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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

#81

Post by jrumbut »

toomuchtodo wrote: post #65
m12k wrote: post #62

Earlier quoted context omitted.

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…

What I worry about is having this data laundered through a couple of vendors.

"How could we know our vendor's vendor was using genetic information in their proprietary risk score?"

"How could we know our client's client was using our score for life, health, or auto insurance/employment/lending/etc decisions?"

It's a "can't unring a bell" situation and the gaps in the regulations and the incentives for bad behavior are enormous.

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

#82

Post by ClumsyPilot »

rumblerock wrote: post #35
m12k wrote: post #25

Earlier quoted context omitted.

One of the other comment threads indicates that the data, that you need to do that kind of annotation of the sequence, is to some extent available for home use as well: https://news.ycombinator.com/item?id=29695449 I'm really hoping someone will work on an open source "23andme@home" solution that ties all this together in an accessible way.

Years ago I used Ancestry, then requested the .txt file and asked them to delete it from their records. Uploaded it to run a report at https://promethease.com/ that cross-references your SNPs against the existing body of genetic research. The results have been pretty astounding. I found markers that pointed to poor response to a specific blood thinner my grandfather was put on before he passed. Currently I'm research…

>"poses a self-diagnosis risk"

Self-diagnosing is not the problem it is made out to be - I live with my symptoms 24/7, doctor sees me for 5 minutes. The amount of times doctors have missed fairly clear sign of trouble in my family is disturbingly high. A simple procedure, done in time, would have saved two people I know.

Unfortunately our educational system teaches you about mitochondrion, but not the practical difference between ibuprophene and paracetomol, or CRP.

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

#83

Post by l-albertovich »

hourislate wrote: post #70
shukantpal wrote: post #50

Earlier quoted context omitted.

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.

Well crap, there you go, giving the lunatics reasons not to get tested and make the whole thing worse than it already is...

I'm joking, I don't think you did anything wrong but I'd hate it if a ridiculous argument such as this example gained any traction :

Example : The government / aliens / whoever released the virus so we willingly gave them our DNA to sequence and match with our assigned ID so they can do XYZ in case the implant in the vaccine doesn't work or if we are smart enough not to get vaccinated.

Scary stuff.

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

#84

Post by albertgoeswoof »

Method-X wrote: post #79
m12k wrote: 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.

When I had 23andme sequence my DNA, I used a fake last name and pre-paid credit card.

But if enough of your relatives get sequenced, they’ll know who you are anyway

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

#85

Post by callesgg »

kingcharles wrote: post #29

So, how long before I can take my DNA "ROM" file and boot it in an emulator that would allow it to grow?

Many years, we still have problems simulating a single protein folding correctly. If we don’t find some new algorithm for simulating cells we would need computers that are billions of times faster than our current ones.

Also your dna is bootstraped from your mothers cells. And the prenatal environment has quite a large effect on development so your simulation might end up quite different from you if we only started with your dna.

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

#86

Post by Teever »

dekhn wrote: post #48
m12k wrote: 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.

I assume this line of reasoning is also why you don't lock your doors at night?

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

#87

Post by authed »

Method-X wrote: post #79
m12k wrote: 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.

When I had 23andme sequence my DNA, I used a fake last name and pre-paid credit card.

If your family members got it done with their real name, they will be able to create a link.

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

#88

Post by sathomasga »

toomuchtodo wrote: post #65
m12k wrote: post #62

Earlier quoted context omitted.

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…

Note that the law does *not* apply to other types of insurance. Life insurance, for example

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

#89

Post by nyolfen »

biophysboy wrote: post #31
AstroDogCatcher wrote: post #12

Earlier quoted context omitted.

Interested outsider here; I work with a lot of HCLS research customers but don't have a biology-related background. Can you explain the problems with the Nanopore sequencer accuracy in more detail? Basically, I was wondering if I could get one for myself and sequence my own genome, then user the data to learn about life-sciences computing techniques. If I were to buy one of the USB-attachable devices and run it, is t…

The instruments do exactly as you say (run the sample N times), but this obviously comes at a cost. Also, keep in mind that sequencing needs to be very, very accurate to be useful. We share most of our DNA, and the small variations make up all the difference.

what cost do you mean? time/electricity? reagents? or the cost of someone else charging more for more reads?

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

#90

Post by makeitdouble »

l-albertovich wrote: post #83
hourislate wrote: post #70

Earlier quoted context omitted.

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

Well crap, there you go, giving the lunatics reasons not to get tested and make the whole thing worse than it already is... I'm joking, I don't think you did anything wrong but I'd hate it if a ridiculous argument such as this example gained any traction : Example : The government / aliens / whoever released the virus so we willingly gave them our DNA to sequence and match with our assigned ID so they can do XYZ in c…

Given the past incidents, it would probably be more in line with a gov. agency getting direct access to everything that goes through a few selected labs for years/decades, so that a significant number of people geting blood/cells sampled for that period would have a high chance of passing their data though these labs at some point.

At the base of it, if the gov. of the country one lives in is the enemy, it can’t be a matter of refusing vaccines here and there, that’s not the scale they should be thinking about.

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