Daily Archives: July 4, 2017

When the first humans left Africa around 100,000 years ago, they got shorter.

The evolutionary shift helped them cope with the colder conditionsa more compact body size helped protect them from frostbite, whileand shorter limbs would be less breakable when they fellbut it also appears to have come with a downside: arthritis.

In a study published in Nature Genetics on Monday, scientists at Stanford University, California, have shown how variants within the GDF5 gene, which are related to reduced growth, was repeatedly favored by our ancestors as they migrated out of Africa and across the continents.

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But GDF5 has also been linked with osteoarthritis,a degenerative joint disease that affects an estimated 27 million Americans. Risk increases with ageit is sometimes referred to as wear and tear arthritisbut it also has a strong genetic component.

Previous research has shown how mutations in part of the GDF5 gene cause malformation in bone structure in mice. In humans, it has been associated with a shortness and joint problems, and two changes in particular are linked with a heightened risk of osteoarthritis.

In the latest research, the scientists find GDF5 provided an evolutionary boost for our ancestors, with arthritis apparently a byproduct of it."The gene we are studying shows strong signatures of positive selection in many human populations," senior author David Kingsley said in a statement

"It's possible that climbing around in cold environments was enough of a risk factor to select for a protective variant even if it brought along an increase likelihood of an age-related disease like arthritis, which typically doesn't develop until late in life."

A display of a series of skeltons showing the evolution of humans at the Peabody Museum, New Haven, Connecticut, circa 1935. Study finds humans became shorter when they first left Africa 100,000 years ago. Hulton Archive/Getty Images

To better understand GDF5, the team studied the DNA sequences that might affect how the gene is expressedspecifically those that are known as promoters and enhancers. From this they found a previously unidentified region they called GROW1.

When they looked for GROW1 in the 1,000 Genomes Project databasea huge database of genetic sequences of human populations around the worldthe team found a single change that is very common in European and Asian populations, but is hardly ever seen in Africans. The team then introduced this change to mice and found it led to reduced activity in the growth of bones.

They then looked at the change to the genetic variant over the course of human evolution, and found it had been repeatedly favored after Homo sapiens left Africa between 50,000 and 100,000 years ago. The team says the benefits of being shorter in colder conditions probably outweighed the risk of developing osteoarthritis in later life.

Because evolutionary fitness requires successful reproduction, alleles that confer benefits at young or reproductive ages may be positively selected in populations, even if they have some deleterious consequences in post-reproductive ages, they wrote.

Researchers believe this change could help explain why osteoarthritis is rarely seen in Africa, but is more common in other populations.Concluding, Kingsley said: "Because it's been positively selected, this gene variant is present in billions of people. So even though it only increases each person's risk by less than twofold, it's likely responsible for millions of cases of arthritis around the globe.

"This study highlights the intersection between evolution and medicine in really interesting ways, and could help researchers learn more about the molecular causes of arthritis."

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Human Evolution: Africa Exodus Made Homo Sapiens Shorter and Gave Them Arthritis - Newsweek

July 4, 2017 Genoeconomics looks for genetic ties to life outcomes and economic behavior. Credit: Janice Kun

When Daniel Benjamin was just beginning his PhD program in economics in 2001, he attended a conference with his graduate school advisers. They took in a presentation on neuroeconomics, a nascent field dealing with how the human brain goes about making decisions.

Afterward, as they took a stroll outside, they couldn't stop talking about what they had learned, how novel and intriguing it was. What would be next, they wondered. What would come after neuroeconomics?

"The human genome project had just been completed, and we decided that even more fundamental than the brain would be genes, and that someday this was going to matter a lot for social science," said Benjamin, associate professor (research) of economics at the USC Dornsife College of Letters, Arts and Science's Center for Economic and Social Research (CESR). Indeed, his excitement that day was the foundation of a visionary academic path.

Fast forward to today. Genoeconomics is now an emerging area of social science that incorporates genetic data into the work that economists do. It's based on the idea that a person's particular combination of genes is related to economic behavior and life outcomes such as educational attainment, fertility, obesity and subjective well-being.

"There's this rich new source of data that has only become available recently," said Benjamin, also co-director of the Social Science Genetic Association Consortium, which brings about cooperation among medical researchers, geneticists and social scientists.

Collecting genetic data and creating the large data sets used by economists and other social scientists have become increasingly affordable, and new analytical methods are getting more and more powerful as these data sets continue to grow. The big challenge, he said, is figuring out how scientists can leverage this new data to address a host of important policy questions.

"We're ultimately interested in understanding how genes and environments interact to produce the kinds of outcomes people have in their lives, and then what kinds of policies can help people do better. That is really what economics is aboutand we're trying to use genetics to do even better economics."

The mission at hand

Only a handful of economists are working with genetics, but this brand of research is perfectly at home at CESR. The center, founded three years ago, was conceived as a place where visionary social science could thrive and where research could be done differently than in the past.

"Being in a place where that's the shared vision is pretty rare," said econometrician Arie Kapteyn, professor (research) of economics and CESR director. "There's no restriction on which way you want to go or what you want to do. It doesn't mean that there are no restrictions on resources, but it's the opportunity to think about your vision of what's really exciting in social science research. Then being able to actually implement it is absolutely fantastic."

The mission of CESR is discovering how people around the world live, think, interact, age and make important decisions. The center's researchers are dedicated to innovation and combining their analysis to deepen the understanding of human behavior in a variety of economic and social contexts.

"What we try to do is mold a disciplinary science in a very broad sense," Kapteyn said. "Because today's problems in society, they're really all multidisciplinary."

Case in point: Benjamin's work combining genetics and economics.

The flagship research effort for Benjamin's CESR research group deals with genes and education. In a 2016 study, the team identified variants in 74 genes that are associated with educational attainment. In other words, people who carry more of these variants, on average, complete more years of formal schooling.

Benjamin hopes to use this data in a holistic way to create a predictive tool.

"Rather than just identifying specific genes," he said, "we're also creating methods for combining the information in a person's entire genome into a single variable that can be used to partially predict how much education a person's going to get."

The young field of genoeconomics is still somewhat controversial, and Benjamin is careful to point out that individual genes don't determine behavior or outcome.

"The effect of any individual gene on behavior is extremely small," Benjamin explained, "but the effects of all the genes combined on almost any behavior we're interested in is much more substantial. It's the combined information of many genes that has predictive power, and that can be most useful for social scientists."

Learning about behavior

While the cohort of researchers actively using the available genome-wide data in this way is still somewhat limited, Benjamin says it is growing quickly.

"I think across the social sciences, researchers are seeing the potential for the data, and people are starting to use it in their work and getting excited about it, but right now it's still a small band of us trying to lay the foundations.

"We're putting together huge data sets of hundreds of thousands of peopleapproaching a million people in our ongoing work on educational attainmentbecause you need those really big sample sizes to accurately detect the genetic influences."

As CESR works to improve social welfare by informing and influencing decision-making in the public and private sectors, big data such as Benjamin's is a growing part of that process, according to Kapteyn.

"What big data reflects is the fact that nowadays there are so many other ways in which we can learn about behavior," he said. "As a result, I think we'll see many more breakthroughs and gain a much better understanding of what's going on in the world and in social science than in the past.

"I think we're really at the beginning of something pretty spectacular. What we are doing is really only scratching the surfacethere's so much more that can be done."

Explore further: Scientists find genes associated with educational attainment

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Can genetics play a role in education and well-being? - Medical Xpress

Artificial intelligence is already being put to use in the NHS, with Googles AI firm DeepMind providing technology to help monitor patients. Now I have discovered that DeepMind has met with Genomic England a company set up by the Department of Health to deliver the 100,000 Genomes Project to discuss getting involved.

If this does indeed happen, it could help bring down costs and speed up genetic sequencing potentially helping the science to flourish. But what are the risks of letting a private company have access to sensitive genetic data?

Genomic sequencing has huge potential it could hold the key to improving our understanding of a range of diseases, including cancer, and eventually help find treatments for them. The 100,000 Genomes Project was set up by the government to sequence genomes of 100,000 people. And it wont stop there. A new report from the UKs chief medical officer, Sally Davies, is calling for an expansion of the project.

However, a statement by the Department of Health in response to a freedom of information (FoI) request I made in February reveals this decision has already been made. The department said in this response that the project will be integrated into a single national genomic database. The purpose of this will be to support care and research, and the acceleration of industrial usage. Though it will inevitably exceed the original 100,000 genomes, we do not anticipate that there will be a set target for how many genomes it should contain, the statement reads.

The costs of sequencing the genome on a national scale are prohibitive. The first human genome was sequenced at a cost of US$3bn. However, almost two decades later, Illumina, who are responsible for the sequencing side of the 100,000 Genomes Project, produced the first $1,000 genome a staggering reduction in cost. Applying machine learning to genomics that is, general artificial intelligence has the potential to significantly reduce the costs further. By building a neural network, these algorithms can interpret huge amounts of genetic, health, and environmental data to predict a persons health status, such as their level of risk of heart attack.

DeepMind is already working with the NHS. As part of a partnership with several NHS trusts, the company has built various platforms, an app and a machine learning system to monitor patients in various ways, alerting clinical teams when they are at risk.

But its been controversial. The company announced the first of these collaborations in February 2016, saying it was building an app to help hospital staff monitor patients with kidney disease. However, it later emerged that the agreement went far beyond this, giving DeepMind access to vast amounts of patient data including, in one instance, 1.6m patient records. The Information Commissioners Office ruled recently that the way patient data was shared by the Royal Free NHS Foundation Trust violated UK privacy law.

Googles ambitions to digitise healthcare continue. I received a response to an FoI request in May which reveals that Google and Genomics England have met to discuss using Googles DeepMind among other subjects to analyse genomic data.

Davies insists that data could be anonymised. The Department of Health always promise that medical data used in such initiatives will be anonymised, yet one of the reasons that Care.data (an initiative to store all patient data on a single database) was abandoned is that this was shown to be untrue. I have also shown that the department has misinformed the public about the level of access granted to commercial actors in the 100,000 Genome Project. In particular it said the data would be pseudonymised rather than anonymised, meaning there would still be information available such as age or geographical location.

What would genomic information add to Googles already far-reaching database of individual information? A hint lies in its self-confessed aspiration to organise our lives for us. The algorithms will get better, and we will get better at personalisation, according to Eric Schmidt, executive chairman of Googles parent company Alphabet. This will enable Google users to ask the question, what shall I do tomorrow?, or what job shall I take?.

With personalisation as their ultimate goal, Google intend to use the machine learning algorithms which track our digital footprint and target users with personalised advertising based on their preferences. They also want to analyse health and genomic data to make predictions such as when a person might develop bipolar disorder or tell us what we should do with our lives.

Let us not forget that data, genomic or otherwise, is the oil of the digital era. What is stopping genomic information from being captured, bought and sold? We cannot assume that people will make life choices based upon their genetic profile without undue pressure commercial or governmental.

As for how genomic data might be used and what decisions will be taken about us, the mass surveillance by government agencies of their own citizens is a chilling reminder of the way information technology can be used. There is something unpalatable about everything being connected and everything being known.

When it comes to genetics, the implications are particularly frightening. For example, there is evidence of a link between genes and criminality. We know that 40% of sexual offending risk is down to genetic factors. A single national knowledge base as the one the UK government is aiming to create might therefore be used for broad genetic profiling. Although early intervention programmes that buy into genetically deterministic notions of crime genes are reductive, serious debate about policies involving genetic information will no doubt happen soon.

We can already see the beginnings of this in the United States. The bill Preserving Employee Wellness Programs Act which has received strong backing from Republicans and business groups would allow companies to require employees to undergo genetic testing. The results would be seen by employers, and should employees refuse to participate they would face significantly higher insurance costs.

Too much personalisation is likely to be intrusive. The challenge, then, will be to harness the potential of genomics while introducing measures to keep government and big business in check. The UK House of Commons Science and Technology Committees inquiry on genomics and genome editing was cut short (due to the recent snap general election). Its recommendations for further lines of enquiry include creating a quasi-independent body, which could be more attuned to broader, social and ethical concerns. This might introduce more balance at a pivotal time for the future of human genetic technologies.

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Google may get access to genomic patient data here's why we should be concerned - The Conversation UK