Category Archives: Human Genetics

The coronavirus crisis has brought to light the societal downside of ignoring patterned, population-based differences. Consider the latest research findings of a specific gene highly prevalent in South Asian populations (but not European ones) that doubles the risk of respiratory failure from COVID-19. COVID has also revealed numerous other examples of susceptibility differences, with study after study (after study after study, and yet more studies) indicating likely population-based (racial) variation in COVID-19 immunity.

Early in the COVID pandemic, we raised the possibilitylikelihood reallythat the genetic make-up of sub-Saharan Africans is the most plausible explanation for why that populous region remains the global cold spot for both infections and deaths from COVID. This is an outcome wholly unanticipated by the medical establishment which unanimously believed the poorest continent in the world, with the worst health care systems, was likely to face catastrophic devastation from the disease. Instead, the opposite happened. Here is a visual representation of deaths per capita (as of March 14, 2022):

Combined with the fact that sub-Saharan Africa is the youngest region in the worldyouth brings fewer co-morbidities and age is the most significant factor in contracting and dying from COVID-19ancestry is likely a significant contributing factor to to the regions comparatively modest case and death count.

What genetic factors could be impacting COVID-19 infection and death rates? Research and informed speculation are already underway. An early study on the possible contribution of genetics to the SARS-CoV-2 infection found significant population-based differences in ACE2 receptors that modulate blood pressure in the cells located in the lungs, arteries, heart, kidneys, and intestines. Africans are considerably less likely than East Asians to express the ACE2 receptors, though slightly higher than Europeans, the researchers believe.

At least two studies show that blood type O could be associated with a lower risk of COVID-19 infection and reduced likelihood of severe outcomes, including organ complications. About 50 percent of Africans have blood group O, the highest in the world. Susceptibility to the coronavirus is negatively associated with having a genetic propensity to absorb Vitamin C, as is the case with black African populations. Across Africa, roughly 50 percent of people carry the Vitamin C-friendly variant and in some African countries, it is as high as 70 percent.

Do Neanderthal genes increase the risk of COVID-19?The answer is yes. In fact, the presence of a Neanderthal gene is the single biggest genetic risk factor for the novel coronavirus, roughly doubling the likelihood of getting the virus. This particular stretch of Neanderthal DNA is carried by around 50 percent of South Asians, 16 percent of those of European descent, but not in any native Africans.

Why have journalists mostly ignored this monumental story while health officials, well aware of this astonishing development, also remain mum? Its the stigma of being associated with those who acknowledge that human biodiversity is a realitythat there are population-based differences that impact disease susceptibility. In contrast to this deafening silence, we addressed the astonishing reality of the situation in Africa, and the strong social and ethical reasons why we should not ignore possible racial differences in susceptibility to COVID-19 (and other diseases).

It is really mind boggling why Africa is doing so well, while in US and UK, the people of African ancestry are doing so poorly, Maarit Tiirikainen, a cancer and bioinformatics researcher at the University of Hawaii Cancer Center, told us in an email. Dr. Tiirikainen is a lead researcher in a joint project at the University of Hawaii and LifeDNA in what some believe is a controversial undertaking considering the taboos on race research. The scientists are attempting to identify those that are most vulnerable to the current and future SARS attacks and COVID based on their genetics.

A spate of new ancestral-linked evidence was brought to light by the novel coronavirus, but a wider perspective shows decades of long-established research on the clear links between genetic ancestry and specific diseases. Because many disorders disproportionately affect poor or marginalized peoples, neglecting such findings can have the worst impact on those most in need. As the distinguished journal Nature has written:

Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry.. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities

For critics arguing to censor all talk of human biodiversity, are you willing to contend that such life-saving research should be supressed lest neo-Nazis begin bragging about both their lactose tolerance- and COVID-superiority? (That is in fact an argument advanced by some post-modernist sociologists and social equity promoting extremists.) Or, would it not be better to use data on genetic differencesthat is, on human biodiversityto advance science to help people who might otherwise die from coronavirus infection?

The growing evidence of the critical importance of pursuing the genetic analysis of populations brings to the fore a fascinating phenomenon in its own right: why many people who classify themselves as liberals or progressives remain reluctant to engage on the fact of evolved human biological diversity, despite overwhelming evidence. Even more startling, they not only wont talk about it, they reflexively attack anyone, including other liberals and progressives, who broach the subject.

This is dangerous territory. Although it is certainly true that all ideas are filtered through a prism of personal beliefs and cultural biases, its dangerous to hyperbolize that if some scientific evidence makes some uncomfortable, it should not be expressed. An overblown fear of racist misrepresentation of human genetics concedes the argument to bigots.

Indeed, by rejecting the fact of evolved human differences in some aspects of human development, well-meaning people undermine their own quest for greater social justice and racial equality. Its far more productive to openly, if carefully, embrace human genetic diversity in the same way we do with cultural diversitya position inspired by biologist E.O. Wilsons emphatic belief that we are not compelled to believe in biological uniformity in order to affirm human freedom and dignity.

Those who question research into human genetic diversity believe that evidence of racial differencebeyond obvious superficial features such as skin coloris socially divisive. It leads inevitably, they say, to racist musings about differences in intelligence and behavior. In the widely-held liberal view, humans are mostly a blank slate, with patterned human differences, random and mostly superficial. The idea that racial differences are more than skin deep is tantamount to promoting racialism (the belief that race determines human traits and capacities). And racialism, according to the analysis of liberal philosopher Michael Hardimon, provides a rationale for racism, slavery, colonization, or genocide:

It motivates the step from (a) representing another group as racially different to (b) taking these differences to be humanly important, to (c) regarding the other group as inferior, and (d) making it the object of hatred and contempt, to (e) imposing upon it involuntary servitude or (f) colonial rule, or (g) attempting the liquidation of all its membersa sequence of steps historically all too familiar.

In other words, if we begin by accepting racial difference, by this measure, critics say, we are on the slippery slope to justifying genocide. This goes to the heart of liberal concern about human biodiversity: the implicit belief that, if racial differences do exist and they are more than superficial, then racism (and worse) is nigh on inevitable. Unfortunately, casting the subject as totally off limits plays right into the hands of the racists themselves, letting them claim they are simply revealing the biological truths that their opponents wish to hide.

Why does this have to be the case? Why should possible evidence of human patterned biological diversity inevitably encourage racism? In fact, history suggests that ignoring this evidence is as likely or more so to promote racist notions.

A tried and tested means to reduce inter-group tension, one enthusiastically adopted by authoritarian regimes throughout history, is to impose cultural uniformity upon the wider population (an obvious recent example being the forced Sinicization of Tibetans, Uighurs and other ethnic groups in modern-day China). In more open societies today, however, cultural homogenization goes against the cherished liberal ideals of freedom and self-expression, where difference is not just to be tolerated but extolled. Except, of course, when focusing on the vexed question of genetic difference, where the ideal of uniformity in the name of equity is strictly enforced.

It neednt be this way. If we can come to value cultural differencedespite the troubling potential for social discordshould we not do the same with biological diversity? Here we can return to the broadminded moral arguments of the late E.O. Wilson:

Perhaps the time has come, he suggested, to adopt a new ethic of racial and hereditary variation, one that places value on the whole of diversity rather than on the differences composing the diversity. It would give proper measure to our species genetic variation as an asset . Humanity is strengthened by a broad portfolio of genes that can generate new talents, additional resistance to diseases, and perhaps even new ways of seeing reality. For scientific as well as for moral reasons, we should learn to promote human biological diversity for its own sake instead of using it to justify prejudice and conflict.

So what would it mean if we adopted Wilsons idealistic new ethic and came to promote rather than to deny deeper human genetic difference? Different human groups, ones that sometimes, but not always, raggedly match the folk categorizations of race, can indeed be genetically distinguishable due to their divergent evolutionary histories. Yet Australian Aboriginals, say, and northern Europeans (and indeed North American Inuit)populations that are almost literally poles apartalso share common ancestry; they are living proof of Wilsons point that, far from being isolated in distinct races, our species is one great breeding system through which genes flow and mix in each generation. Humans move around and fool around.

Here we can begin to address the question with which we began: Is it racist to research or write about human biodiversity? The short answer is no. While modern genomics does reveal broad populationsthat sometimes overlap with popular racial categories, the wider picture shows fuzzy-edged human groupings, sometimes with meaningful phenotypic distinctions and sometimes not. Depending upon how one organizes the data, there could be dozens or hundreds of population groups, with some meaningful connections among groups.

This might appear a good point to conclude. There are numerous scientific and moral reasons to embrace rather than reject human biodiversity in the same way we do or try to do with human cultural diversity. To end here, however, would be to avoid the central, but often unacknowledged, liberal objection to the concept of human racial and hereditary variationwhat it suggests about possible differences in cognitive abilities and behavior. Everyone can acknowledge some patterned human differences shaped by the serendipity of evolution, such as Inuit body shape, say, or East African domination of long distance running driven by their unique physique and physiology. The subject becomes most toxic, however, when it extends to prickly yet nebulous issues such as human intelligence or character. We will explore these issues with care, underscoring each individuals uniqueness.As Wilson himself noted, Hope and pride and not despair are the ultimate legacy of our genetic diversity.

Jon Entineis the foundingexecutivedirectorof theGenetic Literacy Project, and winner of 19 major journalism awards. He has written extensively in the popular and academic press on agricultural and population genetics. You can follow him on Twitter@JonEntine

Patrick Whittle has a PhD in philosophy and is a freelance writer with a particular interest in the social and political implications of modern biological science. Follow him on his websitepatrickmichaelwhittle.comor on Twitter@WhittlePM

Excerpt from:
Part II: How COVID upended the taboo on limiting constructive discussion about human biodiversity - Genetic Literacy Project

Ancestor Trouble does what all truly great memoirs do: It takes an intensely personal and at times idiosyncratic story and uses it to frame larger, more complex questions about how identity is formed. Using her own family tree, with its mix of colorful characters, closet-lurking skeletons, and truly vile monsters, Newton recounts the tall tales about these folks she grew up with before revealing what dogged and thorough research has turned up about their actual lives. Sometimes, these ancestors reveal themselves to be of surprising character. A great-grandfather, Charley Bruce, existed in her mother and grandmothers stories primarily as a man whod once killed another man with a hay hook. But through scraps of news accounts and trial records, Newton discovers a fuller picture: Charley was attacked by a former friend whod been convicted of sexual assault of a young girl; Charley had testified against him at trial, and the subsequent attack was revenge, the fatal blow struck by Charley an act of self-defense.

Others are far less redeemable. Newton turns up far more slave-owners in her lineage than she was expecting, not just on her racist fathers side but on her mothers, as well. And even some potential heroessuch as Mary Bliss Parsons, a distant ancestor in New England once accused of witchcraftturn out to be far from any kind of role model. Maude Newton, the ancestor after whom Maud (ne Rebecca) chose her pen name, was described to her by her mother and grandmother as an idiosyncratic and irascible iconoclast, a woman who chose to live an independent life in Texas. An autodidact who designed and built her own house, and a writer to boot, Maude seemed to have been a kindred spirit, or at least so Newton had hoped. But Maudes published writings (which took the form of a newspaper column from Drew, Mississippi) reveal a figure enamored with George Wallace and Barry Goldwater, who exhorted her readers to defy the Civil Rights Act to save their little white girl[s] from little Negro boys. Summing up this disappointing revelation, Newton writes, Im sorry that Maudes writing turned out to be what it was, but Im not sorry I found it, remembering, as she does throughout, that we do not dispel the ugliness of the past by ignoring it but by recognizing it and, ultimately, seeking restitution for the sins of the fatherand of the great-aunts, as well.

Family stories are one way our forebears pass down legacies to us; Newton also questions the inheritances of genes and heirlooms. The net effect is like watching a deft magician perform one trick after another and then patiently explain the secret and how youve been fooled. Newton will offer scientific research to suggest, for example, that mental health or temperament might be something that could be passed down generations, supplemented with detail from her own life (Later I learned that Charley had died from manic exhaustion, she says of her great-grandfather, and I remembered my own sleepless nights and scrabbling brain). But then shell swiftly move to unpack many of the problems with the same theory. She highlights not only the shaky scientific basis for our beliefs (Our science is only as good as the questions we ask, she reminds us) but also, quite often, the racist and ableist ideologies that underpin them. The idea of inherited mental traits, for example, which gained currency around the dawn of the twentieth century and still holds sway in popular imagination (and not just with people like Newtons father), was itself pushed heavily by eugenicists like Henry H. Goddard and his influential 1912 book, The Kalikak Family: A Study in the Heredity of Feeble-Mindedness. But Goddards central claim that all of the descendants of Martin Kalikak and his wife were normal, while those who descended from an affair with a feeble-minded barmaid turned out to be equally feeble-minded, was later found to be based entirely on altered and invented data.

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The Weight of Family History - The New Republic

Since the first human genome was sequenced in the early 2000s, scientists have touted the breakthrough as a blessing to humanity one that holds promise to promote human health and enhance medical treatment the world over. But around two decades later, the benefits of that scientific advancement have barely rippled out beyond Europe and North America. As of 2018, people of European ancestry who represented approximately 16%of the world population at the time made up 78%of all individuals whose genomes have ever been collected and studied.

DNA profile from a human sample.

Over the last decade or so, international studies on human population genetics have begun to expand genomic libraries to encompass regions of the Global South including Southeast Asia, where I am a science reporter, and the Pacific islands. These international studies, often led by Western scientists, have contributed to a more global understanding of ancient patterns of human migration and evolution. But on some occasions, theyve also sidestepped local regulatory agencies in the developing worldand ventured into murky research ethics terrain as a result.

A recent example a case that simultaneously illustrates the promise, pitfallsand pressure points of international genomics research comes from the largest genetic study ever conducted in the Philippines, published last year in the Proceedings of the National Academy of Sciences. A team led by Mattias Jakobsson of Uppsala University in Sweden and Maximilian Larena, who was a researcher in Jakobssons lab at the time, collected and analyzed DNA samples from more than 1,000 Filipinos representing 115 Indigenous groups. The study determined that todays Filipino population descends from at least five distinct waves of human migration, spanning thousands of years a finding that they said contradicted the prevailing theory of how humans populated the islands.

One could see the Uppsala study as a model of international collaboration. The project was endorsed by the Philippines National Commission for Culture and the Arts, a government body that coordinates, fundsand makes policy for the preservation, developmentand promotion of Philippine arts and culture. It was also done in partnership with more than a dozen local Indigenous and cultural groups in the Philippines; the papers appendix acknowledges more than 100 Filipinos who assisted with the study in some way, and Larena is himself Filipino. And key portions of the research plan were approved by an ethics review board in Sweden.

But many bioethicists would argue that it is not enough for researchers who do a human genomic study on foreign soil to merely collaborate with local groups. Various ethics guidelines on health-related research including UNESCOs International Declaration on Human Genetic Data and international ethical guidelines published by the Council for International Organizations of Medical Sciences, or CIOMS, in collaboration with the World Health Organization advise researchers to seek approval from an ethics committee in the host country. Such reviews are critical, bioethicists say, because cultural and social considerations of research ethics might vary between countries. In low-resource countries especially, ethics reviews are essential to protect the interests of participants and ensure that data are used in ways that benefit local communities.

Nowhere in Larena and Jakobssons paper, or in any of the subsequent publications based on the Philippines study, does the Uppsala team mention obtaining such an ethics approval in the Philippines and Philippines officials say they never granted the team such an approval. Asked whether his group had obtained a formal ethics clearance in the Philippines, Jakobsson pointed to the projects endorsement from the National Commission for Culture and the Artsand wrote that part of the commissions mandate is to ensure that the research they support is in accordance with the ethical principles of research involving participants from the Indigenous communities. But the NCCA primarily supports research that is cultural, not scientific, in nature, and a government website outlining the commissions mandate, powersand functions makes no mention of any duties related to research ethics.

In a 2021 letter, the commissions executive director wrote that the agency has no mandate or authority to give ethical clearance and did not give ethical clearance for the Uppsala study. (I reached out to the commission for this story but did not receive a response.)

A failure to secure formal ethics clearance might be understandable if there were simply no official Filipino agencies equipped to provide that clearance. But the Philippines has such a body the National Ethics Committee, or NEC, which falls under the jurisdiction of the Philippine Health Research Ethics Board and the Uppsala researchers were no doubt aware of this. In 2014, as the researchers were laying the groundwork to begin collecting human samples, they actively sought the NECs approval.

That approval was never granted. Marita Reyes, then the chair of the NEC, said she noticed problems with the initial Uppsala application. For instance, it did not clearly describe how research participants would be recruited, and it lacked the proper paperwork for researchers who intend to ship genetic materials overseas, she told Undark in an email. Reyes asked the Uppsala team to fix the issues and also recommended that they collaborate with local researchers who were doing similar work at the Philippine Genome Center.

According to Jakobsson, the Uppsala researchers took issue with the stipulations levelled at their application, and they say the prospective collaborators at the Philippine Genome Center made troubling demands regarding control of the collected samples. Ultimately, the researchers withdrew their application altogether. Their rationale: They say their population genetics study was cultural, not health-related, and therefore did not fall under the jurisdiction of the NEC or the Philippine Health Research Ethics Board. Given that your good office does not have regulatory mandate on the nature of our study, Larena wrote to Reyes in an email, we humbly withdraw our application. In the ensuing months, the Uppsala team would go on to collect DNA from more than 1,000 Filipinos without ever receiving express ethics approval from the NEC.

The case created an uproar in the Philippines. In a public statement, Allen Capuyan, chairperson of the Philippines National Commission on Indigenous Peoples, condemned the study, saying the researchers showed a blatant disregard of critical policies governing scientific research in the Philippines. Leonardo de Castro, a Filipino bioethicist who now chairs Philippine Health Research Ethics Board, asserted that the Uppsala study did fall under the NECs jurisdiction, and he called on the journal that published the Uppsala work to issue a retraction. (I first learned of the controversy in 2018 from officials at the Philippine Health Research Ethics Board; Maria Corazon De Ungria, a laboratory director at the Philippine Genome Center, later contacted me about the matter as well.)

Meanwhile, the Uppsala researchers have maintained that they are absolutely certain that they abided by basic ethical principles of research involving humans, and they say that investigations by a Swedish ethics review board, by Uppsala University itself, and by scientific journals have cleared them of any wrongdoing.

Nevertheless, I believe the case exposes a glaring shortcoming in the regulation of international genomics research: Even if bypassing a formal ethics review does not violate the letter of the law on human genomic research, it at least seems to go against the spirit of trust and transparency that are the foundation for healthy international scientific collaboration principles enshrined in the UNESCO and CIOMS guidelines. The Uppsala team is hardly the first to wade into this gray area of research ethics. In 2018, I wrote about a team of mostly Danish and American scientists who conducted a genetic study of Bajau traditional divers in Indonesia and also failed to obtain ethics approval from a local review board.

Was the Uppsala team right to conclude that their study fell outside the jurisdiction of the Philippines health research regulatory framework? Some people seem to think so. In a letter of support to the researchers, an attorney with the National Commission for Culture and the Arts the Philippines group that supported the study affirmed that the nature of the Uppsala project was exclusively cultural and fell under NCAAs jurisdiction, rather than that of the National Ethics Committee or the National Commission on Indigenous Peoples. Hank Greely, a professor of law at Stanford University who specializes in biosciences, including bioethics, said that the study published in PNAS didnt appear to be health-related and suggested its reasonable to argue that health research guidelines shouldnt apply in this case, although that wouldnt mean that no ethical standards should apply.

But other bioethics experts including Triono Soendoro, the chair of the Indonesian Society of Ethics Committee for Research and Services say that ethics standards like those developed by CIOMS and enforced by the Philippine Health Research Ethics Board were clearly meant to apply broadly to research involving human biological samples, even studies that have non-medical purposes. Population genetics research that identifies subjects by social or ethnic group, as the Uppsala study does, is certainly covered by CIOMS, said Eric Juengst, a bioethicist and professor at the University of North Carolina at Chapel Hill.

Human genomic science is too important, too consequential, to allow this precarious state of affairs to persist. If we want science to serve the whole of humanity, we need a strong set of universally binding rules on research ethics rules that clearly give local authorities a voice on matters of research ethics in all studies involving human genetic sampling, not just those that are obviously medical in nature.

In the Uppsala case, for instance, a formal ethics review might have offered important safeguards to ensure participants were fully aware of how their samples would be used and stored. Although participants signed informed consent forms that laid out many details of the research, a copy of the form obtained by Undark did not mention that samples would be shipped out of the country, to Sweden, for sequencing and analysis. This information could conceivably have influenced a subjects decision to participate.

Formal ethics reviews are also crucial for ensuring that low-resource countries can freely and independently access data that might benefit the health and wellbeing of their people. Even genetic data obtained for purposes unrelated to health may later prove beneficial for medical purposes. More than 1,000 samples of genetic data collected in the Uppsala study are now stored in the European Genome-Phenome Archive, where a Data Access Committee now has sole power to determine who can use it for future studies although one condition must be that such research is in accordance with consent provided by study participants. (The archives website doesnt specify the members of the Data Access Committee assigned to the Philippines data set, but it lists Larena as the contact person.) There is no guarantee that research institutions in the Philippines will ever be able to make use of the largest human genetic dataset ever collected on its own soil.

The international scientific community must be proactive in raising the standards of global research ethics. Prestigious journals, the gatekeepers of science, should ensure that researchers who collect human DNA samples make every effort to secure formal ethics approvals in the countries where the sample collection is performed. They should also be transparent about investigations of ethics misconduct and involve ethicists from developing countries in those investigations whenever possible.

Human genomic science should not stop at merely satisfying our curiosity. It should also serve the poor and the marginalized. Otherwise, if history is any guide, it will lead only to increasingly extreme disparities between the Global North and the Global South.

This article was originally published on Undark. Read the original article.

See more here:
Genomics' ethical gray areas are harming the developing world - ASBMB Today

Mount Desert Island Biological Laboratory, a non-profit research institute in Maine, is funding a new initiative to increase the use of nonmammalian models in early drug development. The initiative, dubbed MDI Bioscience, aims to turn to species like zebrafish (Danio rerio), C.elegans, axolotls (Ambystoma mexicanum), and African turquoise killifish (Nothobranchius furzeri) to evaluate potential therapeutic compounds at scale before theyre tested in mammals or enter human clinical trials, potentially hastening and honing the decision-making process in early drug discovery and reducing the reliance on mammals such as mice. MDI Bioscience hopes to evaluate drugs before money is spent on costly mammal research, to speed the drug development process, and reduce the number of mammals, and animals in general, used in scientific research. Jim Strickland, the director of MDI Bioscience, says that these goals are aligned the general research practice to reduce, replace, and refine (three Rs) animals in research. The three Rs seek to address the potential ethical issues involved in animal research, which become heightened in higher order animals like rodents and primates.

The Scientistspoke to Strickland about the program and its goals.

Jim Strickland

Anna Farrell, MDI BIOLOGICAL LABORATORIES

Jim Strickland: We wanted to enable more efficient discovery of new drugs and new pharmaceutical compounds by using nonmammalian species such as zebrafish, C. elegans, axolotls, in order to help pharmaceutical companies better characterize early-stage molecules, and be able to quickly select those molecules with the greatest promise before more significant investment is made in mammal studies and other regulatory based activities that we know take quite a bit of time and expense to complete in preparation for human clinical studies.

JS: Were building this organization from the ground up with an eye toward the future. Well have a state-of-the-art facility to work from and to run these studies from, with the goal that eventually, as these models become regulatory models, well be able to quickly transition to a full GLP [good laboratory practices] lab . . . [which are] the requirements that govern whether or not data can be accepted by the FDA for regulatory decisions.

Certainly, to start out and as we grow, we want to leverage the incredible expertise that already exists in the lab . . . . The faculty in the lab . . . will stay true to their basic science objectives, but when their expertise is additive to answering key questions for drug discovery, theyll be consulted and lab staff will also participate in work initially as we grow.

JS: Our primary model at this point is using zebrafish, which are well known as being excellent models for replicating both human physiology, human genetics, and human disease. Zebrafish share over eighty percent homology with human disease-causing genes. They provide excellent comparability to humans in terms of their genetic composition. And that makes them very attractive models for early-stage drug discovery. But additionally, C. elegans . . . also provide a novel model for high throughput assays for evaluating toxicity in early-stage drug development. In the future, were working with two novel nonmammalian models, the axolotl, which has incredible potential to help teach us a lot about how tissue is regenerated. And then also, in a similar light, the African turquoise killifish also has some really unique properties that are specific to tissue regeneration that make it really interesting in terms of evaluating these mechanisms and potential ways of rescuing function.

JS: There are a number of benefits to the nonmammalian models. For one, they can be easily imagedzebrafish embryos are transparent. They work well with microscopy, and that lends the model to high-throughput screening because you can generate a large number of embryos and test multiple different compounds at the same time or at different concentrations. That gives you a really robust early assessment of a compound library to see if youre seeing a desired effect or undesirable toxicity. Then, compared to mammalian species, theyre very cheap to work with. The cost of mammalian research keeps going up and the use of zebrafish and other models is cost and time-efficient compared to mammalian species. . . Lastly, theres tremendous similarity between humans and zebrafish on a structural and a cellular level. If you were to take a slice of a kidney from a human and take a slice of a human or a kidney from zebrafish, if you looked at them under a microscope, theyre almost indistinguishable.

JS: Yes. Zebrafish in particular are becoming more widely used in early phase drug discovery. Were not the only lab that's focused on zebrafish for early-stage work. Theres really a growing consensus that these models can help reduce the use of mammals in the future.

But from a regulatory perspective, were not there yet. The ability to substitute nonmammalian models for mammal models and support . . . an application for human clinical studies . . . isnt currently something that is achievable. However, I think theres a growing amount of data . . . that shows that translation from zebrafish to mammals and ultimately to humans.

JS: Most [studies on drugs that make it to human clinical trials], and those in mice, or rats or dogs follow very specific guidelines set up by the ICH [International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use]. Theres a very prescribed pathway for using mice, rats, and dogs. Thats a different focus than what were working on with zebrafish and C. elegans. What were looking to do is to create genetic models where we can use CRISPR-Cas9 gene editing to essentially replicate the genetic condition that a drug might be trying to target. The important thing is that at this point in development, which is well before you would be contemplating the toxicology studies for initiation of human clinical studies, were able to create those disease models, and also then allow for new drugs to essentially confirm whether or not, based on the disease pathophysiology, theyre actually able to restore function . . . well before they get to regulatory studies.

Most drug discovery work is focused on single-cell systems. Cell analysis is still the predominant mechanism for determining whether or not theres an efficacy signal for a compound. Bringing whole systems biology into drug development brings the ability to ask if there are any downstream toxicology effects beyond the single cell that would involve any other organ systems, or see if there are undesirable secondary effects on a nontarget organ that need to be considered and may ultimately present a problem in later development. From that perspective, it gives you the ability to accelerate the use of whole systems biology earlier in drug development . . . as opposed to waiting to later phases to introduce mammal species.

JS: Our hope is that we can help pharmaceutical companies become more efficient in finding those diamonds in the roughthe molecules that have great potential to influence human disease and sufferingand that using these technologies will drive some of the costs out of development by helping identify those compounds that should move forward, those compounds that should move forward earlier in development, before significant costs are incurred. Ultimately, if we can make drug discovery more efficient, then that translates into reducing costs of drugs, and drug development overall. But the significant costs associated with drug development, which have been estimated at 2.5 billion [US dollars], are tough to reckon with as long as only one in five thousand drugs make it to market.

JS: I think its too early to know whether these models are ultimately going to be more predictive than the mammalian models. But certainly, theres always going to be a need to evaluate novel compounds in other species before they move into and to humans.

JS: These are great models to investigate efficacy at the molecular level, but theyre also great models for investigating rescue of a phenotype. Phenotype drug discovery is certainly a very hot topic because its been shown by some studies to have a higher success rate, and actually finding drugs that are successful and make it to market. Many of these models have excellent phenotypes of disease that enable phenotype-based drug discovery approach. There are strong phenotypes that can be used along with these models that make them attractive.

JS: For example, we can use indicator species [and] fluorescent biosensors. If theres an upregulation of a particular biomarker, the fish or the embryo will actually light up in the presence of those biomarkers. Simple things, like retinal circulation in the eye, arrhythmias of the heart, or glomerular function in the kidney. Even velocity of movement can be good phenotypes for specific diseases.

JS: In the short term, the goal is to provide a really reliable service to pharmaceutical companies that helps to answer either key questions around mechanisms of disease that then provide good feedback on what a desired target would be, or actually replicating models and disease so that if theres a particular target that theyre going after, we have the right tool to help them evaluate compounds and their efficacy and toxicity early on. The longer-term goal is to then take it to the next level and work with regulators in the US and Europe to have these models accepted and to be able to use them. I dont think theyll ever supplant the use of mammals, but they will certainly be good alternative models in cases where they have a really predictive effect.

Editors note: This interview has been edited for brevity.

Correction (Match 15): The original caption for the photo of Jim Strickland was incorrect.The Scientist regrets the error.

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Oust the Mouse: A Plan to Reduce Mammal Use in Drug Development - The Scientist

Ministerial foreword

The UK is a global leader in genetics and genomics. This has never been more evident than in the last 2 years, where collectively we have led the world in virus and human genome sequencing to counter the COVID threat and added 500,000 whole genome sequences to the UK Biobank research dataset.

In 2020 we published our overarching Genome UK the future of healthcare strategy, which set out our vision and clear aspirations for how we will transform genomic healthcare over the next 10 years. In 2025 we will be marking the half-way milestone in the Genome UK 10-year timescale, and measurable progress in the next 3 years will be critical to demonstrating successful delivery. To achieve this progress, we have set out here a series of shared commitments for UK-wide implementation. We are committed to working together along with our delivery partners across the UK to implement these commitments, and, in doing so, realise the potential of genomic healthcare for the benefit of patients across the UK and around the world.

In developing these shared commitments, we have engaged in open dialogue and collaboration across the UK, recognising the differences in our respective healthcare systems and structures.

We believe that these shared commitments will help to ensure better coordination of our joint ambitions for genomics research and healthcare so that these can flourish in each of our nations and across the UK. Through better UK-wide coordination and collaboration, we will further strengthen our ability to share expertise and establish new collaborations and partnerships with others worldwide, securing our global leadership in genomics and the wider life sciences and ensuring we remain an attractive location for research and development investment. These shared commitments present a clear statement of our resolve to work together to deliver better health outcomes across the UK.

In September 2020, the UK government published Genome UK the future of healthcare, setting out the governments 10-year strategy to create the most advanced genomic healthcare system in the world, delivering better health outcomes at lower cost. The strategy also describes a vision for the UK to be the best location globally to conduct genomics research and grow new genomics healthcare companies, with a goal to increase private sector investment.

We want to ensure that patients across the UK can benefit fully from genomic healthcare, through a more preventative approach, faster diagnosis, and personalised and better treatment leading to better long-term outcomes. Researchers and industry will be supported in their research and its applications and incentivised to secure the UKs position at the forefront of genomic research in the world.

In May 2021, the UK government published its 2021 to 2022 implementation plan for Genome UK, setting out priority actions for the financial year 2021 to 2022 in England, with contributions from the Scottish and Welsh Governments outlining their approach to implementation.

Genomics is a fast-moving field and we have therefore adopted a phased approach to research and implementation which will allow us to review our commitments and take action to reflect emerging science and latest research findings. The 2021 spending review, which set departmental budgets and devolved government allocations to 2024 to 2025, provides an important and timely opportunity to collectively agree high-level commitments with which we will progress implementation of the Genome UK vision over the next 3 years. In 2025 we will be marking the half-way milestone in the Genome UK 10-year timescale, and measurable progress in the next 3 years will be critical to demonstrating successful delivery.

There are many areas where UK-wide collaboration in genomics has already been successful, the SARS-CoV-2 genome sequencing in response to the COVID-19 pandemic provided an excellent example of this. In the coming years, UK-wide coordination will continue to provide significant opportunities to enhance benefits for patients, such as joint genomic technology evaluation and better integration of genomic and health data in secure trusted research environments.

We remain committed to delivering genomic healthcare across the UK, while recognising the devolved nature of healthcare policy and the resulting different approaches to the development of genomics in healthcare. In this context, our shared commitments form part of our second phase of Genome UK implementation, setting out joint, UK-wide, high-level commitments for the period 2022 to 2025. Recognising the devolved responsibilities, the shared commitments will be followed by 4 separate implementation plans, with the UK government and the devolved governments each aiming to publish these by the end of 2022. The separate implementation plans will reference the shared commitments, incorporating and building on them, in addition to setting out more detailed commitments for each government.

In taking these commitments forward, we will be guided by the 8 shared principles stated in Genome UK and in particular the following principle, which will underpin our approach to working together:

We will work together across the UK to realise the potential of genomics for the benefit of patients and ensure that the genomics services thrive in each nation. We will engage in open dialogue and collaboration, recognising that health is devolved and there are differences in NHS structures and systems.

The shared commitments have been developed in collaboration with the genomics community and our delivery partners. High-level coordination and delivery progress will be considered by the Genome UK Implementation Coordination Group which is led by the Office for Life Sciences and has UK-wide representation. This arrangement will allow the UK government and the devolved governments to continue with, or put in place, their own reporting and governance arrangements.

The National Genomics Board is chaired by the Minister for Technology, Innovation and Life Sciencesin the Department of Health and Social Care (DHSC) and brings together senior decision makers and representatives from across the genomics sector, including senior officials from the devolved governments. The purpose of the board is to provide strategic oversight and to work collaboratively across the UK to harness the benefits of genomic healthcare ultimately helping to ensure delivery of the vision set out in Genome UK.

As part of these shared commitments, we agree that UK government and devolved government ministers will engage regularly on the outcome of National Genomics Board discussions.

Finally, the UK genomics healthcare policy landscape is vibrant and complex, with a wide range of diverse organisations either delivering or overseeing clinical services and policy programmes. To progress the commitments in this agreement, we will seek to minimise duplication of effort and resource by sharing information about existing processes, groups and structures and, with mutual agreement, utilise these when appropriate.

The following commitments are set out across the 3 pillars of Genome UK:

And the 5 cross-cutting themes covering:

Genome UK vision: tohelppeople live longer, healthier lives byusing genomic technologiesto identifythegenetic causes for disease, to detect cancers earlier and provide personalised treatments to illnesses.

Genomic technologies are already revolutionising the way in which patients are diagnosed and treated across the UK and this is set to accelerate rapidly in the years ahead.

At the same time, the devolution of healthcare and clinical service commissioning means that there are differences in how genomic healthcare has so far been implemented across the UK. However, we have a wealth of experience and leadership in diverse areas of genomics that can be shared across the UK to drive improvements in patient care. For example:

All of these are examples of healthcare systems in each UK nation beginning to transform through adoption of genomic healthcare. It is our ambition to look at current areas of difference in approach and work on how we can address these for patient benefit. For example, the Genomic Test Evaluation Working Groups established by NHS England and Improvement have been designed to bring together UK-wide expertise to collectively evaluate new genomic science and technology for genomic testing of rare and inherited diseases, cancer and for pharmacogenomics, enabling commissioning decisions to be made in our respective health services.

Pathogen genomic sequencing is another area where UK-wide collaboration is important and never more so than in our collective tackling of the COVID-19 pandemic.

At the beginning of the pandemic, in April 2020, the COG-UK (COVID-19 Genomics UK Consortium) was set up to provide a UK-wide SARS-CoV-2 genome sequencingcapacity. COG-UK supported public health agencies in the analysis of SARS-CoV-2 to identify and monitor variants of concern and to track the introduction and spread of COVID-19.

Since 2021, delivery of a national SARS-Cov-2 genomics service has been led by the 4 national public health agencies working with partners including the Wellcome Sanger Institute and CLIMB-COVID. Coordination across the UK was overseen by the UK Strategic Public Health COVID-19 Genomics Advisory Board. At its final meeting the board endorsed the transition to a wider UK Pathogen Genomics Board. Work to take this forward will commence in financial year 2022 to 2023. To date, the UK has shared over 2.25 million genomes on public databases with the international community.

The UK Rare Diseases Framework, published in January 2021, is another important initiative that fosters UK-wide collaboration and outlines a national vision for how the UK will improve the lives of those living with rare diseases. As around 80% of rare diseases have an identified genetic origin, the UKs strengths in genetics and genomics have clear potential to accelerate diagnosis and improve understanding of rare conditions, thereby driving improvements in care for patients with rare disease.

Finally, while diagnosis and personalised medicine, and research form distinct pillars of Genome UK, we are clear that they cannot be implemented in isolation. Our shared principles state that health care systems and research programmes (including those funded by the medical research charities as well as industry) will work in partnership for patient benefit, and it is this interaction and partnership that leads to the many exciting and important advances in genomic research and its applications, opening up new routes for diagnosis and novel treatment opportunities. We are therefore committed that all parts of Genome UK should interact with and cross-fertilise each other to ensure high-quality research outcomes, which are already leading to improved diagnoses for UK patients, more personalised treatment and better patient outcomes.

Our shared commitments are:

NHS Wales (via the Welsh Health Specialised Services Committee) works closely with NHS England and Improvement regarding the implementation of advanced therapy medicinal products (ATMPs) and the enabling pathways needed from the genetics service. This is achieved by NHS England and Improvement sharing their horizon scanning information with NHS Wales to inform capacity planning in Wales for ATMPs and the associated genetic services impact. NHS Wales is also well represented within the National Institute for Clinical Excellence (NICE) committee structures, including the Highly Specialised Technology Committee, which has primary responsibility for considering rare disease ATMPs, which further enhances horizon scanning and involvement in decision making. NHS Wales is also represented within the NHS England and Improvement Specialised Commissioning processes, including attendance at the Rare Diseases Advisory Group.

Genome UK vision: use genomics to:

Genomics is changing the future of health and medicine, and has the potential to transform our model of healthcare from treating illness and disease to preventing illness, or detecting it at very early stages, and supporting healthy lives. Prevention and early detection are key objectives for our healthcare system benefitting the still healthy individual through early, and often cheaper, health interventions, and also benefitting the patient at early stages of diseases offering earlier, more effective treatments. In most cases, early intervention will improve health outcomes, while also reducing treatment and care costs and helping to ensure the sustainability of the NHS into the future.

Screening is the process of identifying healthy people who may have an increased chance of developing a disease or condition, thereby allowing individuals to receive more frequent monitoring or for treatment to be initiated at an earlier stage. Genomic technologies have the potential to play an important role in screening, for example via whole genome sequencing or through the generation of polygenic risk scores, however there is work to be done to consider and address some of the ethical and privacy concerns raised by these technologies, as well as evaluating their utility in our health service. The UK National Screening Committee advises ministers and the health services across the UK about all aspects of screening and will play an essential role in appraising the viability, effectiveness and appropriateness of any new screening programmes.

We will collectively investigate the value of new genomic technologies, such as polygenic risk scores (PRS), that have the potential to identify those at highest risk of future disease and who would benefit from enhanced screening or targeted treatments and health interventions. The concept ofPRS derives from genetic analyses of participants in UK Biobank, the largest and most intensively genetically and phenotypically described longitudinal cohort anywhere in the world, linking into the rich UK health record systems. PRS combines the effects of very large numbers of genetic variants to identify people who are at particularly high risk of a condition. PRS have the potential to transform public health, but many questions remain before determining whether and how they can be used routinely at scale including the most robust disease applications for PRS and how the technology might be rolled out in the health service.

Our shared commitments are:

The UK National Screening Committee (UK NSC) advises ministers and the NHS on screening by drawing on research and consulting stakeholders. Some rare conditions need a more detailed consultation particularly when the science is complex and the evidence more limited. An example of this is tyrosinemia type 1 (TYR1), a very rare serious genetic condition. Newborn blood spot screening for TYR1 could potentially identify affected babies sooner, so they could be treated earlier.

The UK NSC commissioned Warwick University to build a model which compared what happens now with what would happen if screening was introduced. The model was based on an estimate of 7 babies being born each year with TYR1. Without screening, the model predicted that 4 of the 7 would be detected before symptoms develop. With screening, it modelled that all 7 would be picked up.

The UK NSC team used cohort data and information from other countries to provide evidence to support the screening pathway from the point of electronically identifying the babies to be tested, to the point of babies screening as positive and treatment outcomes. The team also worked with experts to understand how it is to live with tyrosinaemia and gain views of the benefits and harms of treatment options. These case histories were used to provide data for the model and to illustrate the consultation document.

The model concluded that screening for TYR1 would do more good than harm, but the costs per unit of additional benefit (quality-adjusted life years, QALYs) are high compared with NICE thresholds. The UK NSC is now consulting on whether it should recommend TYR1 screening given the estimated costs combined with uncertainty around aspects of the evidence. This process is one example of how the UK National Screening Committee uses modelling, expert views and consultation to provide a recommendation on whether an end-to-end screening programme, such as those based on genomics tests, is offered to patients. Delivery of screening programmes is the responsibility of the NHS in each nation.

Genome UK vision: continue to lead the world in genomic research.

The UK has been at the forefront of discovery-led and translational genomics research for decades and we are home to a number of internationally leading genomic research assets. UK Biobank has sequenced the exomes and whole genomes of its 500,000 participants which represents the largest collection of genome sequences anywhere in the world, all of which are linked to participants detailed NHS health records. Similarly, with the 100,000 Genomes Project, Genomics England holds the largest global collection of whole genome sequences from patients with cancer and rare diseases. Both UK Biobank and Genomics England are now also linking imaging data to already available clinical and genomic datasets.

The UK is also a world-leader in clinical and healthcare research thanks to our exceptional health and care research ecosystem including the NHS, world class universities and research infrastructure (including that funded by the National Institute for Health Research in England, Health and Care Research Wales, Health and Social Care Research and Development Division in Northern Ireland and NHS Research Scotland), a strong life sciences sector, and world class medical research charities and regulators.

Our joint vision for UK clinical research delivery highlights clinical research as the single most important way in which we can improve healthcare by identifying the best ways to prevent, diagnose and treat conditions. The UK is already one of the top 3 destinations for delivery of commercial early phase trials and delivered 12% of all global trials for innovative cell and gene therapies in 2020. Our combined strengths in genomics research, clinical genomics and clinical research, therefore, now offer unique opportunities to identify and approach patients who, as a result of genomic or genetic diagnosis, may be eligible for specific studies and who may in the future form part of a recallable clinical cohort for clinical trials, to discover new treatments in rare and common diseases.

The UKs investment and expertise in genomics mean that we now have an unparalleled opportunity to use genomic research assets to drive the next generation of life sciences discoveries. We will therefore work together to support post-pandemic recovery and growth in clinical research to deliver genomics-enabled clinical trials and support the growth and research and development of innovative genomics-focused companies.

In England, the Department of Health and Social Care will publish the final version of its data strategy Data Saves Lives in Spring 2022. The strategy sets out the critical role of health and research data in the transformation of the health and care sector. The current draft strategy includes commitments that will empower researchers across the UK with the data they need to develop life-saving treatments and new models of care, make progress towards bringing together genomics data assets and work with NHS England and Improvement to ensure genomic data generated through clinical care is fed back into patient records. This includes safe environments to securely analyse peoples sensitive health data such as the rich genetic and genomic data hosted by Genomics England, UK Biobank and Our Future Health, alongside one of the worlds most comprehensive collections of disease registries.

Another area where the UK life science sector has a unique opportunity to coordinate, collaborate and combine our expertise is functional genomics. Whole genome sequencing and other genomic tests have identified thousands of genetic variants known to be implicated in disease pathogenesis. But relatively little is known about their function and the challenge now is to understand how these variants mediate their effects, both in order to further our understanding of disease and to speed up successful drug development. Novel molecular and cell biology tools, including single cell sequencing, dynamic gene expression profiling, and systematic CRISPR, combined with insights from genomic datasets and integrated with advanced imaging and pathology, will provide opportunities for high throughput approaches to understand the role of variants and identify novel drug targets. The Medical Research Council and UK Research and Innovation partners, as major funders of discovery and translational science and research, are well placed to convene and coordinate such an initiative.

Given the rapid advances in large-scale genomic and other -omic assays, many of which utilise disruptive technologies that have been developed within the UK (such as Illumina and Oxford Nanopore), the UK is extremely well placed to take advantage of research assets that combine genomic and other -omics data at scale. With large-scale genomic and metabolomic data already available, the UK Biobank a UK-wide and internationally renowned research asset has the ambition to add proteomic data on 500,000 participants to characterise the molecular profile of its study participants in order to further power impactful life sciences research. In addition, its ambition to incorporate the use of long-read sequencing technologies will greatly improve the understanding of the impact of structural variation on human disease and wellness, and may additionally lead to the UK Biobank becoming the worlds largest epigenetic database.

Our shared commitments are:

Genome UK vision: the UK model will be seen as a leader in strong and consistent ethical and research governance of genomic data and apply regulatory standards that support rapid healthcare innovation, and maintain public and professional trust.

Genomic data is unique to every individual. Although small genetic changes will occur in different cells and tissues in our body throughout our lives, our genome will remain our constant, unique identifier. People and patients are therefore right to demand that their genomic data is handled sensitively and securely. The possibility of creating a life-long individual genomic data resource generates distinct questions regarding who should have legitimate access to this data and how, when and to what purpose it should be analysed, processed and communicated to the individual. Other important issues include ensuring that patients have sufficient understanding to support autonomous decision making in genomic healthcare, especially regarding what are likely to be more complex diagnosis and treatment decisions.

In implementing genomic healthcare, we want to harness the tremendous power of genomic and genetic information combined with other health data to be able to provide more timely, improved diagnosis and offer better, equitable and more personalised treatments and access to clinical trials. To enable these advances, it is important that the public and patients can be reassured that ethical questions regarding the handling of genomic data in research have been considered in a comprehensive way, with public and patient participation, and that these questions are addressed with robust data governance and secure data protocols.

Working together on these ethical frameworks for genomic healthcare, we will build on our strong record of examining ethical issues in bioscience and health and in developing robust models of governance and regulation. In doing so, we can lead the world in the ethics and regulation of novel applications in genomic research and healthcare, and most importantly maintain the trust of patients and the public.

Our shared commitment is:

Genome UK vision: build and maintain trust in genomic healthcare, ensuring that patients, the public and the NHS workforce are involved and engaged in its design and implementation.

We are committed to ensuring that patients and the public are at the heart of implementing the vision in Genome UK. As we have set out in our strategy, we must empower and enable patients and the public to have confidence in the potential of genomic healthcare and help shape equitable delivery. A recent report by the Government Office for Science includes evidence that suggests the public can generally see the potential benefits of genomics but are also aware of its potential negative impacts on privacy. A public dialogue by Genomics England on its whole genome sequencing research pilot came to a similar conclusion there was broad support for such an initiative provided that the right safeguards were in place.

The DHSC Data saves lives draft strategy also recognises the need to deliver truly patient-centred care, which puts people before systems, so people will have better access to their personal health and care data and can understand exactly how it is used. People will only share their information with confidence if they feel that there are proper safeguards in place, and that those entrusted with their data will keep it safe.

An important part of empowering people is to ensure greater understanding and awareness of the benefits of genomic healthcare and allowing people to make informed choices. The COVID pandemic has raised public awareness of the power and benefits of clinical research and provided an example of the relevance and importance of concepts such as genetic variation in population health. We hope that in implementing our vision for Genome UK we can build on this awareness and interest.

Our shared commitments are:

Genome UK vision: deliver UK-wide, coordinated approaches to data and standardise the way in which genomic data is recorded.

Genomic data is already transforming the way in which patients are diagnosed and treated for diseases and is enabling researchers to discover the next generation of medicines and diagnostics. The UK is home to many world-leading institutions that house genomic data. However, these have tended to be developed in isolation for a specific purpose, leading to poor interoperability and difficulty in co-analysing different datasets. To implement our vision for data set out in Genome UK, we plan to link, or federate, trusted research environments (TREs), including those hosted by UK Biobank, Genomics England and Our Future Health, creating secure spaces where accredited researchers can access and securely analyse sensitive data without breaching privacy. This means that in-depth analysis can be undertaken on rich multimodal datasets, but without identifiable information ever being seen by researchers and analysts. In March 2022, initiatives to progress this work were announced in England.

In Genome UK we set out a number of ambitions to transform our capabilities in genomic data over a 10-year period, based on a set of agreed principles and use of shared data standards that would allow a federated approach to data sharing and improved use of AI and machine learning tools across databases.

We aim to collectively build on our successful UK-wide data collaboration during the COVID-19 pandemic, such as those pioneered by the COG-UK consortium and the UK Joint Biosecurity Centre. We also aim to work closely with units developed following the pandemic such as the UKHSA Centre for Pandemic Preparedness, leveraging connections with the WHO on their Genomics Strategy, the International Pathogen Surveillance Network (IPSN) and other bi- and multi-lateral agreements on surveillance, modelling and forecasting.

Genomic data is much more useful when combined with wider healthcare information, such as scanned pathology and radiology images, blood tests or hospital admission statistics and data initiatives such as the SAIL (Secure Anonymised Information Linkage) database in Wales are already aiming to achieve this. When combined, this data allows researchers to make more informed links between genetic changes and disease development, improving the accuracy of diagnosing genetic conditions and providing a platform to launch drug discovery programmes. This kind of analysis is accelerated by the latest developments in artificial intelligence and machine learning.

Across the UK, multiple pathogen genomics services already exist, delivered at varying levels across England and the devolved administrations. Many of these services have ISO 15189:2012 medical laboratory accreditation, and all are dependent upon digital infrastructure to enable the generation of actionable information from sequence data. These services often exist in silos, creating barriers to sharing approaches and data across the UK, creating inequalities of service across the UK because of the current digital systems that exist to provide current services.

In contrast to existing pathogen genomics services, the sequencing response to the COVID-19 pandemic has seen unprecedented co-creation across the UK, and across healthcare/public health, academia and government. In response to an urgent need, a complete analysis platform for UK SARS-CoV-2 sequence data, CLIMB COVID, was built in less than 3 days in March 2020. This platform was put in place to provide a single data sharing and analysis platform which would bring together all UK SARS-CoV-2 genomes, wherever they were generated, and enable their analysis in real time. Providing real-time analysis on a single, combined UK dataset has enabled the generation of actionable intelligence at multiple scales ranging from outbreak analyses for infection prevention and control in hospitals, up to information on the shape and progression of the pandemic across the UK, to inform government policy. Collectively CLIMB COVID currently stores and analyses over 2 million SARS-CoV-2 genomes from across the UK, with the data and analysis outputs being actively used by the 4 UK public health agencies as well as numerous NHS trusts.

The exploitation of pathogen genomics data as part of the COVID-19 pandemic paints a picture of what is possible in a future where pathogen genomics data is rapidly shared across the UK as required. With shared data and common analysis approaches, expertise can also be more effectively pooled and analyses can be undertaken more collaboratively across the UK public health agencies for the benefit of patients and the public. The federated model also means that each nation is able to use the data to meet their local needs.

The success of the SARS-CoV-2 genomics efforts in the UK has been a federated approach to sequencing and analysis underpinned by a multi-node data processing infrastructure which works to standardise analysis and enables work to be undertaken on a UK-wide basis. This infrastructure, underpinned by data sharing agreements that span the UK public health agencies, provides a validation of a future federated approach, and demonstrates the enormous potential that exists through working collectively across the UK to improve how we link, combine and use our genomic data.

Our shared commitments are:

Genome UK vision: support and enable healthcare staff to deliver the benefits of genomics by training and supporting them to acquire the relevant knowledge and skills, and developing clinical pathways and standards of care.

The ambition of the Genome UK vision cannot be achieved without ensuring that the workforce have the necessary skills and knowledge to deliver genomic healthcare. Staff need to understand how genomic tests fit into clinical pathways, identify which patients require which type of test, and be able to interpret and communicate the results of these. For UK patients to receive the benefits of the latest advances in genomic technology and infrastructure, we need a workforce that develops in parallel, so that we empower healthcare professionals with the confidence and up to date knowledge needed to deliver these innovations. This will involve embedding formal education in genomics into speciality training programmes, as well as providing clinical staff with the resources to stay up to date with the latest advances in the area and utilise the available clinical pathways. By creating a National Framework for genomics education, we can ensure consistency of capability across the UK.

Key delivery partners in this work are Health Education England (HEE) and its Genomic Education Programme, which supports the NHS Genomic Medicines Service and ensures that the 1.2 million-strong NHS workforce has the knowledge, skills and experience to keep the UK at the heart of the genomics revolution in healthcare, and the Academy of Medical Royal Colleges, which sets the standards for how doctors are educated, trained and monitored through their careers.

Our shared commitments are:

Genome UK vision: make the UK the best location globally to start and scale new genomics healthcare companies and innovations, attracting direct investment in genomics by the global life sciences industry and increasing our share of clinical trials in the UK.

In July 2021, the government and the life sciences sector published its Life sciences vision. The vison sets out the governments and the sectors collective ambition for the UK to build on the scientific successes and ways of working, from COVID-19 to tackling future disease challenges (including cancer, obesity and dementia), ageing, secure jobs and investment and become the leading global hub for life sciences.

The vision recognises that to remain competitive in the life sciences and deliver on its ambition, the UK will need to focus relentlessly on areas in which it already has, or can gain, a competitive advantage such as genomics and health data. It also recognises that, for genomics, our ambition needs to be to create scale. We already have fantastic expertise, tools and world-leading initiatives in UK genomics our challenge is how to bring these together in a way that is transformative and places the UK firmly ahead of its competition, while making it a valued partner for international collaboration and an attractive location for investment.

This can be achieved through working closely with the sector on the existing and planned initiatives included in these shared commitments, such as enhancing our genomic UK-wide research infrastructure, large pilot studies to evaluate variants and their role in predicting disease risk, evaluation of new genomic tools for early disease detection, new tools for improved cancer diagnosis and delivering a world class offer to support functional genomics studies.

The UK has a diverse industrial life sciences sector, comprised of large multinationals, SMEs and spinouts all of which bring unique value and expertise to the UKs genomics ecosystem. The innovations coming from the commercial UK genomics sector and their international partners and collaborators will underpin developments in research and healthcare for years to come. It is vital that we capitalise on the UKs existing strength by continuing to foster an environment that allows companies to develop new treatments, deliver effective innovations to patients and grow at scale.

Our shared commitments are:

In our Genome UK strategy, we set out, for the first time, a comprehensive and ambitious vision for the future of genomic healthcare: a future where genome sequencing, genomic tests and integrated genomic and other health data will help to detect the risk and very early stages of disease to support early intervention, and where genomic and other -omic technologies can speed up diagnoses and support the development of better, more precise treatments for many diseases, including cancer.

Here we commit to following through on this vision by working together we will achieve better coordination and collaboration on genomic healthcare for the benefit of patients across the UK, while recognising the differences in our respective healthcare systems and structures. Our commitments will strengthen our ability to share expertise and establish new collaborations and partnerships to progress genomic healthcare not only across the UK but worldwide, securing our global leadership in genomics and the wider life sciences.

See the article here:
Genome UK: shared commitments for UK-wide implementation 2022 to 2025 - GOV.UK

Capillary Electrophoresis (CE)is a technique used in the laboratories that can separate ions based on their electrophoretic mobility with the use of an applied voltage without overheating. The advantages of the system include high accuracy, efficiency and higher reproducibility. This electrophoresis technique is widely used in biosciences and clinical research.

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Growth by Region

North America accounted for the largest market share owing to the increasing focus by stakeholders on research projects that involves proteins, associated biomolecules and also genes. The growth in Europe, is due to the growing research activities in the fields related to genomics and proteomics coupled with stringent regulatory requirements in pharmaceutical manufacturing industries. Asia-Pacific region is also one of the lucrative markets showing noticeable growth due to rising focus on structure-based drug design developments.

Drivers vs Constraints

The market is mainly driven by advantages over other molecular separation and analysis technologies due to its improved efficiency, high accuracy as well as greater reproducibility. However, the growth of the market is hindered by the high cost of the equipment as well as the availability of other electrophoresis systems in the market.

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Industry Trends and Updates

Agilent Technologies, Inc., an American public research, development and manufacturing company had completed its acquisition of Advanced Analytical Technologies, Inc., a provider of capillary electrophoresis solutions for fully automated analysis of a wide range of molecules for USD 250 million in cash.

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Thermo Fisher Scientific, an American biotechnology product development company had launched its new capillary electrophoresis (CE) system which is designed to offer a low-throughput, cartridge-based system for Sanger sequencing as well as fragment analysis at European Society of Human Genetics (ESHG) conference held in Copenhagen, Denmark.

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Capillary Electrophoresis Market predicted to experience noticeable growth in the future ChattTenn Sports - ChattTenn Sports

From mesmerizing symmetry of spiraling sunflower seeds to mirror-like sides of the human body, patterns dominate nature. Aesthetic appeal aside, what advantage does repetition afford?

The question baffles experts, but a group of scientists have a controversial answer: It's the wrong question. A young professor at the University of Bergen, Dr. Iain Johnston, asked a different one: Can something inherent about evolution explain the prevalence of symmetry?

According to Johnston, the answer lies in probability. Evolution favors simple genetic codes over complex ones a principle called "simplicity bias" drawn from theoretical computer science before natural selection even comes into play. Patterns in organisms are just a symptom of that preference.

"The beautiful symmetry that we see everywhere is primed to appear," Johnston told Salon. "Simplicity bias in biology exists, and it's favored without needing to invoke any specific mechanism."

In other words, the Fibonacci spiral evidence in a nautilus shell or a head ofRomanesco broccoli is a byproduct of nature being efficient in its genetic code.

RELATED:What makes Romanesco broccoli so mathematically perfect?

Given the diversity of organisms that do so across every branch in the tree of life and every scale down to the molecular level, evolutionary biologists have generally hypothesized that symmetrical forms emerge frequently as a result of natural selection. Long-standing debate has surrounded the precise mechanism, but with the understanding that life must prefer patterns for some competitive edge.

"It's too much to be JUST natural selection," tweeted Dr. Chico Camargo. "This simplicity appears in vertebrates and invertebrates, in plants and bacteria, in RNA secondary structures and in the cell cycle, in the shape of the goddamn COVID-19 virus. There's no selective pressure that can explain all that."

The research team published a paper last Friday in Proceedings of the National Academy of Sciences that could topple that assumption. What they found was that the presentation of phenotypes, displayed traits, from genetic code, resembled the selectivity of a computer algorithm.

"We don't need to look at a flower and say, 'That was selected because it was symmetric,'" he continued. "There's some preference just from the way evolution works as an algorithm."

Using computational modeling the team demonstrated how their hypothesis, based on algorithm information theory, functions at the genetic level.

"Nature is exponentially biased towards these simple outputs, and in the RNA, you see this very nicely," asserted corresponding author, Dr. Ard Louis. "Rather than it being a bias toward symmetry, it's a bias towards these low outputs with low descriptional complexity."

With a twist on the "infinite monkey theorem" given enough time, paper, and ink a monkey could hypothetically replicate a work of Shakespeare Louis explained that genetics could be vastly more complex and disordered than they are. The odds are not likely though. He compared the greater number of genetic materials they found in the model to files one might zip on a computer.

"Symmetry emerges from what evolution is not necessarily through a specific selective pressure in a given circumstance, and at the same time it has the corollary advantage of making things more robust in biology," concluded Johnston.

From an engineering standpoint, repetition breeds stability. Compare a pile of randomly stacked rocks of various shapes and sizes to a stone building. Congruent, organized stones give the latter construction structural integrity. Patterns in nature can be similar. The approach taken in this study does not imply that natural selection has no role, but evolution can not account for all of these.

"Evolution has literally trillions of shapes to pick from, and yet, biological structures often show symmetry and simplicity," Camargo wrote.

Natural selection is process not an engineer. It is unable to anticipate what traits may or may not be advantageous, Camargo added.

"Elsewhere, there's evidence of this simplicity bias in models of neuron development, in studies of plant morphology, in teeth shapes and leaf shapes, and cell differentiation," Camargo elaborated.

Read more:
The weird reason symmetry abounds in nature may have to do with our genes striving for efficiency - Salon

G

rew up with a grumpy parent? The fear dawns that with every passing year youre unstoppably trudging towards that testy transformation your temper shortening in inverse proportion to wrinkles lengthening. With every sarcastic comment muttered to a forgetful waiter, with every idiot involuntarily barked at Question Time, the miserable metamorphosis feels pre-ordained. And science seemed to support the idea that resistance was futile against this coming curmudgeonliness. As recently as 2005, an influential paper claimed that 50 per cent of peoples happiness was determined by their genes. Becoming a grumpy git was part of your inheritance.

But if I may momentarily stop swearing at the TV, pause the dour determinism and deliver some good news: we now know that were not entirely doomed by our parents genes. Not just the doom and gloom DNA, but the genes linked to all manner of dispositions and diseases youd rather werent passed on like diabetes and heart disease. Thats because the rapid leaps and bounds in genetics in recent years have transformed how we understand the nuanced role that genes play in our health and wellbeing and its all looking a lot less pre-determined.

We once believed that having the genes for a complex disease was the key to explaining why some people are more likely to be affected by an illness such as diabetes. Not anymore, says Professor Vittorio Sebastiano, an epigeneticist at Stanford University. Whats crucial, he says, is in fact gene expression. In very basic terms, whether genes are activated or not. In other words, having a good gene but not being able to express it or activate it in the right way could lead to illnesses, relates Professor Sebastiano.

Conversely, you might have a genetic predisposition to diabetes or depression, heart disease, or hundreds of other genetically linked conditions but if the offending combination of genes is not activated, then youre unlikely to develop the condition.

The idea that genes can be switched on/off that its not determined that well take on the ailments of our ancestors is a game changer. Professor Sebastiano estimates that as much as 70 per cent of our health outcomes come down to gene expression. Its the most important factor affecting our health from ageing and immunity, to even how we feel.

So our tempers can get longer and the wrinkles shorter; but how to get our genes to play ball in this radically-changed game? Well, the good news is that an awful lot of gene expression lies in our hands. Because our lifestyles the day-to-day of how we live can actually switch on/off those inherited traits. For example, exercise, stress, pollution, sleep and meditation can all impact genes as can behaviour towards others. One of the authors of that 2005 paper later found that simply performing small acts of kindness for other individuals can impact human gene regulation.

Gene expression is the most important factor affecting our health - from ageing and immunity, to even how we feel

As can connecting with nature, the alternative medicine guru Deepak Chopra told me when I was exploring on my sceptical BBC wellness podcast All Hail Kale how to somehow shift my genetic tendency towards being a morning person.

As can leaving earth. After astronaut Scott Kelly returned from the International Space Station, Nasa found his gene expression was seven per cent different from his identical twins.

But the single biggest way to impact gene expression with all the benefits that can have for mind, body, immunity, ageing etc is through what we eat. The nutrients we ingest go deep inside our cells, interact with DNA and can actually flip switches to turn genes on or off. Food as molecular medicine.

Studying the relationship between our diet and genes is a breakthrough branch of science called nutrigenomics. And its captivated me.

Seeing how something as natural and accessible as nutrients can affect this vital process of gene expression compelled me to go from cynic on the sidelines to, well, getting stuck in. To team up with the Stanford Professor Sebastiano and Dr Uma Naidoo Harvard Medical Schools pioneering nutritional psychiatrist to bring nutrigenomics research to the masses. Cards on the table, weve launched Karmacist the worlds first nutrigenomics-based supplement with formulations for Mood, Relax, Immunity and Energy. Weve always known that plants are powerful. Mankind has been turning to them for more than 60,000 years. Plants power an estimated 40 per cent of modern pharmaceuticals. But its geekily fascinating to use nutrigenomics to drill down deeper to see how and why botanicals might be working their magic.

Take saffron. The active components in this precious Persian spice have been found to help regulate the gene that transports serotonin the happy hormone thats key to our moods. Saffron has also been shown to increase the expression of the feel-good chemical dopamine in the brain. Indeed, Dr Naidoo notes, its been shown that Saffron is as effective as Prozac in decreasing depressive symptoms. Theres perhaps good reason now revealed by cutting-edge science why saffron has been coveted for millennia, and is pound for pound more expensive than gold.

Another ancient botanical yielding its cellular secrets is ashwagandha. Prized for its rejuvenating qualities in Ayurvedic tradition, research now shows how ashwagandha can prevent the expression of certain genes that can drive inflammation a known factor in stress and anxiety. Reishi mushrooms contain phytochemicals which, studies show, can help regulate the immune system.

That herbs and plants can have such deep, transformative potential also tallies with our understanding of the gut-mind link: the two-way highway running between brain and belly. Because, as Deepak Chopra told me, humans arent just carrying around their 25 thousand or so genes but another two million extra genes which are not human, they are bacteria. Technically-speaking, youre a few human genes hanging onto a bacterial colony which is known as the microbiome, or second genome, and its totally dependent on your lifestyle.

So, the way we live especially what eat doesnt just impact our own DNA, but the several million genes of the mass of bacteria were shlepping around that seems to have a direct line to our brains.

The nutrients we eat deeply impact our molecular and cellular processes - and directly affect mental health

Were still in the nascent days of nutrigenomics and in understanding precisely how the gut-mind axis works.

But at Massachusetts General Hospital, where Dr Uma Naidoo directs the USs first hospital-based Nutritional Psychiatry Service, she uses nutrients as part of her clinical practice and has no doubt about the mood-food connection. The nutrients we eat deeply impact our molecular and cellular processes and directly affect our brains and our mental health, Dr Naidoo says.

Psychiatry has been too slow to realise the rest of the body and what we feed it affects our moods and stability. Nutrition is the pioneering new frontier for better mental health and resilience.

With enough gene-expression-friendly nutrients along with meditation, exercise, sleep, and exposure to nature a grump-free future might beckon where waiters can take as long as they want, particularly if theyre bringing saffron risotto.

The benefits packed in herbs and spices are mind-blowing, says Harvard nutritional psychiatrist Dr Uma Naidoo. Were not just adding more flavour to our food these seasonings can be good for our moods too, she notes.

To help combat depression, Dr Naidoo suggests:

Oregano: research shows its active component has promising antidepressant activity and is likely to help protect brain tissue.

Saffron: the ultimate mood-enhancing spice (see main article for its serotonin and dopamine prowess).

Turmeric: shown in studies to adjust brain chemistry and protect cells against toxic damage that leads to depression, Dr Naidoo writes. Always add freshly ground pepper to maximise absorption.

Excerpt from:
How to hack your genes and eat your way younger - Evening Standard

Name: Emily Ozdowski

Position: Instructor in the Duke Department of Biology Meet Emily's Nominator

Emily was nominated by Dr. Sheila Patek, professor of Biology and one of Ozdowskis mentors.Emily exemplifies the very best of Duke. She is dedicated to undergraduate education and has tirelessly put student needs first throughout the pandemic. She gave tremendous effort and planning into teaching during the pandemic so that students could safely take lab classes in person - a lifeline for many students. No matter the setback and challenge, Emily has kept positive and constructive attitude - always finding a way to make things work and always supporting student learning, engagement, and growth. It has been an absolute privilege working with Emily and I hope we can express our Duke gratitude in the Blue Devil of the Week way!"

Years at Duke: 15

What she does at Duke: In high school in Ringgold, Virginia, Emily Ozdowski read an article about the genetics of schizophrenia in a Virginia Tech magazine and knew right away that she wanted to become a researcher.

That curiosity eventually landed her at Duke as a postdoctoral researcher in 2006.

Today, as an instructor in the Department of Biology, Ozdowski continues to ask important and interesting questions for the sake of her own research, while helping the next generation of researchers discover their passions in science.

Every spring semester, Ozdowski teaches a class that puts junior and senior-level undergraduates in the drivers seat of their own research projects, using zebrafish and mussels in the classroom to explore their interests. The students work with Ozdowski to determine the subject of their research, exploring topics such as climate change or the affect of chemicals excreted by the human metabolism into water sources on mussels.

I love the curiosity factor, Ozdowski said. The fact that we can brainstorm these amazing connections and look up all sorts of new information is a great way to learn to test a hypothesis with lab experiments. Whether its super focused on human health or ecology, in this lab, were able to ask some fun questions and go try to figure out the answer.

Outside the classroom, Ozdowksi works with Dr. Nina Sherwood to research Autosomal Dominant Hereditary Spastic Paraparesis (ADHSP), a rare genetic neurological disorder that causes muscle weakness and tightness in the lower half of the body.

Using fruit flies, which have a similar gene to humans that causes the disorder, Ozdowski studies how neurons signal to muscles and how glial cells help make those developmental connections.

I wanted to do something that was both basic science but also could have human application, so the fruit fly really appealed to me all the way since undergrad and graduate school, she said.

Best advice received: Ozdowskis parents taught her that you have to find the places where youll be most happy. That became important when Ozdowski received her doctorate from the University of Virginia and contemplated what was next.

Ozdowski came to Duke, where shes been ever since.

When youre looking for either a school or a job or the next stage of life, having it be a good fit for you is just as important as prestige or money. I have been so lucky to find the things that fit my personality, she said. That is really important for happiness.

Something unique in her workspace: Working with fruit flies in her research, Ozdowski naturally has all sorts of insect-themed dcor in her office, including from attending many of the annual Drosophila Research Conferences, affectionately known in the field as The Fly Meeting.

My office has fruit fly postcard art, jewelry, ornaments, and toys that I've collected over the years, Ozdowski said. My daughter loves art and has given me paintings of insects to decorate my shelves.

What she loves about Duke: Ozdowskis favorite part of her job is interacting with students, who come from all over the country and world but whose curious and creative minds led them to her class.

She has the opportunity to encourage them to explore why science appeals to them.

I get to design the courses that I wish Id had, she said. So if theres something that I didnt get to do as an undergraduate, then its really fun to be able to have that freedom here.

When shes not at work, she likes to: Since she came to Duke in 2006, Ozdowski has enjoyed pickup volleyball at the outdoor court on East Campus with a group of faculty, staff, students and Durham residents.

Its a great group of friends and just friendly competition, she said.

Lesson learned during the pandemic:

Teaching lab-based classes during the pandemic has meant plenty of lessons in flexibility. With COVID-19 forcing quarantine, Ozdowski has had to learn to adjust her teaching, hold frequent makeup labs and instruct students while theyre socially distanced across two different classrooms.

Were all more flexible than we realize or we can be more flexible than we gave ourselves credit for before, Ozdowski said. Since the pandemic, it seems like almost all of the classes are more laid back. Weve all been forced to become resilient and flexible, so whatever happens were going to make it work.

Originally posted here:
Blue Devil of the Week: A Curious Researcher and Dedicated Teacher - Duke Today

In the United States, cardiovascular disease (CVD) is a major health problem accounting for nearly 40 percent of all deaths each year, according to the US National Library of Medicine. Now, scientists from University of Utah Health have confirmed that artificial intelligence (AI) can better predict cardiovascular disease, including risk factors, onset, and course.

Fortunately, several risk factors for heart diseasesuch as tobacco use, hypertension, obesity, elevated low-density lipoprotein cholesterol (LDL-C), and hypercoagulable states can be modified. Much like detecting cancer early, therapeutic lifestyle changes and drug treatment can be highly effective at reducing a patients risk of heart attack and stroke if risk factors can be identified in patients early. But AI technology could improve this process, with the potential of saving lives before adverse events occur.

The Centers for Disease Control and Prevention (CDC) lists heart disease as the #1 leading cause of death in the US, followed by cancer and Covid. Cardiovascular disease is a grave concern in the field of medicine. Here in Utah, University of Utah Health researchers have been working closely with physicians at Intermountain Primary Childrens Hospital to develop computational tools that accurately measure the combined effects of existing medical conditions on a patients heart and blood vessels.

While the initial research is limited to cardiovascular disease, its only the beginning. Researchers see the vast potential of AI technology and how it can essentially help identify and pinpoint risk factors in a broad range of medical diagnoses.

We can turn to AI to help refine the risk for virtually every medical diagnosis, [including] the risk of cancer, the risk of thyroid surgery, the risk of diabetesany medical term you can imagine, says Martin Tristani-Firouzi, the studys corresponding author, a pediatric cardiologist at U of U Health and Intermountain Primary Childrens Hospital, and scientist at the Nora Eccles Harrison Cardiovascular Research and Training Institute.

The current methods for calculating various risk factors on cardiovascular diseasessuch as medical history and demographicsare subjective and imprecise, says Mark Yandell, senior author of the study, professor of human genetics, and co-founder of Backdrop Health. Since these methods fall short, they fail to identify those interactions that can profoundly affect the health of a persons heart and blood vessels.

Instead, the researchers focused on measuring comorbidities and how they influence patient health. Yandell, Tristani-Firouzi, and their colleagues from Intermountain Primary Childrens Hospital and U of U Health sorted through more than 1.6 million anonymous electronic health records (EHRs) utilizing AI. These EHRs included detailed information about patients, including lab tests, diagnoses, medication prescribed, and medical procedures, which helped researchers identify which comorbidities were most likely to aggravate cardiovascular disease.

The important thing is that we can now calculate any outcome given multiple combinations of prior events in the patients medical record, Yandell says. This allows us to refine a patients risk for a medical diagnosis and understand how prior events influence future ones.

The researchers found that patients with a previous diagnosis of cardiomyopathy, a disease of the heart muscle, had an 86 times higher risk of needing a heart transplant than those without cardiomyopathy. Individuals with viral myocarditis had about a 60 times higher chance of needing a heart transplant. Transplant risk for those who used the drug milrinone (used to treat heart failure) rose by 175 timesthe strongest predictor of a heart transplant.

In certain cases, the combined risk was significantly higher. When individuals took milrinone and had cardiomyopathy, for instance, their risk of needing a heart transplant jumped to 405 times higher than individuals with healthier hearts.

This novel technology demonstrates that we can estimate the risk of medical complications with precision and even determine better medicines for individual patients, Josh Bonkowsky, director of the Primary Childrens Center for Personalized Medicine, told U of U Health.

Continue reading here:
This AI device is changing heart attack prevention - Utah Business - Utah Business