Sequencing your DNA with a USB dongle and open source code (opens in new tab)

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

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.

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

It’s out the bag now - you can be identified via relatives DNA.

https://www.latimes.com/california/story/2020-12-08/man-in-t...

It’s not exactly DIY but there are in theory ways to ‘encrypt’ your DNA before it gets sequenced. Something like amplifying/enzymatically modifying the DNA in a way that changes the sequence which you can undo computationally once you get the data back.

Its only valuable if somebody also interprets it for you, such as telling you whether you have a genetic predisposition for certain diseases.

Note that Oxford Nanopore seems to have very much a "sell the ink/razor/etc" business model with their devices: that $1,000 package comes with one flow cell, which is a consumable and costs $900. They're essentially giving the device away for free.

On some of their larger devices (eg, the PromethION), they've moved outright to a "we lend you the device for free, you buy the consumables" model.

Yep that’s the one. They update the flow cells over time. The bit they don’t tell you is the stuff you need, like a qubit, to properly run the thing.

yes. if you wanted to annotate your genome you could “easily” do it on your brand new macbook (this is ram intensive, you probably need 32G). you’d need a reference genome, like https://www.nist.gov/programs-projects/genome-bottle

then you’d need a program like bwa http://bio-bwa.sourceforge.net/ to map your data.

then use https://samtools.github.io/bcftools/howtos/variant-calling.h... or something else to produce variants from the mapping results.

then compare your resultant vcf file to something like dbSNP: https://www.ncbi.nlm.nih.gov/snp/

at this point you can start generating a raw version of a 23andMe report.

A used laboratory grade NGS system can be had for less than 10K

https://www.ebay.com/itm/265148387179

Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

Sounds like a fediverse project?

Yep

I think you would have to two scenarios at hand:

1. A completely genetically determined disease; a rare 100%-going-to-happen deal. (Which you would probably know about already, because your mother, or grandfather died from it...)

2. Some significant, but abstract risk modification.

With 1., you would know, you will get sick/die some time soon in the future, allowing you to live your life accordingly, die without regrets, prepared and so on. You can take that into consideration when planning for a family, taking job offers, procrastinating on the good life with work and retirement plans. Burn bright.

With 2., there is a very, very high chance lifestyle choice influence the stated risk, as obviously not everybody who got the polymorphism gets sick. So you can get your ass up, exercise, quit smoking and drinking, reduce stress, get regular check ups, ..., and avoid getting sick or reduce the impact/progression, in case you do.

I think, logically, knowing is always better than not knowing. But I understand how anxiety does tell a different story.

well, build a whitelist of the conditions you are interested in knowing. then just run the report through a sed filter so that it strips out all the information you’re not interested in. destroy the original report. problem solved: infohazards avoided.

Knowing something about your prospects doesn't doom you to negative thoughts. In fact, the way the human mind works is often the obverse.

"Inaction breeds doubt and fear. Action breeds confidence and courage. If you want to conquer fear, do not sit home and think about it. Go out and get busy." --Dale Carnegie

"You gain strength, courage and confidence by every experience in which you really stop to look fear in the face. You are able to say to yourself, 'I have lived through this horror. I can take the next thing that comes along.' You must do the thing you think you cannot do." --Eleanor Roosevelt

"Fear is the path to the Dark Side. Fear leads to anger, anger leads to hate, hate leads to suffering." --Yoda

"The brave man is not he who does not feel afraid, but he who conquers that fear." --Nelson Mandela

"Nothing in life is to be feared. It is only to be understood.' --Marie Curie

"The key to change... is to let go of fear." --Roseanne Cash

"He who is not everyday conquering some fear has not learned the secret of life." --Ralph Waldo Emerson

"We should all start to live before we get too old. Fear is stupid. So are regrets." --Marilyn Monroe

"Fear keeps us focused on the past or worried about the future. If we can acknowledge our fear, we can realize that right now we are okay. Right now, today, we are still alive, and our bodies are working marvelously. Our eyes can still see the beautiful sky. Our ears can still hear the voices of our loved ones." --Thich Nhat Hanh

How about affinities to possible health issues, which could be avoided if you started now and not in 20 years?

An idea just popped into my head reading your comment:

What if you could take the (binary) data file of your DNA and use it as input in the (recently remastered) Monster Rancher games to generate a monster? Apparently those games use external user-provided data (like music CDs, game discs etc.) to generate the monsters the player would then train and use (something I only recently learned about through gaming livestreams).

I'd actually like to see the level of jank that would come out of something like that.

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.

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

There was some interest in the information retrieval research community 10-15 years ago, but I don't think anyone ever found a good application for it. Some limitations of the BWT always got in the way.

The BWT sees strings as integer sequences. Either "ABC" and "abc" are two unrelated strings, or you normalize before building the index and lose the ability to distinguish between the two.

Search proceeds character-by-character backwards, jumping arbitrarily around the BWT using the same LF-mapping function as when inverting the BWT. You get cache misses for every character.

BWT construction is expensive, because you want a single BWT for the entire string collection. There is a ridiculous number of papers on BWT construction, as well as on updating and merging existing BWTs, but the problem has still not been solved adequately. If your data is measured in gigabytes, you can just pay the price and build the index, but a few terabytes seems to be the practical upper limit for the current approaches.

You can of course partition the data and build multiple indexes, but then you have to search for each pattern in each index. There is no way to partition the data in a way that different indexes would be responsible for different queries.

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.

Initially, the DNA is brought near the pore through diffusive (brownian) motion + any small attraction it'll have to the membrane. Close to the pore it uses a combination of the electrophoretic and electro-osmotic effects to draw the DNA molecules through. The application of an external magnetic field will cause the charged DNA molecules to migrate along the field (electrophoresis). This is independent of the fluid, and happens to any ions under voltage. The electro-osmotic flow, on the other hand, is a motion of the fluid itself, pulling the DNA molecules along with it. EOF is a really interesting phenomenon which is caused by the interaction between the surface chemistry (vis-a-vis charge distribution) and the concentration gradient of charge carriers in the fluid. I'd recommend Fundamentals and Application of Microfluidics by Nguyen et al if you're looking for a good primer on electrically induced flows in microfluidics.

It’s a weird quote anyway since there is commercial, proprietary software for DNA sequence analysis. Just a few examples of companies in this space are Sentieon, Edico (acquired by Illumina) and Parabricks (acquired by Nvidia). And Michael knows this (they’re sufficiently well known, and his own research laid some of the earliest foundations that Parabricks would ultimately build upon) so I’m assuming the quote was taken out of context or he was talking specifically about his own lab.