The $100 Genome has Arrived? AD Breakthrough!

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J11
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Re: The $100 Genome has Arrived? AD Breakthrough!

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Circ, thank you for replying (and getting me back on the track of this thread)

Yes, being an early adopter of technology does have its inconveniences. By the time we do reach the $100 price point all the kinks will need to be worked out. Just saying "Here you go, here's a 100 Gig download file enjoy" will not cut it.
They need to work on the back end software etc. to make full genomes a manageable experience. There is a lot that they could do to make the experience more pleasant though with a small enough market they never seem to get around to it. One of the more surprising aspects of my full genome report was they did not seem to include MAF etc etc.. Once we reach the load up the buggy stage all of that will probably be figured out quite quickly.

With privacy I think it is mostly a lost cause. As soon as you have millions of full genomes in the databases, they might not need to even bother with the sequencing. They could simply ask you for your genochip file and then they could impute your results from there. It would be a fairly shady business practice (though highly profitable) while still probably giving quite a accurate genome results.

They have a humanity family tree under construction which could be extremely powerful in searching for disease variants. You could simply locate yourself in this tree and report your phenotype to some database. The large variant risks might immediately pop out when even a few people in the tree report a related phenotype (e.g. AD). In such a scheme, there could be very rapid unlocking of the genome at the personal scale. Most of the research to date has been more GWASy. Going done to the microlevel can be too much effort. With the human family tree, EVERYTHING could unlock very fast.
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Re: The $100 Genome has Arrived? AD Breakthrough!

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J11 wrote: Mon Jul 25, 2022 8:14 pm Brian4, thank you for your comment! Yes, I have been following Oxford Nanopore very carefully, though I had not been aware that we had reached the $1,000 full genome price point with them. That is moving into consumer level pricing
Hi J11– Just a quick clarification. That is the price they quoted me as a researcher looking to do 20 or so at once. I think the price would be higher if it were offered to just one person, and I don't even know whether they're considering doing that yet.

But there are some other companies working on long read sequencing. We should have some great options within a year.
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Re: The $100 Genome has Arrived? AD Breakthrough!

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J11 wrote: Tue Jul 26, 2022 7:25 pm They have a humanity family tree under construction which could be extremely powerful in searching for disease variants. You could simply locate yourself in this tree and report your phenotype to some database. The large variant risks might immediately pop out when even a few people in the tree report a related phenotype (e.g. AD). In such a scheme, there could be very rapid unlocking of the genome at the personal scale. Most of the research to date has been more GWASy. Going done to the microlevel can be too much effort. With the human family tree, EVERYTHING could unlock very fast.
Ah yes, I saw that! The Buddhists (and others) were right all along … we are interbeings; there is no separate self. Once we all fully grasp that in unison, war can take a back seat and solving Alzheimer's through shared full genomes a front seat.

What sequencing technology is the All of Us team using to sequence their participants? That will be a large dataset available to researchers.

NIH’s All of Us Research Program Releases First Genomic Dataset of Nearly 100,000 Whole Genome Sequences
The genomic data is available via a cloud-based platform, the All of Us(link is external) Researcher Workbench(link is external), and also includes genotyping arrays from 165,000 participants. Whole genome sequencing provides information about almost all of an individual’s genetic makeup, while genotyping arrays, the more commonly used genetic testing approach, capture a specific subset of the genome.
Brian4 wrote: Hi J11– Just a quick clarification. That is the price they quoted me as a researcher looking to do 20 or so at once. I think the price would be higher if it were offered to just one person, and I don't even know whether they're considering doing that yet.
Brian I'm guessing from this that All of Us either doesn't provide the long reads you seek, and/or you need to collect additional information from the participants that isn't available from All of Us.
ApoE 3/4 > Thanks in advance for any responses made to my posts.
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Re: The $100 Genome has Arrived? AD Breakthrough!

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circ, very insightful idea about us interbeings. Yes humanity as a Gaia force. It is fairly remarkable to realize that bits and pieces of our genomes are spread across our living genomes out in the world. It's fairly interesting because we now have insights into what some of these genetic modules actually do. With my genome in hand I am aware of quite a few odd pieces of my being; it would be amusing to see some of these features isolated in those who shared such pieces of DNA.

The approaching complete unlock of the human polygenic genome is cosmically important. We have learned bits and pieces about the genome over the last 20 years. However, when people load up their buggies and pay $100 for their full genome sequence, we could know everything. This is now plausible over the mediumish term. That could be truly startling. There are likely a fair number of things that are lurking around in the genome that we are not aware of. Finding them could have monumental consequences.
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Re: The $100 Genome has Arrived? AD Breakthrough!

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Brian4, wow a year? That is closer than I would have thought.

Some of the genome companies have these 10 million dollar genome boxes. The nanopore technology is more like a $1,000 toaster -- something that you might have in your kitchen or something. Given how devastating COVID has been, it can only be hoped that nanopore tech will now go deep into the wild and will let us be much more ready for the next viral outbreak. Perhaps we could even stop such pandemics before they went world wide. With COVID it might have been circulating for months before anyone noticed what was happening.
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Re: The $100 Genome has Arrived? AD Breakthrough!

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J11 wrote: Tue Aug 02, 2022 10:39 pm Brian4, wow a year? That is closer than I would have thought.
That's my educated guess. Could be wrong, but demand for long read sequencing grew substantially because of the pandemic. And then of course there are all the new ideas for cancer therapies, which would require long read sequencing.

But where I could be wrong is about how quickly that translates into a consumer product, since the rapidly growing demand right now is mostly from researchers.
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Re: The $100 Genome has Arrived? AD Breakthrough!

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Hmm, yes they are doing massive scale circulating cancer cell genomic studies. That could be such an enormous breakthrough ... take a blood sample, full genome sequence and find some of the earliest circulating cancer cells. You could treat not at stage 4 or 3 or 2 or even 1 but at stage 0!

Similar logic might even apply to AD. Some recent AD research has found that AD also has genomic effects on cells (brain cells). What if you could play the same circulating cell game and grab some of these cells? Once again you might be able to find pathology years before there were even proteinopathy (such as amyloid or tau).
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