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

Re: A new era of personalised medicine: or how I got myself sequenced for free

#70

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…

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.

Post reply on HN