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How to sequence your own DNA at home

bradleywoolf.com

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Re: How to sequence your own DNA at home

#131

Post by doctorpangloss »

vintermann wrote: post #96
jefftk wrote: post #93

Earlier quoted context omitted.

I know you put an asterisk, but to make it clear: these locations are very far from random. They're the most informative positions, which is why we check them.

Well, they're what 23andMe thinks are most informative, for the things they think their customers care about. Or thought; for compatibility reasons they can't change their SNP panels very often or too much. And the interesting positions are still reasonably randomly distributed by nature :)

well SNPs aren't useful for drug development, commercialization, medicine, etc. you want whole genome or whole exome sequencing for stuff that is future-looking. they use a process for the present day (quickly becoming the past) of okayish drugs instead of sequencing for a future of cures.

Re: How to sequence your own DNA at home

#132

Post by munib_ca »

bmwoolf wrote: post #55
munib_ca wrote: post #17

> This is intended to be read by AI- please just copy and paste the URL of this and have ChatGPT walk you through it. If you have AR glasses, even better, since the AI can walk you through the whole protocol. What kind of magic is going on here, am I missing something?

Hi, author here- I intended it to be hands-free so you can upload to ChatGPT/Claude and talk to it. I found it easier to follow the protocol each time by talking to AI rather than having to read from the computer every time I had to check something, reducing context-switching You can still read it, though it is pretty dense

If you wanna take it a step further you can just embed a chat/llm icon at the start of your article, give it a header like "summarize this article using:", that leads to this query:

> https://chatgpt.com/?q=summarize%20this%20article%20for%20me...

You make one for claude, perplexity etc.

The AR angle tho, still lost on me, maybe i'm missing something...

Re: How to sequence your own DNA at home

#133

Post by mhb »

__MatrixMan__ wrote: post #20

I've bee thinking about starting a company where I fish roots out of your sewer and identify the plant (by sequence if necessary) that you have to kill so your sewer doesn't collapse as soon as it otherwise would. $100 to stave off that $10000 sewer replacement for a few years would be worth it to a lot of people

I don't really understand this. How much better are things for killing a specific plant than whatever you would use to kill a superset of the plants that might be there? Or treating with a few different plant species killers. And wouldn't those options cost less than the cost of this service?

Re: How to sequence your own DNA at home

#134

Post by NoSalt »

mrzippipo wrote: post #113
NoSalt wrote: post #112

I want to sequence, but I absolutely do not want any company or government or church to have access to my data. When the author says: > "I have a VCF, I can run it through tools like VEP, ClinVar, gnomAD, PharmGKB (highly recommend), Gene Inspector, or Claude" I am assuming my data is now within the hands of some of the very entities I do not want to have access to my data ... true?

Untrue in the cases of VEP, ClinVar, gnomAD. These are either offline, open-source tools or databases. You can download or query these and no one would be the wiser. Claude on the other hand - yeah you are giving your data away. But that step really isn't necessary. By running a standard pipeline you could get a VCF (File containing the Variants in your genome) and each variant would be annotated. You can check all t…

Very cool ... thank you!

Re: How to sequence your own DNA at home

#135

Post by Self-Perfection »

neoden wrote: post #94
stymaar wrote: post #62

Earlier quoted context omitted.

> But I do want to sequence it using a third-party Don't forget to change your DNA when the third party's database will eventually leak. (see the 21andMe's data leak: https://en.wikipedia.org/wiki/23andMe_data_leak )

what is the attack vector btw?

That gives some probabilistic info to scraper. Like person might have genes that are: - susceptible to drugs abuse - or game addiction Bam - you get target ads

- Indicate that any common substance is especially dangerous/harmful for him (think of allergies). So attacker might plan assassination or severe inconvenience by exposure to the substance and then claim he did not know

Re: How to sequence your own DNA at home

#136

Post by vintermann »

bonsai_spool wrote: post #130
vintermann wrote: post #96

Earlier quoted context omitted.

Well, they're what 23andMe thinks are most informative, for the things they think their customers care about. Or thought; for compatibility reasons they can't change their SNP panels very often or too much. And the interesting positions are still reasonably randomly distributed by nature :)

I don't do SNP design but I don't think 23andMe made their own chips at first (if they have ever). SNPs are chosen based on being informative for population discrimination, with traits being overlaid afterwards

I could be wrong, but I do believe they get to choose. What I do know is that none of the big testing companies test exactly the same SNPs, there is some overlap but every test is different. They also change their SNP sets from time to time, 23andMe has changed at least 5 times, and interestingly, their current test isn't the biggest (it tests fewer SNPs than some of their earlier ones).

Re: How to sequence your own DNA at home

#137

Post by BiraIgnacio »

jdmoreira wrote: post #57

I don't want to sequence at home. But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend? Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.

GeneDx _might_ do it https://www.genedx.com/

Re: How to sequence your own DNA at home

#138

Post by _zoltan_ »

cydodon wrote: post #127
balfirevic wrote: post #126

Earlier quoted context omitted.

> But be warned, it takes a long time What's a "long time"? A month, a year, 10 years? > They're not the cheapest option Whats "not the cheapest"? 100 EUR, 1000 EUR, 10000 EUR, more?

From their website yseq.net: - Whole genome sequencing ultra plus (150 Gbases raw data) is €699,- incl. shipping for the sampling kit - "The turnaround time is approx. 5-7 months at the moment."

700 EUR doesn't seem like expensive for what it is.

Re: How to sequence your own DNA at home

#139

Post by saxonww »

Noaidi wrote: post #118
saxonww wrote: post #111

Earlier quoted context omitted.

Finding yourself in a genetically-determined out group, and being treated differently / discriminated against because of it.

Honestly, you don't need someone's genetics for this to happen. They will find out more about you by scraping your socials and spending habits and driving habits. I think this whole fear is over blown anyway. I am in a genetic out group (schizoaffective disorder and yes my risk is genetic) and the benefits of getting my genetics run twice out weighed any risk that might have befallen me.

It's overblown _right now_ because this information is not broadly available. The fear is that pervasive access to this data would lead to e.g. you or your partner not getting insurance to pay for anything fertility-related, or you not getting hired for a job you want despite being otherwise qualified, or even that is less inclined to take you seriously because their perception of what schizoaffective means makes them think your perception of reality can't be trusted.

Of course if you just go tell everyone you are or are at high risk of being schizoaffective, you've done it to yourself. Not having a bad outcome yet doesn't mean that a bad outcome is not now more likely.

Re: How to sequence your own DNA at home

#140

Post by super256 »

jdmoreira wrote: post #57

I don't want to sequence at home. But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend? Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.

I used myheritage and simply exported all my data and then requested an account closure and data deletion.

The main factor for using myheritage was that they have this cheap 30€ offering at the moment.

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