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Sequencing your DNA with a USB dongle and open source code

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Re: Sequencing your DNA with a USB dongle and open source code

#61
post #59
post #45

Earlier quoted context omitted.

it's unlikely we would ever be able to achieve this. Even simulating a single cell at high resolution is a serious challenge.

You seriously underestimate the continuous growth of computer power. And quantum computers after, which are perfect for simulating chemical reactions. What was unthinkable 50 years ago, playing chess better than a human, it's now trivial for a $100 device. And it's not necessarily required that to simulate the growth of a human you'll need to simulate the entirety of chemical reactions in all 50 trillion cells and al…

It's possible I underestimate, but I have worked in all the relevant fields of simulation, ~20 years of running various simulations on large HPC, built the largest instance of folding@home using idle cycles inside google data centers, published papers simulating proteins, developed infrastructure to process the voluminous data, etc, etc. Quantum computing remains fantasy (in terms of being useful for science).

It's unlikely even if we improved computing hardware many orders of magnitude beyond all reasonable predictions, that the calculations would be able to simulate all the necessary details; most of our simulations now are based on many approximations due to hardware limitations.

As to the question of "what level of fidelity is required to turn a FASTQ of somebody's genome into an accurate model of the resulting human, with some sort of realistic environment also provided", that's so far beyond what is even remotely comprehensible it's not worth speculating about in terms of science fact; it's just fiction.

Re: Sequencing your DNA with a USB dongle and open source code

#62
post #36

Earlier quoted context omitted.

Imagine insurers refusing to give you a service due to your predisposition to certain diseases...

Protection from this comes from laws that ban DNA-based policies, not by being secretive about sequencing. If it is allowed, insurers will have no need to obtain DNA sequences in devious ways, they will just ask and refuse cover or charge more when clients refuse to get sampled.

Sure, but being secretive about your DNA seems like the prudent course of action until those laws are in place

Re: Sequencing your DNA with a USB dongle and open source code

#63
post #46

Folks are free to analyze my genome, https://my.pgp-hms.org/profile/hu80855C Last time it was analyzed the conclusion was that there was nothing actionable.

Have you ever encountered any insurance implications from it? eg: questioned whether you have ever had a genomic test etc. and had to answer yes and then them wanting to see results?

I guess in your case where nothing actionable is found it's benign. It will be the cases where there are risk factors for late onset things - cancer, diabetes, heart disease etc. where it would get sticky.

Re: Sequencing your DNA with a USB dongle and open source code

#64
post #53
post #36

Earlier quoted context omitted.

Imagine insurers refusing to give you a service due to your predisposition to certain diseases...

It's amazing how many problems you avoid by having public health system.

You resolve part of them, but immediately generate others. Hybrid systems are the way to go.

In Spain, for example, we have a private system but it is extremely inefficient in some areas (and very good in others). Of course, you can have private insurance, but you still have to pay your social security. Curiously, the only ones who can decide which system they want are the public servants...

Re: Sequencing your DNA with a USB dongle and open source code

#65
post #62

Earlier quoted context omitted.

Protection from this comes from laws that ban DNA-based policies, not by being secretive about sequencing. If it is allowed, insurers will have no need to obtain DNA sequences in devious ways, they will just ask and refuse cover or charge more when clients refuse to get sampled.

Sure, but being secretive about your DNA seems like the prudent course of action until those laws are in place

“Passed in 2008, a federal law called the Genetic Information Nondiscrimination Act (GINA) made it illegal for health insurance providers in the United States to use genetic information in decisions about a person's health insurance eligibility or coverage.”

Also prevents employment discrimination based on genetics.

https://www.genome.gov/about-genomics/policy-issues/Genetic-...

(disclosure: have had my DNA sequenced by multiple organizations, and it's publicly available)

Re: Sequencing your DNA with a USB dongle and open source code

#67
post #63
post #46

Folks are free to analyze my genome, https://my.pgp-hms.org/profile/hu80855C Last time it was analyzed the conclusion was that there was nothing actionable.

Have you ever encountered any insurance implications from it? eg: questioned whether you have ever had a genomic test etc. and had to answer yes and then them wanting to see results? I guess in your case where nothing actionable is found it's benign. It will be the cases where there are risk factors for late onset things - cancer, diabetes, heart disease etc. where it would get sticky.

No, my health insurance company doesn't care about my whole genome data. Health Insurance companies are already quite skilled at (and profitable due to) their ability to model life expectancy and health issues without genomic data, and they are legally prohibited from using this data, in my country anyway. Life insurance is different (they are allowed to incorporate much more information) but I've never been asked for anything like that.

As for the case where nothing actionable is found- it's not benign. It's absence of information, not information of absence.

Re: Sequencing your DNA with a USB dongle and open source code

#68
post #48
post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

Note that you are literally shedding identifiable DNA from your body at all times and a truly motivated adversary would have no problem obtaining enough sample material to do high quality sequencing.

In the near future (or arguably now depending on your purpose) you don't even need that. Assuming enough of your relative's sequences are available, the probability of you having certain genes/mutations can be narrowed down so much that having your individual genome doesn't add much.

Re: Sequencing your DNA with a USB dongle and open source code

#69

Earlier quoted context omitted.

Your DNA is almost exactly the same as other people's, just a unique mix. Not sure what you are concerned about. What would you expect a bad actor to do with your DNA sequences? I'm genuinely curious.

Your DNA is almost exactly the same as other people's, just a unique mix. Music is exactly the same notes, just a unique mix. So why is Sony upset that I want to stream their entire library? But jokes aside... A few decades ago I fought the military on collecting my DNA. I stalled them long enough to get my honorable discharge and avoid that all together. It's funny you ask because the commander asked the same thing…

From a more paranoid perspective:

I'm curious about the possible abuse scenarios given the ubiquitous use of PCR-testing for nearly two years, now.

If I'm informed correctly for a viable sample for NGS you need like 2mL saliva (which sounds little but it really takes some time: >1 min) not those trace amounts which gets usually collected by the swabs?

Re: Sequencing your DNA with a USB dongle and open source code

#70
post #48

Earlier quoted context omitted.

Note that you are literally shedding identifiable DNA from your body at all times and a truly motivated adversary would have no problem obtaining enough sample material to do high quality sequencing.

At scale?

I'm curious whether a Covid PCR test could be used to sequence your DNA. Is there enough of a specimen in the process.
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