genetics (4)

Haplotypes and Neanderthals...


a, Manhattan plot of a genome-wide association study of 3,199 hospitalized patients with COVID-19 and 897,488 population controls. The dashed line indicates genome-wide significance (P = 5 × 10−8). Data were modified from the COVID-19 Host Genetics Initiative2 ( b, Linkage disequilibrium between the index risk variant (rs35044562) and genetic variants in the 1000 Genomes Project. Red circles indicate genetic variants for which the alleles are correlated to the risk variant (r2 > 0.1) and the risk alleles match the Vindija 33.19 Neanderthal genome. The core Neanderthal haplotype (r2 > 0.98) is indicated by a black bar. Some individuals carry longer Neanderthal-like haplotypes. The location of the genes in the region is indicated below using standard gene symbols. The x-axis shows hg19 coordinates.

Topics: Biology, COVID-19, Genetics, Research


A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in South Asia and around 16% of people in Europe.


The COVID-19 pandemic has caused considerable morbidity and mortality and has resulted in the death of over a million people to date3. The clinical manifestations of the disease caused by the virus, SARS-CoV-2, vary widely in severity, ranging from no or mild symptoms to rapid progression to respiratory failure4. Early in the pandemic, it became clear that advanced age is a major risk factor, as well as being male and some co-morbidities5. These risk factors, however, do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Thus, genetic risk factors may have a role in disease progression. A previous study1 identified two genomic regions that are associated with severe COVID-19: one region on chromosome 3, which contains six genes, and one region on chromosome 9 that determines ABO blood groups. Recently, a dataset was released by the COVID-19 Host Genetics Initiative in which the region on chromosome 3 is the only region that is significantly associated with severe COVID-19 at the genome-wide level (Fig. 1a). The risk variant in this region confers an odds ratio for requiring hospitalization of 1.6 (95% confidence interval, 1.42–1.79) (Extended Data Fig. 1).

The genetic variants that are most associated with severe COVID-19 on chromosome 3 (45,859,651–45,909,024 (hg19)) are all in high linkage disequilibrium (LD)—that is, they are all strongly associated with each other in the population (r2 > 0.98)—and span 49.4 thousand bases (kb) (Fig. 1b). This ‘core’ haplotype is furthermore in weaker linkage disequilibrium with longer haplotypes of up to 333.8 kb (r2 > 0.32) (Extended Data Fig. 2). Some such long haplotypes have entered the human population by gene flow from Neanderthals or Denisovans, extinct hominins that contributed genetic variants to the ancestors of present-day humans around 40,000–60,000 years ago6,7. We, therefore, investigated whether the haplotype may have come from Neanderthals or Denisovans.

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals, Hugo Zeberg, & Svante Pääbo, Nature

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Snake Oil...

Image Source: Link below

Topics: Biology, DNA, Genetics

"Extraordinary claims require extraordinary evidence." Carl Sagan

I'm guessing "I did Ancestry" is going to become the "I used to do Amway" in the 21st Century?

I participated, thinking it was legitimate science. It did somewhat jive with my own experiences of being consistently identified by Nigerians as resembling someone from the Igbo. This again is pure conjecture, and likely only a polite guess.

I can see the desire to know about our roots, especially if you're a part of the African Diaspora is tempting as well as an opportunity for confidence rackets and quackery.

In the spring of 2017, a college student named Mary spit into a tube and sent it to the DNA testing company Ancestry, which analyzed it and sent back a breakdown of her family history.

But Mary wanted to know more. The human genome contains, in theory, an extraordinary wealth of pre-programmed information about who we are and who we might become: whether she was at risk for the same types of cancer that killed her parents, for instance, or if she had medical conditions she could unknowingly pass on to her children.

For that information, Mary — we’re withholding her last name to protect her privacy — turned to a dubious new sector of the genomics industry, in which startups claim to provide vastly greater insights than prominent companies like Ancestry and 23andMe do. She uploaded a copy of her raw genetic code, which Ancestry provided as a 17.6 megabyte text file, to a site called Genomelink, which advertises tests for everything from medical conditions and mental illnesses to ludicrously specific personality traits including “loneliness,” “social communication problems,” and “vulnerability to helicopter parenting.”

But when her results arrived, Mary immediately noticed that many were “wildly inaccurate.” Genomelink said she was “less easily depressed,” but Mary was diagnosed with clinical depression at a young age. The startup predicted that she had a peanut allergy, but Mary told Futurism that “peanut butter is one of the true loves of my life.” Other errors in Mary’s report included traits like blood iron levels, body fat measurements, hearing problems, height, and skin complexion.

“I felt that much of it was off-base and unhelpful,” she told Futurism, “as it didn’t fit me at all.”

Genomelink is just one of a growing number of shady DNA testing startups now operating in the regulatory Wild West of commercial genomics.

There’s GenePlaza, for instance, which sold a DNA test that claimed to predict users’ sexual preferences — and still sells tests that purport to measure intelligence and risk of depression. A company called Soccer Genomics claims to examine a child’s DNA to create a sports training regimen to turn them into the perfect soccer player. An outfit called GenoPalate told a Milwaukee Journal Sentinel reporter that their DNA demanded a diet of elk meat and passion fruit. A venture called Vinome claims it can recommend the perfect wine for each person based on their genetic code.

The problem, according to experts, is that these companies are promising information about DNA with a granularity that even scientists can’t deliver. Deanna Church, a geneticist at the biotech company Inscripta, told Futurism the tests are “all equally useless.”

“There is not a scientific basis for this sort of testing,” she said. “I certainly would not recommend anyone spend any money on this sort of thing.”


"Like Horoscope Readings!": The Scammy World of DNA Startups, Dan Robitzki, Futurism

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Twin Paradox...

Retired astronaut Mark Kelly (left) cracks a slight smile while posing with his identical twin brother, astronaut Scott Kelly (right). As part of NASA's Twins Study, Scott took a long trip to space, while Mark remained on Earth. Researchers then monitored how their bodies reacted to their differing environments. NASA


Topics: Astronaut, Astrophysics, Genetics, NASA, Spaceflight

Brothers compete. So in 2016, when astronaut Scott Kelly returned to Earth after spending a year in space, it must have really annoyed his identical twin brother — retired astronaut Mark Kelly — that Scott was two inches taller than when he left. However, Scott's temporary increase in height was not the only thing that changed during his trip.

As part of NASA's Twins Study, while Scott was in space, Mark went about his daily life on Earth. Over the course of the year-long mission, researchers tracked changes in both brothers' biological markers to pinpoint any variances. Because the twins share the same genetic code, researchers reasoned that any observed differences could tentatively — though not definitively — be linked to Scott's time aboard the International Space Station (ISS). This allowed them to take advantage of a unique opportunity and explore how an extended stay in space may impact the human body.

Based on their results, which were published this week in the journal Science, spaceflight can definitely trigger changes in the human body. But the vast majority of these changes disappear within just a few short months of returning to Earth.

Most notably, the researchers found that living in a microgravity environment can: damage DNA; impact the way thousands of individual genes are expressed; increase the length of telomeres (the shielding caps that protect the ends of our chromosomes); thicken artery walls; modify the microbiome; and increase inflammation — just to name a few.

"This is the dawn of human genomics in space," said Andrew Feinberg, a distinguished professor at Johns Hopkins University and one of the lead investigators for the Twins Study, in a press release. "We developed the methods for doing these types of human genomic studies, and we should be doing more research to draw conclusions about what happens to humans in space."


NASA's Twins Study: Spaceflight changes the human body, but only temporarily
Jake Parks, Astronomy

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Ethics of Genesis...



Topics: Biology, Ethics, Genetics, Science Fiction

Note: The article "went there" before I could.

"Beware the beast man, for he is the devil's pawn. Alone among God's primates, he kills for sport or lust or greed. Yea, he will murder his brother to possess his brother's land. Let him not breed in great numbers, for he will make a desert of his home, and yours. Shun him... for he is the harbinger of death." Internet Movie Database, Planet of the Apes (1968) Synopsis



Human intelligence is one of evolution’s most consequential inventions. It is the result of a sprint that started millions of years ago, leading to ever bigger brains and new abilities. Eventually, humans stood upright, took up the plow, and created civilization, while our primate cousins stayed in the trees.

Now scientists in southern China report that they've tried to narrow the evolutionary gap, creating several transgenic macaque monkeys with extra copies of a human gene suspected of playing a role in shaping human intelligence.

“This was the first attempt to understand the evolution of human cognition using a transgenic monkey model,” says Bing Su, the geneticist at the Kunming Institute of Zoology who led the effort.

According to their findings, the modified monkeys did better on a memory test involving colors and block pictures, and their brains also took longer to develop—as those of human children do. There wasn’t a difference in brain size.

Su’s monkeys raise some unusual questions about animal rights. In 2010, Sikela and three colleagues wrote a paper called “The ethics of using transgenic non-human primates to study what makes us human,” in which they concluded that human brain genes should never be added to apes, such as chimpanzees, because they are too similar to us.

“You just go to the Planet of the Apes immediately in the popular imagination,” says Jacqueline Glover, a University of Colorado bioethicist who was one of the authors. “To humanize them is to cause harm. Where would they live and what would they do? Do not create a being that can’t have a meaningful life in any context.”



Not to go all Cassandra on you, but...

At the story's heart is Caesar (Andy Serkis), a chimpanzee who gains human-like intelligence and emotions from an experimental drug. Raised like a child by the drug's creator, Will Rodman (James Franco) and a primatologist Caroline Aranha (Freida Pinto), Caesar ultimately finds himself taken from the humans he loves and imprisoned in an ape sanctuary in San Bruno. Seeking justice for his fellow inmates, Caesar gives the fellow apes the same drug that he inherited. He then assembles a simian army and escapes the sanctuary - putting man and ape on a collision course that could change the planet forever. Internet Movie Database, Rise of the Planet of the Apes (2011) Storyline


Chinese scientists have put human brain genes in monkeys—and yes, they may be smarter
Antonio Regalado, MIT Technology Review

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