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Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Sarcany
Date: July 07, 2020 10:47PM
It might help to know how much Neanderthal DNA you have when trying to calculate your risk from COVID-19...

[www.nytimes.com]

A stretch of DNA linked to Covid-19 was passed down from Neanderthals 60,000 years ago, according to a new study...

This piece of the genome, which spans six genes on Chromosome 3, has had a puzzling journey through human history, the study found. The variant is now common in Bangladesh, where 63 percent of people carry at least one copy. Across all of South Asia, almost one-third of people have inherited the segment.

Elsewhere, however, the segment is far less common. Only 8 percent of Europeans carry it, and just 4 percent have it in East Asia. It is almost completely absent in Africa...

Researchers are only beginning to understand why Covid-19 is more dangerous for some people than others. Older people are more likely to become severely ill than younger ones. Men are at more risk than women.

Social inequality matters, too. In the United States, Black people are far more likely than white people to become severely ill from the coronavirus, for example, most likely due in part to the country’s history of systemic racism. It has left Black people with a high rate of chronic diseases such as diabetes, as well as living conditions and jobs that may increase exposure to the virus.

Genes play a role as well. Last month, researchers compared people in Italy and Spain who became very sick with Covid-19 to those who had only mild infections. They found two places in the genome associated with a greater risk. One is on Chromosome 9 and includes ABO, a gene that determines blood type. The other is the Neanderthal segment on Chromosome 3...

“The jury is still out on ABO,” said Mark Daly, a geneticist at Harvard Medical School who is a member of the initiative.

The new data showed an even stronger link between the disease and the Chromosome 3 segment. People who carry two copies of the variant are three times more likely to suffer from severe illness than people who do not.




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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: sekker
Date: July 07, 2020 10:52PM
I've been following, seems like BS to me.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: NewtonMP2100
Date: July 07, 2020 10:53PM
....they can also help to catch cold case.....serial killers.......they just nabbed the Golden State Killer......



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I reject your reality and substitute my own!
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Steve G.
Date: July 07, 2020 11:50PM
You don't have to do tests for these near-human relatives, you'll spot them wearing red caps and not wearing masks at any crowded bar in the city.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Racer X
Date: July 08, 2020 01:45AM
Sounds very credible. It has been proven that those with a higher percentage of Neanderthal DNA have weaker immune systems, are are more susceptible to inflammatory response issues like arthritis, allergies and asthma.

My partner's family on their dad's side are Wallaces, descended from Bigfoot Wallace and William Wallace. Everyone in that gene line that I know of has at least one inflammatory medical issue, some 3+, and have high relative Neanderthal DNA. Bigfoot Wallace, the Texas Ranger, was VERY tall, and had huge feet. He had some inflammatory issues according to his biography, as researched through his children and grand kids.

I have more than normal, and suffer from VERY bad allergies and asthma.

Covid 19 weakness could easily fit into that puzzle.

Wonder if Peter B will weigh in.



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The police have no duty to respond. See Castle Rock v. Gonzales, 545 U.S. 748 (2005) or Warren v. District of Columbia[1] (444 A.2d. 1, D.C. Ct. of Ap. 1981)
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Filliam H. Muffman
Date: July 08, 2020 02:53AM
Don't put down Neanderthals. There is was some speculation that people with certain segments are better at math. Just because it is thought of as less evolved overall, it's not necessarily less wise/smart.



In tha 360. MRF User Map
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Racer X
Date: July 08, 2020 03:25AM
Very true. More robust immune system doesn't mean smarter, just better equipped as a species to survive.

I truly wonder if modern medicine is allowing the frail and less equipped for survival to survive, weakening the gene pool.



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The police have no duty to respond. See Castle Rock v. Gonzales, 545 U.S. 748 (2005) or Warren v. District of Columbia[1] (444 A.2d. 1, D.C. Ct. of Ap. 1981)
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: RgrF
Date: July 08, 2020 03:45AM
I truly wonder if modern medicine is allowing the frail and less equipped for survival to survive, weakening the gene pool.

Sounds much like a proposition advanced about a hundred years ago, it was called Eugenics, you may have heard of it.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Racer X
Date: July 08, 2020 04:14AM
proposing we do something about it is very different than wondering if we are screwing with natural selection and evolution.

Eugenics is DOING something about it. "to arrange reproduction within a human population to increase the occurrence of heritable characteristics regarded as desirable"



********************************************
The police have no duty to respond. See Castle Rock v. Gonzales, 545 U.S. 748 (2005) or Warren v. District of Columbia[1] (444 A.2d. 1, D.C. Ct. of Ap. 1981)



Edited 1 time(s). Last edit at 07/08/2020 04:54AM by Racer X.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Sarcany
Date: July 08, 2020 06:40AM
Quote
Racer X
I truly wonder if modern medicine is allowing the frail and less equipped for survival to survive, weakening the gene pool.

We've been allowing "the frail and less equipped" to survive for the entire time that our species has existed.

It's a good thing. It broadens the gene pool, which allows us to adapt to new environmental stresses, and in the case of the elderly it provides for childcare and the passing on of knowledge to new generations.

...Except in the modern United States and a lot of the Western world where we mostly isolate and persecute the frail and the elderly. It's probably too soon to show much in the way of evolutionary change, but given a few thousand years of this it could be responsible for the end of our species.



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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: deckeda
Date: July 08, 2020 06:43AM
Wondering if something is happening lends it credibility that often leads to a proposal to try it out before considering if what’s being wondered is worthy of the effort.

And so we had eugenics until society essentially said, “we don’t care if it’s true because creating a master race/culture/whatever isn’t the goal.”
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: PeterB
Date: July 08, 2020 09:55AM
OK ... so I've just had a chance to glance both at the article, as well as the actual study to which it refers, here: [www.biorxiv.org] (PDF here: [www.biorxiv.org] ) ...

It's interesting, but far from conclusive. At once, they claim to make an association with this stretch on chromosome 3, while also NOT seeing an association on chromosome 9 (the one involved in ABO blood groups) ...

The major issue I have with studies of this type is, as they say: correlation is not causation. Just because you more frequently see two things together, does not mean that one causes the other. In this particular case, the study raises some rather obvious additional questions:

1) If this stretch of Neanderthal DNA is more commonly seen in people with poorer COVID-19 clinical outcomes, and it's more common in people of South Asian (especially Bangladeshi) heritage-- then why are we not seeing this more commonly here in the US? (The prediction would be that Bangladeshi-Americans and Indian/Pakistani-Americans would be at higher risk, but to my knowledge, nobody has seen that.) This stretch is also supposed to be nearly absent from people of African descent, yet African Americans in the US have some of the worst clinical outcomes from the virus -- which we already know is largely due to socioeconomic factors and not genetics.

2) They also argue the lack of involvement of the blood group haplotype, yet repeated studies have shown that this does seem to be a factor-- NOT necessarily from the blood type itself, but possibly from some linked genes that are associated with immune response.

3) The big question here is, what is it in this stretch of DNA that's causing the problem? (DNA doesn't do much of anything on its own, it's the encoded RNA and proteins that are the "actors".) According to another NYT article, in that stretch of six genes, "one of those gene candidates encodes a protein known to interact with ACE2, the cellular receptor needed by the coronavirus to enter host cells. But another gene nearby encodes a potent immune-signaling molecule. It is possible that this immune gene also triggers an overreaction that leads to respiratory failure." ... so it may not be a single gene but rather a combination of particular gene/protein variants that's leading toward a poorer clinical outcome.

Svante Pääbo is well known and respected in the evolutionary genomics field, he practically started it by his use of PCR to amplify "ancient" DNA. So while I don't disbelieve the results presented in the paper, the question is what actual meaning / relevance it has.

If anyone is curious about these six genes:



... they include at least 3-4 chemokine receptors, so this is not completely farfetched. Interesting though that the one of the six known to interact with ACE2, SLC6A20, is NOT one of the chemokine receptors.

Edit: I could make a pretty good argument for involvement of the CCR9 receptor: [www.hindawi.com]




Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)



Edited 3 time(s). Last edit at 07/08/2020 10:08AM by PeterB.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: sekker
Date: July 08, 2020 12:00PM
Quote
Racer X
Sounds very credible. It has been proven that those with a higher percentage of Neanderthal DNA have weaker immune systems, are are more susceptible to inflammatory response issues like arthritis, allergies and asthma.

This is an interesting idea in the field, not validated with any prospective work and there is no experimental confirmation.

Indeed, there is a strong counter-argument that the immune loci are largely retained in current homo sapiens (like yours truly) from non-homo sapiens (like neanderthal) to give us more immunological ammo against pathogens. The negative is that we would get more allergies and other auto-immune diseases. But that trade-off is ok if it also means we do not die from novel pathogens!

The problem I have with these specific studies is that there is no epidemiological evidence to substantiate this genetic work. In the US, genetic groups that are the most sensitive (POC) tend to have the least amount of Neanderthal DNA. So, on a macro scale, this is quite counter-intuitive.

People have picked up on these studies because they sound good. I am just not convinced they have actually taught us anything, scientifically speaking.



Edited 2 time(s). Last edit at 07/08/2020 12:03PM by sekker.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Filliam H. Muffman
Date: July 08, 2020 03:13PM
PeterB, thank you for the review. smiling smiley



In tha 360. MRF User Map
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Racer X
Date: July 08, 2020 04:55PM
Thanks Peter!

I just pointed out what my partner's family line experienced and how it sounded plausible. NOT saying I believe its true.



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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: PeterB
Date: July 08, 2020 05:44PM
Quote
Filliam H. Muffman
PeterB, thank you for the review. smiling smiley

Sure ... and I should have mentioned that CXCR6 is another really good candidate: [europepmc.org]

... and here's another paper finding association with the region and more severe clinical outcome, where they go into more discussion about the causative issues: [www.nejm.org]

from that paper:

"On chromosome 3p21.31, the peak association signal covered a cluster of six genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, and XCR1), several of which have functions that are potentially relevant to Covid-19. A causative gene cannot be reliably implicated by the present data. One candidate is SLC6A20, which encodes the sodium–imino acid (proline) transporter 1 (SIT1) and which functionally interacts with angiotensin-converting enzyme 2, the SARS-CoV-2 cell-surface receptor.28,29 However, the locus also contains genes encoding chemokine receptors, including the CC motif chemokine receptor 9 (CCR9) and the C-X-C motif chemokine receptor 6 (CXCR6), the latter of which regulates the specific location of lung-resident memory CD8 T cells throughout the sustained immune response to airway pathogens, including influenza viruses.30 Flanking genes (e.g., CCR1 and CCR2) also have relevant functions,31 and further studies will be needed to delineate the functional consequences of detected associations."

And the next two paragraphs providing supportive info and also commenting about the blood group associations:

"The preliminary results from the Covid-19 Host Genetics Consortium32 include suggestive associations within the same locus at chromosome 3p21.31, which lend considerable support to our findings (Fig. S11 in Supplementary Appendix 1). The consortium analysis also used population-based controls, but the patients included persons with mild Covid-19 and those with severe Covid-19. The parallel findings nevertheless underscore an important point about the ascertainment of patients and controls in genetic studies of Covid-19. Because the majority of patients with SARS-CoV-2 infection are asymptomatic, any sample involving patients with a positive nasopharyngeal RNA test is likely to hold a bias toward some degree of symptomatic burden. Two of the identifiers for inclusion in the current study were a positive result for the presence of SARS-CoV-2 according to PCR testing and receipt of respiratory support (an extreme Covid-19 phenotype). As such, it seems reasonable to conclude that the chromosome 3p21.31 locus is involved in Covid-19 susceptibility per se, with a possible enrichment in patients with severe disease. This latter interpretation is supported by the significantly higher frequency of the risk allele among patients who received mechanical ventilation than among those who received supplemental oxygen only as well as by the finding of younger age among patients who were homozygous for the risk allele than among patients who were heterozygous or homozygous for the nonrisk allele.

Nongenetic studies that were reported as preprints33,34 have previously implicated the involvement of ABO blood groups in Covid-19 susceptibility, and ABO blood groups have also been implicated in susceptibility to SARS-CoV-1 infection.35 Our genetic data confirm that blood group O is associated with a risk of acquiring Covid-19 that was lower than that in non-O blood groups, whereas blood group A was associated with a higher risk than non-A blood groups.33,34 The biologic mechanisms undergirding these findings may have to do with the ABO group per se (e.g., with the development of neutralizing antibodies against protein-linked N-glycans)36 or with other biologic effects of the identified variant,37-39 including the stabilization of von Willebrand factor.40,41 The ABO locus holds considerable risk for population stratification,42 which is increased by the inclusion of randomly selected blood donors in the current study (for which there is an inherent risk of blood group O enrichment). Alignment of the allele frequencies at the ABO locus in our control population with those in several non–blood-donor control populations would suggest that this is not a major bias, and at least one study34 that tested for association with blood type used disease controls with no affiliation to blood donors."

... putting this all together ... I wouldn't be at all surprised if it turns out that people with a particular haplotype are more susceptible (for example, the Neanderthal-derived one), as well as individuals who happen to have particular mutations in one or more of the genes in this region or in the one for the blood groups. We really have a lot more to learn about all this. I'm sure someone has already done it, but it'd be interesting to see microarray results with severe COVID infection to see which genes are getting up/downregulated, and whether these differ from someone who is more successfully fighting it off. That might give us more specific ideas about which genes/proteins to target in cases of severe infection to help the person survive... very useful info until we get an effective/safe vaccine.




Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)



Edited 2 time(s). Last edit at 07/08/2020 06:33PM by PeterB.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Racer X
Date: July 08, 2020 09:02PM
eek2 smiley



********************************************
The police have no duty to respond. See Castle Rock v. Gonzales, 545 U.S. 748 (2005) or Warren v. District of Columbia[1] (444 A.2d. 1, D.C. Ct. of Ap. 1981)



Edited 1 time(s). Last edit at 07/08/2020 09:02PM by Racer X.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: PeterB
Date: July 08, 2020 11:01PM
Quote
Racer X
eek2 smiley

Sorry if that was too much for you! grinning smiley




Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Don C
Date: July 08, 2020 11:07PM
WWWAAAYYYY above my pay grade to understand this stuff! Glad there are people who do and it's pretty neat that some of the people who do reside and comment here.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: PeterB
Date: July 09, 2020 08:47AM
Quote
Don C
WWWAAAYYYY above my pay grade to understand this stuff! Glad there are people who do and it's pretty neat that some of the people who do reside and comment here.

Bottom line / summary for the nonscientists in the group: there is some Neanderthal DNA in all of us, but how much and which particular DNA we have varies, and these researchers have found an association between a particular stretch and an apparently poorer clinical outcome with coronavirus. WHY that association seems to exist is still a question... there are at least six genes in this stretch, and some of them might affect the ability of the virus to infect and/or response to infection. This particular stretch is most commonly found in people of South Asian (especially Bangladeshi) descent, but it's possible that people of other ethnic groups could have mutations in some of the genes as well.




Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)



Edited 1 time(s). Last edit at 07/09/2020 08:48AM by PeterB.
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Re: Turns out that there may be some value in those stupid personal DNA testing services where they sell all of your personal data down to the genome for the low low price of $99...
Posted by: Racer X
Date: July 09, 2020 09:10AM
Quote
PeterB
Quote
Racer X
eek2 smiley

Sorry if that was too much for you! grinning smiley

To be honest, in HS AP Bio, I was distracted by enchanting redhead named Suzanne............. so I have an excuse.



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The police have no duty to respond. See Castle Rock v. Gonzales, 545 U.S. 748 (2005) or Warren v. District of Columbia[1] (444 A.2d. 1, D.C. Ct. of Ap. 1981)
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