The $100 Genome has Arrived? AD Breakthrough!

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J11
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The $100 Genome has Arrived? AD Breakthrough!

Post by J11 »

The human genome to a large extent is still unlocked.
The current full genome sequencing cost is still somewhat pricey at ~$300 and this might even be
a loss leader price.

We need lower genome sequencing costs. When we hit the magic price point of ~$100 per genome
then people are expected to storm the shopping malls/crash the online servers and load up their buggies!
Load up their buggies, Yeah! We have seen this before with genochips, once you hit $100, the price
resistance evaporates.

If we could have 3-4 million AD dementia full genomes sequenced then the entire genetic architecture of
AD dementia genetics would unlock. At the moment AD GWAS scale is fairly unimpressive at around ~100,000.
We need to scale up!

Well, it appears that the $100 genome is on the short term time horizon!
Ultima Genomics is revealing this technology.
$1 / Gig ---> $ $100/100 Gig = 1 full human genome!!!

https://www.ultimagenomics.com/

This could give us a great opportunity to upload our full genomes to a server and be part of the unlock.
The AD pharma companies could also play their part by including optional full genome sequencing in their
trials. AD clinical trials now largely have true AD patients, so sequencing these patients could be especially
powerful. Biogen has played a constructive role in funding AD and other genetic studies. Considering
that AD drugs could generate tens of billions of dollars in revenue, a $500 million AD genomics project
does not seem an unreasonable ask. Unlocking the AD genome would alert people who might be unaware of their
genetic risk decades before actual cognitive onset. The cost savings to the medical system for such knowledge would be large.

This is a very exciting development!
After all of these years it is still unclear to me what is the genetic cause of my family's dominant AD.
Resolving this question is becoming increasingly important because effective treatments are
within sight over the near term. It is important to know what risk we face from our genetics.
With $100 genomes, this question should finally be answered!!
Last edited by J11 on Mon Jul 25, 2022 11:21 pm, edited 2 times in total.
J11
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Re: The $100 Genome has Arrived? AD Breakthrough!

Post by J11 »

Somewhat off-topic though recent research found that rs10423769_A in Africans with APOE e4 had lower AD risk.
This allele has frequency of ~10% in Africans and ~.1% in Europeans. The thinking here is that through evolutionary time Africans have been able to genetically adapt to APOE e4 in a way that those of other ancestries have not been able to.

https://pubmed.ncbi.nlm.nih.gov/35788729/
circular
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Re: The $100 Genome has Arrived? AD Breakthrough!

Post by circular »

J11 wrote: Sat Jul 09, 2022 7:39 pm Well, it appears that the $100 genome is now on the short term time horizon!
Ultima Genomics is revealing this technology.
$1 / Gig ---> $ $100/100 Gig = 1 full human genome!!!

https://www.ultimagenomics.com/

This could give us a great opportunity to upload our full genomes to a server and be part of the unlock.
Good to hear!
ApoE 3/4 > Thanks in advance for any responses made to my posts.
J11
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Re: The $100 Genome has Arrived? AD Breakthrough!

Post by J11 »

Thank you for your response Circ!

This is now getting so exciting!
We are days away from ICAD!
This will be epic.

There are multiple topline reportables that are now imminent ...
... and then there's Clarity and then there's Ganten ... so much to celebrate!


I need to stock up for the celebration ... cashews, chocolate bars, Macadamia nuts ....

No better way to start off the new era of treatable AD then to have a lost month or two.
If you don't hear from me, I'll be in the 12 step program of recovery from cashew addiction.
Choose your addictions carefully -- make sure you choose the ones with the tasty little nuts.
Last edited by J11 on Mon Jul 25, 2022 11:23 pm, edited 1 time in total.
circular
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Re: The $100 Genome has Arrived? AD Breakthrough!

Post by circular »

J11 wrote: Sun Jul 17, 2022 8:25 pm Thank you for your response Circ!

This is now getting so exciting!
We are now days away from ICAD!
This will be epic.

There are multiple topline reportables that are now imminent ...
... and then there's Clarity and then there's Gantenu so much to celebrate!


I need to stock up for the celebration ... cashews, chocolate bars, Macadamia nuts ....

No better way to start off the new era of treatable AD then to have a lost month or two.
If you don't hear from me, I'll be in the 12 step program of recovery from cashew addiction.
Choose your addictions carefully -- make sure you the ones with the tasty little nuts.
Do tell! What is ICAD? I find at least three organizations that go by that acronym. Maybe it is the International Conference of Addiction to NuttyDooDads? Clarity? Gantenu? Apologies if you've posted about these and I've missed it. I haven't been able to frequent the forum much for a long time.
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, it's ICAD! You know, the big one; once a year .... ICAD. San Diego California, yeah!

This will be such a monumental event for the Alzheimer dementia community.
This is the road back to normal for a lot of people including me.
Modern technology has if anything intensified our life challenges. Now finally medical treatments
will significantly alter the course of disease progression.

It's hard to imagine; I will be able to claim victory for all those centuries of my ancestors.
Even in the most recent generations in which we coped with AD all we had to help was memantine and anti-Aches. There are now waves and waves of approaching treatments with clinically verified cognitive benefits.
When we were coping we tried all sorts of silly things that had very unclear benefit. We wanted to help, though there is such a mountain of research and it is so unclear how it might specifically relate to our particular flavor of AD. Current AD research is now clarifying the various dimensions of differential response. Removing all of that uncertainty is such a blessing. When you are care giving 24/7 for moderate/severe AD, it is too much to also expect that you can invent your own dementia cure. Aside from treatment there are also numerous diagnostics that will be profoundly helpful. The diagnostics that are even now being approved will allow for treatment years before apparent clinical decline.

Life has been so disordered for my family for the centuries that we have struggled with this.
There is supposed to be a wheel of fortune in life; you know:

life is good --> life is on the down slide --> life is bleak --> life is not so bleak there is light at the end of the tunnel --> life is good again.

There's a cycle. Good --> Bad --> Good repeat.

With us it's been more life is bleak ... there is no light at the end of the tunnel ... things will probably get worse.
All the time.
That's the way it's been for us for centuries.
There were no good times.

With dominant AD there really is no ray of sunshine out there. Life never moves to the up cycle. Most of the people in our community likely found this fairly odd -- how can people never be able to move from the bottom? I mean if you're the kid in the class who has the worst academic performance -- there's only one way to go isn't there? Going from the worst to the middle of the pack is likely a highly achievable goal for all but the most stubborn under-achievers.

For us we have pretty much always been at the bottom of society. It doesn't really even matter about nominal success, because for us even nominal success has merely highlighted our inherent disadvantages. We have been part of the permanent Alzheimer dementia underclass: broadly defined as 5-10% of the population.

Our genomes are saturated with social disadvantages. It's probably naive to think that we can all just start happy dancing after an effective AD cure is reported (possibly at ICAD?), for us there are other challenges to confront. However, I would guess our problems are 90% AD. So, yeah, happy dancing will be on the ticket.
We do have other medical type challenges, though mostly these are more inconveniences than having a progressive and irreversible neurodegenerative illness leading to complete disability. I mean when you think about it in the grand scheme of things when you compare most other life challenges to AD, most other problems are typically orders of magnitude below AD in life impact.


This is such an epic moment for so many tens of millions of people.
This is on the scale of once in centuries event that redefines the social landscape.
Few medical advances over the last century or projecting into the next century have had/ will have such
substantial impact on population health.

I am so grateful for all those who have been part of this journey: those of the community,
those more of the guardian type who really do not understand dementia but are willing to help
out people who are at extreme life disadvantage and yes the frenemies who might not always
be on the right side of the cheering section though have the the best interests of the demented
at heart.


Yes, it's true that they gave up on the ICAD name quite a while ago, though the replacement AAIC, I mean it's not even pronouncable. ACK? ICK?

J11 dares to be different.
I can't pronounce an acronym with three consecutive vowels and a soft consonant; ain't gonna happen, not even gonna try.

ICAD? No worries! That's almost too easy. I am going to stick with ICAD.

However, as you noted you could wind up at the International Convention of Anterior Design by mistake.
I can drone on endlessly about Alzheimer's Disease ... but with Anterior Design ... really can't think of anything to report. If I get stuck at their convention I'll just smile nod my head politely and do my best not to look completely confused.
Last edited by J11 on Mon Jul 25, 2022 11:27 pm, edited 1 time in total.
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Re: The $100 Genome has Arrived? AD Breakthrough!

Post by barbS »

Still reading thru... but scrolling on apoe searches, this came up: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8073598/
ApoE 3/4
MTHFR A1298C
VDR Taq
all the other ++
MAO R297R MTHFD1L GAMT PEMT CCL2 SOD3 NSUDS7 ATG16L1 FOXE1 do these matter? :?: (I believe in "woo" cuz pharma never helped me)
circular
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Re: The $100 Genome has Arrived? AD Breakthrough!

Post by circular »

J11 wrote: Sat Jul 23, 2022 6:13 pmYes, it's true that they gave up on the ICAD name quite a while ago, though the replacement AAIC, I mean it's not even pronouncable. ACK? ICK?

J11 dares to be different.
I can't pronounce an acronym with three consecutive vowels and a soft consonant; ain't gonna happen, not even gonna try.

ICAD? No worries! That's almost too easy. I am going to stick with ICAD.

However, as you noted you could wind up at the International Convention of Anterior Design by mistake.
I can drone on endlessly about Alzheimer's Disease ... but with Anterior Design ... really can't think of anything to report. If I get stuck at their convention I'll just smile nod my head politely and do my best not to look completely confused.
:D

Didn't they register for the Acronym 101 Zoom event? :shock: :roll:

I finally began going through my loved one's digitial devices … content, what's this doohickey?, what's that doohickey?, … Among them was a 2 TB hard drive, USB 3 … I think this will be large enough to hold my genome when I have it :D, maybe even software to work with it, although I took note that you suggested the tools may be available in the cloud. This will allow me to keep my current external HD in service as a 2 TB Time Machine backup.

It will be interesting to see how the privacy issues play out when whole genomes are more commercially accessible to consumers. The US is already behind the curve in privacy regulation, generally speaking. One of the most interesting questions in my mind is whose genome really is it? Of course it's uniquely mine, but it contains so much of others' genomes too that in a way it doesn't all belong just to me.
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!

Post by Brian4 »

The $100 genome is at hand, but I think we should wait until long read technologies come down to that same price. There are too many regions that cannot be read accurately with standard sequencing techniques. Oxford Nanopore is now down to $1000 or so for long read sequencing. We're getting there!
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Re: The $100 Genome has Arrived? AD Breakthrough!

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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.

I am excited about the potential for a $100 full genome. This is the price level that mainstream consumers capitulate and load up the buggy. If this were to happen over the next 2-3 years then the entire human genome could unlock! That would be a monumental event in human history. We could know everything about our genetics and not just some of it! I have been trying to unlock whatever dementing variants might be present in my family though it has been largely unsuccessful. We just do not have that many genotypable relatives, and those who could be genotyped refuse to.

Now that $100 genomes are on the horizon everything could unlock soon! That would be great! I am still unclear whether another generation of my family is at AD risk -- I am not even that sure about my risk either. With millions and millions of full genomes sequenced even super rare variants with large dementia effects and other variants even with small effects will be discoverable. All that's needed to be a hero is to pay $100, spit and post. That should be doable for most people. If hero had meant run a full marathon in under 3 hours, then it would have been trickier to chalk up a win.
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