Category Archives: Transhuman News

from the knowing-too-much dept

The cost of sequencing every DNA "letter" in a human genome has fallen faster than Moore's Law, from around $100 million in 2001, to under $1,000 today (although some say the overall cost in a clinical context is higher). This brings with it the prospect of routinely carrying out full-genome sequencing for everyone. That's precisely what Matt Hancock, the UK's Health Secretary, has said he wants to see as a part of the country's National Health Service (NHS), reported here by The Telegraph:

"My ambition is that eventually every child will be able to receive whole genome sequencing along with the heel prick test [a basic test for genetic conditions]," he told the conference.

"We will give every child the best possible start in life by ensuring they get the best possible medical care as soon as they enter the world. Predictive, preventative, personalised healthcare -- that is the future of the NHS -- and whole genome sequencing and genomics is going to play a huge part in that," he said.

Creating a massive database of near-complete genomes will probably ring alarm bells for Techdirt readers. Just recently, US police have started obtaining warrants to search entire DNA databases, even of people who opted out of allowing law enforcement to access their genomic data. That's despite the fact that "touch DNA" is mostly guesswork, and that crime lab testing is beset with problems. Moreover, a mistaken belief that DNA is infallible can lead to innocent people being charged with serious crimes like murder.

It's true that DNA can be a very powerful tool for solving crimes by finding distant matches in publicly-available genetic data, and then constructing family trees to narrow down the possible suspects. But that fact also exposes why routinely obtaining someone's DNA, as Hancock proposes for newborns in the UK, has an important impact on anyone related to the person whose whole genome is sequenced.

Even when DNA databases of a complete population are not set up for the purposes of mass surveillance, as Kuwait proposed (but then scaled back), and as China is implementing in Xinjiang as a way of controlling the local Uyghur population, there are other serious issues that need to be considered.

For example, the Telegraph article notes that full-genome sequencing of newborns means "parents could choose to be alerted to the fact their child faced heightened risks of specific diseases, and allow the NHS to offer more tailored treatment." But would parents necessarily welcome knowing that their child is more likely than the average individual to develop some serious genetic condition at some point in their lives? And what about if that condition had no treatment at present? What is gained by knowing of the risk? Might parents, and later the affected children themselves, find that knowledge almost too much to bear -- a genetic sword of Damocles hanging over them all their lives? Equally, parents might feel guilty if they don't ask for this information, which could allow for earlier treatment of diseases.

There's no doubt that full-genome sequencing will have a major impact on medicine in the decades to come, and offers the hope of more targeted and more effective medicines for many conditions. But for the benefits to be realized, doctors and genetic counselors will need to find effective ways to talk to people about what the detailed but probabilistic information revealed by their complete genomes will mean for their future health and treatments. Only then can we make informed decisions that enhance our well-being and happiness.

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Filed Under: babies, dna, health minister, matt hancock, nhs, privacy, surveillance, uk, uk health secretary

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Health Minister Wants Full-Genome Sequencing Of Every Newborn Child In UK To Become Routine - Techdirt

SOMETIME NEXT year, if all goes to plan, a gay male couple in California will have a child. The child in question will have been conceived by in vitro fertilisation. In this case a group of eggs from a female donor are now being fertilised by sperm from both fathers (half from one, half from the other). Of the resulting embryos, the couple will choose one to be implanted in a surrogate mother. An uplifting tale of the times, then, but hardly a newsworthy event. Except that it is.

Where the story becomes newsworthy is around the word choose. For the parents, in conjunction with a firm called Genomic Prediction, will pick the lucky embryo based on a genetically estimated risk of disease. Such pre-implantation testing is already used in some places, in cases where there is a chance of parents passing on a condition, such as Tay-Sachs disease, that is caused by a single faulty gene. Genomic Prediction is, however, offering something more wide-ranging. It is screening embryos for almost 1m single-nucleotide polymorphisms (SNPs). These are places where individual genomes routinely differ from one another at the level of an individual genetic letter. Individual SNP differences between people rarely have much effect. But add them up and they can raise or lower by quite a lot the likelihood of someone suffering a particular disease. Generate several embryos and SNP-test them, then, and you can pick out those that you think will grow up to be the healthiest.

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Much fuss was made last year about a researcher in China, He Jiankui, who edited the genomes of two human embryos in order to try, he claimed, to make them immune to infection by HIV, the virus that causes AIDS. What Genomic Prediction proposes is different. No editing is involved. There is thus no risk of harming a child by putting it through a risky experimental procedure. Whether Genomic Predictions particular technique will actually deliver super-healthy children remains to be seen. The principle seems plausible, though. History may therefore look back on this moment as the true beginning of designer babies. And the tool that has made that possible is called GWAS.

GWAS stands for genome-wide association study. It is the endpoint of a historical process that began in the mid-19th century with Gregor Mendel, a Moravian abbot and amateur botanist. Mendel worked out the first set of rules of heredity. This led to the idea of a gene. And that, when allied with the discovery that the material of heredity is a chemical called DNA, which encodes genetic information in the order of its component units, known as nucleotides, led to the idea of a gene being a particular piece of DNA that carries in its nucleotides the blueprint of a particular protein. This protein goes on to contribute, in combination with environmental effects such as nutrition, to a particular bodily or behavioural characteristic, known as a phenotypic trait.

Since the 1950s, researchers have tried to quantify the relative contributions of genes and the environment to such traits. Mostly, this is in the context of disease. But behavioural characteristics, personality and cognitive ability have also been matters of interest. GWAs expands this process by looking not just at the effects of individual genes, but across the whole genomefor protein-coding genes make up only about 2% of a persons DNA.

Comparisons, over several generations of a family, of the prevalence of a particular trait yield estimates of its heritabilitya measure of how well individual genetic differences account for variations in that trait in a given population. A heritability of 100% indicates that any differences in a trait between individuals in that population are accounted for solely by genetic factors, while 0% suggests the environment alone is responsible. The phrase given population is important. Some populations may be exposed to relevant environmental variables unknown to others. Conversely, genetic factors present in one group (better response to oxygen scarcity in those evolved to live at high altitude, for example) may be absent in another.

An analysis published in 2015 of more than 2,700 studies of heritability shows that its average value, for all traits looked into in those studies, is about 50%. That includes physical traits like susceptibility to heart disease (44%) and eye disorders (71%), and mental ones, including higher-level cognitive functions (47%) such as problem-solving and abstract thought.

Other, less obvious traits are heritable, too. The amount of time a child spends watching television was assumed for many years to have a heritability close to zero. In 1990, however, a study led by Robert Plomin, now at Kings College, London, compared the habits of adopted children with those of their birth mothers. It found television-watching has a heritability of about 45%. Similar surprisingly heritable traits include a childs tendency to be bullied at school (more than 70%) or to be accident-prone (51%). Even someones likelihood of being religious (30-40%) or of getting divorced (13%) is heritable.

In 1989 James Watson, the first head of the Human Genome Project, summarised the mood of many by declaring that We used to think our fate was in our stars. Now we know, in large measure, our fate is in our genes. There was hope then that the genome project would locate those genes. No one was naive enough to think that there existed, say, such a thing as a gene for television-watching. But it was reasonable to believe that there might be a handful of genes which combined to encourage television-watching indirectly. More important, there was an expectation that the heritable causes of things like heart disease might be pinned down to such genetic handfuls. These might then be investigated as drug targets. To everyones frustration, though, few such genes revealed themselves. And in most cases the contributions they made to a conditions heritability were small. Where, then, was the missing heritability?

With hindsight, the answer was obvious. The number of variants that play a role in disease risk is far higher than Mendel-blinded researchers had imagined. Though human beings are genetically more than 99.9% alike, they have 6bn genetic letters in their genomes. This is where the SNPs are hidden, for a diversity of less than 0.1% still leaves room for millions of them. And when SNPs contributions are combined, their effects can be significant. For height, for example, the number of relevant SNPs is reckoned to be about 100,000each adding or subtracting, on average, 0.14mm to or from a persons adult stature. Furthermore, most of these SNPs are in parts of the genome that do not encode proteins at all. Rather, they regulate the activities of other genes and often have no obvious connection to the trait in question.

To be fair, it was mainly human geneticists who were captivated by the simple Mendelian model of single genes with big effects. According to Peter Visscher of the University of Queensland, Australia, many plant and animal scientists knew of traits genetic complexity long before the Human Genome Project started. But they were more interested in breeding better crops or livestock than in understanding the biology behind such complexity.

Dr Visscher was one of the first to realise that human studies would need to recruit more participants and screen for many thousands more SNPs if they were to capture in full the genetic components of most traits. In 2007 he and his colleagues used models to show that for a condition with a prevalence of 10% in the general population, approximately 10,000 volunteers are required to identify the SNPs marking the 5% of those at highest risk of developing that condition. Earlier studies, often with just a few hundred participants, had simply not been powerful enough to see what was going on. And thus was GWAS born.

Ideally, a GWAS would obtain a full sequence of the genome of every participating individual. However, even though the cost of such sequences has fallen dramatically since the completion of the genome project, to about $1,000 a shot, this would still be prohibitively expensive. Instead, researchers use devices called SNP arrays. These detect hundreds of thousands of the most common SNPs for a price of $50 or so.

A combination of SNP arrays, larger samples of volunteers and better computing methods means it is now possible to find millions of variants that contribute to a trait. An individuals score from these variants, known as his polygenic score, can then be calculated by adding up their contributions to give, for example, his risk of developing a particular disease in later life.

Another advance has been a change in the way volunteers are recruited. Institutions called biobanks have come into existence. These hold both tissue samples from, and a range of medical and other data about, large numbers of people who have agreed to make those data available to researchers who meet the criteria employed by the bank in question.

Among the largest of these repositories is the UK Biobank, in Britain. This has 500,000 depositors. One study that drew on it, published in 2018 by Sekar Kathiresan of the Massachusetts General Hospital in Boston and his colleagues, worked out polygenic risk scores for five diseases, including coronary heart disease and type 2 diabetes. By totting up scores from over 6m genetic variants, they were able to elucidate SNP patterns that identify those who are at a threefold higher risk or worse than the general British population of developing one of these diseases. For heart disease, 8% of the population are at such risk. For type 2 diabetes, 3.5%.

Nasim Mavaddat of the University of Cambridge and her colleagues have similarly calculated polygenic risk scores for breast cancer. These showed that a British womans average ten-year risk of developing breast cancer at the age of 47 (the earliest that Englands National Health Service begins screening for the disease) is 2.6%. The study also found that the 19% of women who had the highest risk scores reached this level of risk by the age of 40. Conversely, the 10% at lowest risk did not cross the threshold until they were 80.

Using these and similar studies, it is possible to draw up lifetime risk profiles for various medical conditions. A British firm called Genomics has done that for 16 diseases (see chart). This will help screening programmes to triage who they screen, by offering their services earlier to those at high risk of developing a condition early in their lives. It will also permit the dispensing of risk-appropriate advice about diet and exercise to those who need it most, and the early offering to those who might benefit from them of things like statins and antihypertensive drugs. In light of all this Englands National Health Service announced in July that 5m healthy Britons would be offered free gene tests.

A third study that drew on the UK Biobank is rather different. It was published in October and demonstrated the power of GWAS to reach beyond non-medical matters. It examined patterns of internal migration in Britain, and showed that there has been an outward migration from former coalmining areas of people with SNP patterns associated with high educational attainmentprecisely the sorts of individuals economically deprived places can least afford to lose.

Educational attainment also demonstrates how heritability varies with environment. In Norway, for example, heritability of educational attainment increased after the second world war as access to education widened. Since all children now had more or less the same opportunities at school, environmental variation was largely ironed out and the effects of genetic differences consequently exaggerated.

Both of these examples foreshadow how the sort of genetics made possible by GWAS can have political consequences. The implication of the internal-migration study is that the geographically left-behind are dimmer, on average, than the leavers. The implication of the Norwegian study might likewise be seen by some as suggesting that those who have done well at school and thus snagged the best (and best-paid) jobs are part of a genetic elite that deserves its success, rather than being the lucky winners of a genetic lottery.

And that is just within a country. Start comparing people from different parts of the world and you enter a real minefield. Because most of the genetic data now available come from populations of European ancestry, their predictive power is poorer for people from elsewhere. Alicia Martin of the Broad Institute in Massachusetts and her colleagues scored West Africans for height based on SNPs drawn from studies on European or European-derived populations. The scores predicted that West Africans should be shorter than Europeans. Actually, they are not.

As more people of non-European ancestry are sequenced, these problems may abate. But if group-based differences emerge or persist in the face of better data, that would be cause for concern. Differences between groups in things like height are rarely cause for prejudice beyond a jocular level. For something like educational attainment, by contrast, there is a risk that politically motivated groups would try to exploit any differences found to support dubious theories of racial superiority.

To some historians, this looks horribly familiar. They fear that the old spectre of eugenics risks rising in a new guise. As Nathaniel Comfort of Johns Hopkins University, in Baltimore, observes, The IQ test was invented in order to identify students who needed extra help in school. But within about a decade, it was being used as a tool to weed out the so-called feebleminded, not just from school but from the gene pool. Such fears of genetic stratification would become particularly acute if polygenic scores were applied to embryos for the purpose of selecting which to implant during IVFas Genomic Prediction is just about to do.

Genomic Prediction and a second firm, MyOme (which is not yet accepting customers), claim to be able to build up an accurate picture of an embryos genome. That is tricky because the sequencing has to be carried out using the tiny quantities of DNA in a few cells taken from that embryo. A sequence so obtained would normally be full of errors. The two companies say they can deal with this by comparing embryonic sequences with those of the biological parents. All of the DNA in the embryo has come from one or other parent, so blocks of embryonic DNA can be matched to well-established sequences from their parental progenitors and an accurate embryonic sequence established. That makes working out the embryos SNP pattern possible.

Genomic Prediction thus says it is able to offer couples undergoing IVF a polygenic risk score for each embryo for a variety of diseases including type 1 diabetes, type 2 diabetes, breast cancer, testicular cancer, prostate cancer, basal-cell carcinoma, malignant melanoma, heart attack, atrial fibrillation, coronary artery disease, hypertension and high cholesterol. At the moment it does not offer scores for non-medical traits like height or educational attainment. But there is nothing to prevent it from doing so should it so wish.

Even for medically relevant scores, however, some worry about this approach. One concern is pleiotropythe phenomenon of the same piece of DNA influencing several apparently unrelated traits. Choosing an embryo with a low risk of heart disease might accidentally give it, say, a higher chance of developing epilepsy. Single-mindedly maximising scores for positive traits like intelligence or height may therefore increase the risk of genetic disorders.

Stephen Hsu of Michigan State University, one of Genomic Predictions founders, acknowledges the theoretical risk of this, but argues that serious pleiotropic effects are unlikely. If you looked at a bunch of kids with IQs of, say, 160 or 170, he says, I doubt youd find much seriously wrong with them. Theyd just be a bunch of geeks. Dr Hsu, who in 2014 predicted that reproductive technologies would soon be used to select for more intelligent offspring, estimates that an IQ gain of between 10 and 15 points would be possible if couples were allowed to choose between ten embryos. He also thinks that further gains would probably accumulate if people selected in this way went on to select their own offspring on the basis of intelligence.

This is plausible. Before 2008, when the first SNP chips for cattle became available, the annual milk yield of dairy cows in America had been increasing at about 50kg per year. After six years of chip-based polygenic selection, the rate of increase had doubled to more than 100kg per year. This suggests the technique is powerfulin cattle at least. Despite Dr Hsus optimism, however, pleiotropism has reared its head in these animals. They have become less fertile and have weaker immune systems.

In the end, then, it is generally a good idea to remember that human beings have already been optimised by a powerful agent called natural selection. Trade-offs between different pieces of physiology, even in domestic animals, will have been forged in the crucible of evolution and will generally be optimal, or close to it. Genetic tinkering may sometimes improve things. But by no means always.

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Modern genetics will improve health and usher in designer children - The Economist

As of today, Podcasts on Pandora are now available for all users on the Pandora website and on its desktop app for Mac and Windows. The company first launched podcasts on its app last year, leveraging its Podcast Genome Project, an offshoot of Pandoras Music Genome Project, which can personalize podcast recommendations down to an individual episode level.

Pandora is banking on this hyper-personalization, and says its system uses more than 1,500 attributes from the shows MPAA ratings to a users listening history to drill down on shows it thinks youd like to listen to, along with specific episodes. This is mostly done with the Podcast Genome Projects algorithms, but theres still a human curation component involved to help guide recommendations.

Since launching podcasts in 2018, Pandora says its podcast offerings have grown from around 100,000 episodes to over 600,000 episodes, spread across a variety of genres like comedy, music, news, and more. Backing this effort, the platform also introduced its self-service Pandora for Podcasters online hub earlier this year, providing a centralized place for podcast creators to submit their shows for inclusion in Pandoras catalog.

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Podcasts are now available on Pandoras website and desktop app - The Verge

The University of Vermont Health Network, along with partners Invitae and LunaPBC, launched a pilot project on November 1, to offer the Genomic DNA Test as part of its clinical care. The test will provide information for 147 genes that are indicators of increased risk for certain diseases including hereditary cancers, cardiovascular conditions, and other medically important disorders for which clinical treatment guidelines are established. The test also screens for carrier status for other diseases.

Our overall health and longevity are determined about 30% by genetics, said Debra Leonard, M.D, Ph.D., chair, Pathology and Laboratory Medicine at UVM Health in a press release. But until now, most of our clinical health care decisions have been made without understanding the differences in each individuals DNA that could help guide those decisions.

The Genomic DNA Test will be offered over the next year to 1,000 patients who are over 18 years old, are treated by a UVM Health Network Family Medicine provider, are not pregnant, or the partner of someone who is currently pregnant, and are part of the OneCare Vermont Accountable Care Organization (ACO). The testing will be conducted by Invitae on healthy individuals who opt in to the pilot and will be provided with information about their potential risk of developing diseases like cancer or heart disease based on their genetic make-up, with the potential to adjust their healthcare and lifestyle to help mitigate some of these risks.

Nearly one-in-six healthy individuals exhibit a genetic variant for which instituting or altering medical management is warranted, said Robert Nussbaum, M.D., Invitaes chief medical officer in a prepared statement. Genetic screening like the Genomic DNA Test in a population health setting can help identify these risk factors so clinicians can better align disease management and prevention strategies for each patient.

The test and any pre- and post-test genetic counseling services will be provided to pilot project participants at no charge and results will become a part of each patients medical record and available to the patient and all of his or her healthcare providers.

In addition to providing patient-specific information that can help determine health and wellness decisions, patient genomic data can also be used in for broader research applications that are helping to unravel the genetic basis for a number of diseases.

Patients who are interested in making their data available for research purposes can share their data through LunaDNA, the sharing platform of pilot project partner LunaPBC. Patients who choose to share their data with researchers will become shareholders in LunaPBC, a public benefit corporation owned by the individuals who provide their genomic data to the company. Data provided by LunaDNA to researchers I de-identified to protect the privacy of its member-owners. In the future the patients will also be able to shareand receive additional LunaPBC share forlifestyle, nutrition and environmental data.

Vermonters who choose to share their genomic data for research will play a leading role in the advancement of precision medicine, said Dawn Barry, LunaPBC president and co-founder. This effort puts patients first to create a virtuous cycle for research that doesnt sacrifice patients control or privacy.We are proud to bring our values as a public benefit corporation and community-owned platform to this partnership.

According to UVM Health, the pilot program, run through the ACO is a step toward moving to a value-based healthcare system.

Vermont and other states are moving away from fee-for-service health care and toward a system that emphasizes prevention, keeping people healthy, and treating illness at its earliest stages, Leonard said. Integrating genetic risks into clinical care will help patients and providers in their decision-making.

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UVM Health Taps LunaPBC, Invitae on Genomic Testing Pilot Project - Clinical OMICs News

By Michael Le Page

Beverley Thain / EyeEm/Getty Images

A project to sequence the genomes of 60,000 species of animals, plants, fungi and complex cells such as amoeba found in the British Isles is about to get under way. The Darwin Tree of Life project has raised the 9 million needed to collect and barcode the first 8000 species, and to sequence 2000 of them.

Barcoding involves finding distinctive DNA features so species can be identified by simple, quick tests. The Wellcome charity, which aims to improve health, is providing the funding because it thinks the work could have many benefits for people as well as wildlife, from finding new treatments for diseases to helping to feed a growing population.

To start with, the project aims to sequence one organism from each of the 4000 families of plants, animals, fungi and protists complex single cells in the British Isles, says Mark Blaxter, who is leading the Tree of Life programme at the UKs Wellcome Sanger. Species will also be chosen on the basis of how important, interesting and iconic they are, he says.

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Read more: Biologys moonshot: The mission to decode the DNA of all life

The first set will include badgers, red squirrels, all 59 British butterflies, 40 moths and a set of beach animals and seaweeds used in climate studies.

The project is part of a larger international push to sequence the genomes of the 1.5 million species of complex life on the planet, the Earth BioGenome project, formally launched last year. The organisers say it can be done for around $5 billion or around $3000 per species. Critics say simply getting samples of rare species could cost this much.

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The grand plan to sequence the genomes of 66,000 UK and Irish species - New Scientist News

Foodborne illnesses are not only an unpleasant personal experience for millions of Americans each year, theyre a logistical concern for businesses, with the potential to drive and keep people (and their dollars) away for good. As our food supply becomes increasingly global, the ability to accurately and quickly identify the source of any pathogen causing a foodborne illness has become exponentially more difficult. To ensure the safety of what we eat, the Food and Drug Administration (FDA) plans to build upon its early success with digital technology and whole-genome sequencing for its New Era of Smarter Food Safety.

Whole-genome sequencing

At its simplest, a genome is the information a cell needs to create an organism. Since an organisms genome is as unique as a fingerprint, sequencing that genome is the first step in being able to quickly identify just what is making a person sick. Scientists generate the sequence by gathering samples of a particular food in a sterile environment, mashing it up, and conducting the genome analysis. The result is the fingerprint for that specific entity.

The problem is, having this information on hand at the local level is useful only under very limited circumstances. For instance, it would be enough if a group of people became ill after eating a single meal with food sourced locally, in a single sitting at a single event. With a few calls, it might be possible to identify the food causing the illness and take steps to keep it from being shipped to new locations.

More common is the case in which a number of people with nothing in common at first become ill within days of one another. Making a match between the pathogen causing the illness and the pathogen in each food involved is still fairly straightforward if everything is sourced locally. But what if some of the food comes from sources across the globe? How are the fingerprints for those foods going to be of use in stopping the spread of the illness to additional locations when there is no way to readily communicate with other localities?

GenomeTrakr

So, to bring whole-genome information into play on a global scale, the FDA created a United States-based open-source distributed network of labs in 2013. The result is GenomeTrakr the stuff of foodie-sci-fi. It makes whole-genome sequences from foods around the world available globally. Any health agency, anywhere on the network, can upload data from a pathogen causing illness in their locality and receive information about entities that match or closely approximate that sequence. In effect, the power of the digital fingerprinting and related DNA sampling now in use in law enforcement can be put to work for foodborne illness outbreaks by either making a match or reporting that the match is likely to be found within a certain cluster of related genome sequences. This game-changing use of whole-genome sequencing has already helped to halt the spread of global foodborne pathogens several times.

A digital framework

But global genome sequencing is still not all that is needed to safeguard the food supply and your health. Being able to readily access a whole-genome sequence can tell you which food is the culprit, but how do you know where the food originated, what path it took from field to plate, and where any additional product is currently located on its journey from field to plate?

The FDAs remedy to this part of the challenge is to digitize the records kept at each step of a foods journey through the global system. Rather than filling out a paper form that remains local or creating a paper-based dossier that travels with a food shipment, each step along the way will be documented in a globally accessible, digital format. The result will be a system that complements the GenomeTrakr by making it possible to trace the source of a foodborne pathogen to its point of origin in minutes rather than weeks or months.

Why does it matter? It matters because ready access to the genome, the origin, and the trail it traveled will make it possible to stop the flow of this food through the system: It will keep additional people from becoming ill.

A blueprint

As the first step in the FDAs Strategic Blueprint for this New Era of Smarter Food Safety, agencies and companies from all parts of the food sector met in October to discuss the logistics of the new approach and offer input. Considerations ranging from ownership of the data to concerns about data transfer were among the many raised. These issues are not not only vital to the integrity of the data in the system, but will also result in a system we can count on when we sit down to eat.

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When it Comes to Identifying the Source of Foodborne Illness, The Future is Now - The Spoon

Anxious couples are approaching fertility doctors in the US with requests for a hotly debated new genetic test being called 23andMe, but on embryos.

The baby-picking test is being offered by a New Jersey startup company, Genomic Prediction, whose plans we first reported on two years ago.

The company says it can use DNA measurements to predict which embryos from an IVF procedure are least likely to end up with any of 11 different common diseases. In the next few weeks it's set to release case studies on its first clients.

Handed report cards on a batch of frozen embryos, parents can use the test results to try to choose the healthiest ones. The grades include risk estimates for diabetes, heart attacks, and five types of cancer.

According to flyers distributed by the company, it will also warn clients about any embryo predicted to become a person who is among the shortest 2% of the population, or who is in the lowest 2% in intelligence.

The test is straight out of the science fiction film Gattaca, a movie thats one of the inspirations of the startups CEO, Laurent Tellier. The companys other cofounders are testing expert Nathan Treff and Stephen Hsu, a Michigan State University administrator and media pundit.

So far, fertility centers have not leaped at the chance to offer the test, which is new and unproven. Instead, prospective parents are learning about the designer baby reports through word of mouth or news articles and taking the companys flyer to their doctors.

One such couple recently turned up at New York Universitys fertility center in Manhattan, says David Keefe, who is chairman of obstetrics and gynecology there. Right off the bat it raises all kind of questions about eugenics, he says.

Keefe, who has seven children, worries that couples who think they can choose kids from a menu could be disappointed. Its fraught with parenting issues, he says. So many couples just need to feel they have done enough.

Picking your baby

The companys project remains at a preliminary stage. While some embryos have been tested by the company, Tellier, the CEO, says he is unsure if any have yet been used to initiate a pregnancy.

The test is carried out on a few cells plucked from a days-old IVF embryo. Then Genomic Prediction measures its DNA at several hundred thousand genetic positions, from which it says it can create a statistical estimate, called a polygenic score, of the chance of disease later in life.

Genomic prediction

In October, the company pitched the test, which it calls LifeView, from a trade-show booth at the annual meeting of fertility doctors in Philadelphia. A promotional banner read: She has your partners ears and smile. Just not their risk of diabetes.

Criticism of the company from some genetics researchers has been intense.

It is irresponsible to suggest that the science is at the point where we could reliably predict which embryo to select to minimize the risk of disease. The science simply isnt there yet, says Graham Coop, a geneticist at the University of California, Davis, and a frequent critic of the company on Twitter.

The company has raised several million dollars in venture capital from investors including People Fund, Arab Angel, Passport Capital, and Sam Altman, the chairman of Y Combinator and CEO of OpenAI.

At an investor event last April, Genomic Prediction compared itself to 23andMe for IVF clinics and boasted it was preparing for a massive marketing push.

Our reporting suggests the company has struggled both to validate its predictions and to interest fertility centers in them. Its customers so far seem to be a scattering of individuals from around the world with specific family health worries. The company declined to name them, citing confidentiality.

The company is expected to soon present its first case reports, describing clients and their embryo test results. One case involves a married gay couple who have begun IVF using donor eggs and plan to employ a surrogate mother. That couple wants a child with a low risk for breast cancer.

How will it be used?

Genomic Prediction thinks it can piggyback on the most common type of preimplantation embryo test, which screens days-old embryos for major chromosome abnormalities, called aneuploidies. Such testing has become widespread in fertility centers for older mothers and is already employed in nearly a third of IVF attempts in the US. The new predictions could be added to it.

Fertility centers can also order tests for specific genetic diseases, such as cystic fibrosis, where a gene measurement will give a definite diagnosis of what embryo inherited the problem The new polygenic tests are more like forecasts, estimating risk for common diseases on the basis of variations in hundreds or thousands of genes, each with a small effect.

In a legal disclaimer, the company says it cant guarantee anything about the resulting child and that the assessment is NOT a diagnostic test.

Santiago Munne, an embryo testing expert and entrepreneur, thinks patients already undergoing aneuploidy testing would likely want the add-on test, but that doctors could object if it introduces uncertainty: For monogenic disease, if the embryo is abnormal, we will tell you, and it is. With a risk score, it may be affected. And some patients will only have embryos with higher risks. Then what?

As well, he says it wont be possible with a test to optimize a child for many features at once: My personal opinion is once you start looking, some embryos will be brighter, some will be taller, some will have longevity, and none will have those qualities all together. And in an IVF cycle, you produce maybe six embryos on average. You wont be able to get all the traits that you want.

Despite such inherent limits, theres a bigger plan afoot. Treff, the startup's chief scientist, believes even fertile couples might begin to undergo IVF just so they can select the best child. I do believe this is going to be the future we can start to ... reduce the incidence of disease in humans through IVF, Treff told an audience at a conference in China last month.

How many people will be willing to go through the trouble of IVF if they dont need it to have a baby? IVF involves weeks of hormone shots and two medical procedures (one to collect eggs, another to implant the embryos) and typically costs around $15,000. Add to that the companys fee to test embryos, which is $1,000, plus $400 for each embryo scored.

If someone is fertile, unless there is a family history of disease, I dont think that it is going to be popular, says Munne.

Can you get a smarter baby?

Genomic Prediction has so far won the most attention for the possibility of using genetic scores to pick the most intelligent children from a petri dish. It has tried to distance itself from the controversial concept, but thats been difficult because Hsu, a cofounder, is frequently in the media discussing the idea.

Hsu told The Guardian this year that accurate IQ predictors will be possible if not in the next five years, the next 10 years certainly. He says other countries, or the ultra-wealthy, might be the first to try to boost IQ in their kids this way.

During his talk in China, Treff called improving intelligence via embryo selection an application that many people think is unethical." In private, Treff tells other scientists he thinks it's doable, but wants to promote the technology for medical purposes only.

Ms Tech

For now, the company is limiting itself to alerting parents to embryos it predicts will be the least intelligent, with the highest chance of an IQ which qualifies as intellectual disability according to psychiatric manuals.

Some experts see a transparent maneuver to avoid controversy. They say theyre going to test for the medical condition of intellectual disability, not for the smartest embryos, because they know people are going to object to that, says Laura Hercher, who trains genetic counselors at Sarah Lawrence College. They are trying to slide, slide into traits without admitting as much.

A May report from the Hebrew University of Jerusalem found that trying to pick the tallest or smartest embryos might not work particularly well. Researchers there estimated that using polygenic scores to locate the tallest or smartest child from a batch of sibling embryos would result in an average gain of 2.5 centimeters in height, and less than three IQ points.

They modeled what everyone is scared of happening, Treff said of that study. Its not what we are doing.

The predictions, however, could be more effective at helping people avoid children with specific diseases. Treff, during his speech in China, said that a couple choosing between two embryos would see, on average, a 45% reduction in risk for type 1 diabetes. That is a serious disease from which Treff suffers and which runs in families, although it has complex causes. The more embryos there are to choose from, he says, the more the risk will go down.

Demand for the test

Patients and doctors are mostly on their own when it comes to deciding if the tests really work. While federal and state agencies do oversee laboratory accuracy, the oversight is limited to whether analytes like DNA are correctly measured, not what they mean. So Genomic Prediction doesnt need to prove that the test is useful before selling it. In fact, it could take decades to ascertain if tested kids fare better than others.

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And its not only whether the test works or not. Uptake will depend on demand from patients and the degree of pushback from doctors and genetic counselors. In the US, tests for genderthat is, picking a boy or a girl embryoare accepted and relatively routine. But thats never become the case for choosing eye color, which is also possible. In terms of eye color, the pressure not to do it, to not offer it, was met with a weak market demand. So it doesnt exist, says Hercher.

Genomic Prediction provided a map of 12 fertility clinics it says will order its test, including five in the US and others in Nigeria, Peru, Thailand, and Taiwan.

MIT Technology Review was able to independently locate two IVF clinics where customers have recently requested the embryo predictions. Michael Alper, founder of Boston IVF, one of the worlds largest fertility clinics, says his center was approached by a couple a few weeks ago but he decided the request needs to be weighed by the centers ethics committee before he would agree to order it.

This is the first case we have had, says Alper. To me its a 23andMe type of prediction: theres a propensity, but how strong? That is the problem. We dont have any problem testing for cystic fibrosisthat is a lethal disease, it strikes young. But we are not there yet with these other tests. Its soft; its not that predictive.

At NYU, Keefe says the test raises profound questions. His center is in Midtown Manhattan, just blocks from a hub of finance and legal offices. He says his clientele are typically well-off professionals, people who have programmed everything in life and feel they are in control. They sometimes even ask out loud if a mere doctor is smart enough to help them.

The case he is working on involves a family that has two children with autism. They now want a child without the condition, and they hope the intelligence feature of the test will help them. Treff says he counseled the family that the Genomic Prediction test wasnt likely to helpautism can have specific genetic causes that the intelligence prediction isnt designed to capture.

Yet the family remains interested. They want to do whatever they can to have a healthy kid. Keefe says hes so far supporting their choice, but he is concerned by all that it implies. There is potential psychological harm to the kid, he says. God forbid the kids ends up with autism after spending this money.

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The world's first Gattaca baby tests are finally here - MIT Technology Review

11 November 2019

Twenty thousand babies are to have their genomes sequenced at birth in an NHS-based pilot announced by Matt Hancock on Monday 4 November at the Genomics England Research Conference.

The announcement by the Secretary of State for Health and Social Care did not receive the fanfare or focus it deserved. There has not been a press release from the Department of Health and Social Care, and it was only picked up by the papers on Wednesday 6 November, just before the government and the civil service entered the pre-election purdah period.

The Sun, and the Times welcomed the news, sharing that 'around 3000 of the 660,000 babies born a year in England and Wales are thought to have a treatable, early-onset disease', while other coverage (Futurism, New Scientist)raised ethical challenges and privacy concerns.

It is not hyperbole to state that England will shortly lead the world in genomic diagnosis. The new NHS England Genomic Medicine service will offer all acutely ill children with a likely monogenic condition, and all children with cancer, a whole-genome sequence. The list of diagnostic grade genes on Genomics England's curated PanelApp which allows experts to review genes and the evidence for their relation to conditions, was at 3139 in August 2019 at PanelApp's fourth birthday, with 56,640 gene-disease curations.

In the UK we are in an unusual position. We are at the forefront of diagnosing people with rare diseases but are among the countries screening for fewest rare conditions at birth (see BioNews 1008). The announced pilot offers one route to bridge this disparity. We are behind most countries in Europe and other high-income countries when it comes to identification of babies at risk of genetic conditions at birth.

The UK National Screening Committee currently recommends that the NHS screens for nine conditions at birth few enough to list here: phenylketonuria (first screened for in 1969), congenital hypothyroidism (1981), sickle cell disease (2006), cystic fibrosis (1983 in Northern Ireland, 1997 in Wales, 2003 in Scotland and 2007 in England), and four further metabolic conditions: medium-chain acyl-CoA dehydrogenase deficiency, maple syrup urine disease, isovaleric acidaemia, glutaric aciduria type 1 and homocystinuria (all began in 2015 in England and Wales, and 2017 in Scotland, with no screening in Northern Ireland).

For comparison, Italy screens for 43 conditions, the Netherlands 34, Australia 28, the Czech Republic 20, while Spain screens for seven, Ireland six, and France five.

Diagnosis of symptomatic individuals and screening at birth are two different things: clinical diagnoses are performed with a combination of genomic information from testing and phenotypic information from consultation and a screening approach is clearly not appropriate for all conditions listed in PanelApp. While the disparity between the UK's adoption of each is so great, it can appear to our community that the NHS is waiting for children to get ill instead of intervening sooner.

The benefits of diagnosis to families affected by rare conditions are accepted, but the benefits of screening to identify these families in advance of symptoms developing are ignored. For the affected child, screening can prevent a future lengthy diagnostic odyssey, provide access to treatments that are best delivered before symptoms develop, enable participation in clinical trials and ensure the best possible quality of life by beginning care pathways at the optimum moment.

To the family, screening can identify a risk to future births and enable reproductive decision-making, as well as giving time to prepare for the expected condition. More broadly, newborn screening can improve our knowledge of the incidence and nature of rare conditions and enable research.

In July 2019, Genetic Alliance UK launched our Patient Charter on Newborn Screening: Fixing the Present, Building for the Future. Our community recommended that a pilot of newborn screening using genome sequencing should go ahead as soon as possible for the key reason that the number of conditions that can be identified is much greater than when using traditional metabolic screening technology, which relies on early metabolic indications of the condition. Genomic screening can identify future risk before there are any symptoms. The US-based research project BabySeq labelled 885 gene-disease pairs as having 'definitive or strong evidence to cause a highly penetrant childhood-onset disorder'.

The community also identified the challenges that must be addressed in a pilot. Some of these were picked up in concerns aired in reporting of the announcement. Futurist raised that: 'It would also mean that kids' entire genetic sequence will be mapped out long before they can understand what that means or agree to having it done. As genomic science develops, dilemmas about personal privacy and what happens to the data after its collected are still far from being sorted out.'

Our workshop participants noted that we 'are struggling to adequately inform patients and families about the screening done now within the NHS' but felt that 'we should press on, but recognise that communication and standards need to improve'.

The concern about children's health data being examined before they gain the capacity to understand the implications was one of the many concerns around this initiative that have already been dealt with in some form. Parental choice and how it affects children as they grow up is not a new issue, and the approaches taken to explore this question in the past will be applicable to this pilot.

New Scientist's coverage focused on the challenge of dealing with a screening result for a late-onset condition, which raises the question as to which conditions should be screened for and how they should be selected. Again, this is a question that has been solved before in a different context. The means by which the 100,000 Genomes Project identified whether to report findings and which additional findings to offer can be adapted to address this question.

Other familiar questions will need to be examined again from a different perspective: how to manage a parallel health and research consenting process, the ethics of storing genome sequences, and how genetic information will be shared within families.

New questions that need to be addressed in the pilot include where this methodology fits alongside the current newborn screening programme, and whether this approach is a good use of NHS resources.

The key element of what little we know about this initiative so far is that it is a pilot. Genomics has vast potential to deliver benefit to the currently undeserved community of people living with rare, genetic and undiagnosed conditions. We need to take every opportunity to find answers to the challenges instead of letting them hold us back.

Link:
Let's grasp this opportunity to examine the potential future of screening - BioNews

New technology reduces amount of time spent preparing treatment plans in cancer genomic medicine by half in verification trials conducted with the Department of Hematology and Oncology

KAWASAKI, Japan, Nov 7, 2019 - (JCN Newswire) - Fujitsu has announced the results of a joint research project it has been conducting with the Institute of Medical Science at the University of Tokyo since April 2018. As part of this joint research, Fujitsu Laboratories Ltd. has successfully developed and verified AI technology to improve the efficiency of treatment planning in cancer genomic medicine, demonstrating its effectiveness through verification experiments at the Institute of Medical Science at the University of Tokyo.

In the field of cancer genomic medicine, creating treatment plans derived from genomic information remains a costly and time-consuming process. The newly developed technology extracts from a vast body of research and academic papers to generate a knowledge graph of cancer genomic medicine that can be used for creating treatment plans, including the effects of a given course of treatment. Verification trial experiments using this technology have allowed the Department of Hematology and Oncology at the Institute of Medical Science, the University of Tokyo to reduce the amount of work required to determine a treatment plan for acute myeloid leukemia by more than half, delivering improved efficiency.

Moving forward, Fujitsu Laboratories will support the work of medical doctors by expanding the technology to deal with a greater range of cancer types and contribute to the overall advancement of cancer genomic medicine.

The technology will be on display at "Fujitsu Forum Munich 2019" in Munich, Germany, from Wednesday, November 6.

Development Background

The goal of cancer genomic medicine is to provide optimal medical care for each patient by identifying genomic mutations in cancer patients and predicting the likelihood of disease, as well as drug response and side effects. Starting from June 2019 in Japan, cancer gene panel testing has been covered by health insurance, and industry experts anticipate an increasing number of patients to seek further testing.

Presently, in the field of cancer genomic medicine, it remains necessary for specialist physicians to painstakingly search for relevant articles one by one from a database and determine appropriate treatment methods as well as their effects on the patient (Figure 1). To address these challenges, Fujitsu Laboratories and the Institute of Medical Science at the University of Tokyo's launched a joint AI research project beginning in April 2018 to improve the efficiency and sophistication of the work of physicians specializing in cancer genomics, subsequently conducting a verification trial for the technology.

Outline of the Verification Trials

1. Trial PeriodJuly 2018 to September 2019

2. Trial LocationDepartment of Hematology and Oncology, the Institute of Medical Science at the University of Tokyo

3. Developed technologyThe new technology automatically generates a database of knowledge on the relationship between gene mutations and therapeutic drugs, and the relationship between therapeutic drugs and their effects, drawing from medical papers. This is accomplished by integrating Fujitsu's AI technology for language processing, which identifies terms and phrases used in research papers from context, as well as insight of information needed to discuss treatment policies identified by the Institute of Medical Science at the University of Tokyo.

4. Verification Trial DetailsWith the newly developed technology, 2.4 million elements of relationships from 860,000 medical papers are automatically extracted as knowledge to construct a knowledge graph database for cancer genomic medicine.

In this study, the time required for 4 physicians specializing in hematological malignancies at the Institute of Medical Science at the University of Tokyo to search and examine papers using the technology based on past cases of acute myeloid leukemia is measured, and the efficiency of examination work with and without the newly developed technology is evaluated(1) (Fig. 2). For this verification experiment, a database developed by Fujitsu Limited in cooperation with the Japan Agency for Medical Research and Development as part of the "Program for an Integrated Database of Clinical and Genomic Information"(2) is used as part of the knowledge graph.

5. ResultsThe technology reduced the burden of reading the entire paper by presenting the knowledge extracted from each paper and enabled users to focus on pertinent aspects of research alone. As a result, it was confirmed that the new technology can reduce the amount of time spent on this task by more than half, compared with the average of about 30 minutes per each study it took in the past. At present, it is estimated that more than 12,000 people suffer from leukemia annually in Japan(3), and if genomic medical treatments are administered to all of them using this new technology, the 6,000 hours of examination work normally required for experts can be shortened to 3,000 hours or less, considerably expediting the process of determining the a treatment appropriate for each patient.

Future Plans

Technology developed at Fujitsu Laboratories to explain the reason and rationale behind AI decision-making(4) is to be used in conjunction with this technology in order to further improve the efficiency of the genomic mutation curation process. Fujitsu will further use the knowledge graph for precision medicine developed through this joint research to improve the efficiency of the study of gene mutations for a wide range of cancer types, and actively promote the development of cancer genomics in clinical practice.

Comment from our Research Partners

Professor Seiya Imoto, Health Intelligence Center, the Institute of Medical Science at the University of Tokyo

"The promise of new genomic medicine, which harness the wealth of information contained in the human genome, remains extremely difficult to fully exploit given the limited time of doctors. This trial demonstrates that AI technology can be used to support planning for treatments that target blood tumors, helping physicians to process the research literature that forms the basis of therapeutic best practices in less than half the time it has previously taken. We hope that the further development of AI technology for various genome-related medical contexts will enable more patients to receive precision medicine, contributing to the realization of medical care in Japan that can beat cancer."

(1) The efficiency of examination work with and without the newly developed technology is evaluatedIn the actual verification work, apart from searching relevant research papers, doctors engage in various additional work, such as interpreting sequence data, analyzing data, and creating reports.(2) The Japan Agency for Medical Research and Development as part of the "Program for an Integrated Database of Clinical and Genomic Information"A program based on the interim report of the Council for Promotion of Genome Medicine Implementation, to verify the relationship between genome information and disease specificity and clinical characteristics, to develop a database that comprehensively handles clinical information and genomic information that can be used for clinical and research purposes, and to promote advanced research and development that makes use of the research infrastructure.(3) At present, it is estimated that more than 12,000 people suffer from leukemia annually in JapanCancer Information Service, National Cancer Research Center "Cancer registry and statistics"(Source).(4) Press Release"Fujitsu Fuses Deep Tensor with Knowledge Graph to Explain Reason and Basis Behind AI-Generated Findings" (September 20, 2017)

About Fujitsu

Fujitsu is the leading Japanese information and communication technology (ICT) company, offering a full range of technology products, solutions, and services. Approximately 132,000 Fujitsu people support customers in more than 100 countries. We use our experience and the power of ICT to shape the future of society with our customers. Fujitsu Limited (Code: 6702) reported consolidated revenues of 4.0 trillion yen (US $36 billion) for the fiscal year ended March 31, 2019. For more information, please see http://www.fujitsu.com.

About Fujitsu Laboratories

Founded in 1968 as a wholly owned subsidiary of Fujitsu Limited, Fujitsu Laboratories Ltd. is one of the premier research centers in the world. With a global network of laboratories in Japan, China, the United States and Europe, the organization conducts a wide range of basic and applied research in the areas of Next-generation Services, Computer Servers, Networks, Electronic Devices, and Advanced Materials. For more information, please see http://www.fujitsu.com/jp/group/labs/en/.

Technical ContactsFujitsu Laboratories Ltd.Artificial Intelligence LaboratoryE-mail: qa_fy2019@ml.labs.fujitsu.com

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Fujitsu Improves Efficiency in Cancer Genomic Medicine in Joint AI Research with the Institute of Medical Science at the University of Tokyo -...

REDWOOD CITY, Calif., Nov. 7, 2019 /PRNewswire/ --Genomic Health, Inc.(NASDAQ: GHDX) announced that its stockholders voted to approve the company's proposed combination with Exact Sciences Corp (NASDAQ: EXAS) at a special meeting held earlier today.

As previously announced, on July 29, 2019, Genomic Health and Exact Sciences entered into the merger agreement by which Exact Sciences will acquire Genomic Health in a cash and stock transaction. With the receipt of the required stockholder approval, Genomic Health and Exact Sciences expect to close the transaction on Friday, November 8 subject to satisfaction of the remaining customary closing conditions.

Final vote tallies from the Genomic Health special meeting of stockholders are subject to certification by the Company's inspector of elections and will be included in a report to be filed by the Company with the Securities and Exchange Commission (the "SEC").

AboutGenomic HealthGenomic Health, Inc. (NASDAQ: GHDX) is the world's leading provider of genomic-based diagnostic tests that help optimize cancer care, including addressing the overtreatment of the disease, one of the greatest issues in healthcare today. With its Oncotype IQGenomic Intelligence Platform, the company is applying its world-class scientific and commercial expertise and infrastructure to lead the translation of clinical and genomic data into actionable results for treatment planning throughout the cancer patient journey, from diagnosis to treatment selection and monitoring. The Oncotype IQ portfolio of genomic tests and services currently consists of the company's flagship line of Oncotype DXgene expression tests that have been used to guide treatment decisions for over 1 million cancer patients worldwide.Genomic Healthis expanding its test portfolio to include additional liquid- and tissue-based tests, including the Oncotype DXAR-V7 Nucleus Detecttest. The company is based inRedwood City,California,with international headquarters inGeneva,Switzerland. For more information, please visitwww.GenomicHealth.comand follow the company on Twitter:@GenomicHealth,Facebook,YouTubeandLinkedIn.

This press release contains statements, including statements regarding the merger that are forward-looking statements within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, that are intended to be covered by the "safe harbor" created thereby. Forward-looking statements, which are based on certain assumptions and describe future plans, expectations and events, can generally be identified by the use of forward-looking terms such as "believe," "expect," "may," "will," "should," "would," "could," "seek," "intend," "plan," "anticipate" or other comparable terms. All statements other than statements of historical facts included in this press release regarding the expected closing of the merger are forward-looking statements. Forward-looking statements are neither historical facts nor assurances of future performance or events. Instead, they are based only on current beliefs, expectations and assumptions regarding future business developments, future plans and strategies, projections, anticipated events and trends, the economy and other future conditions. Because forward-looking statements relate to the future, they are subject to inherent uncertainties, risks and changes in circumstances that are difficult to predict and many of which are outside of Genomic Health's control. Actual results, conditions and events may differ materially from those indicated in the forward-looking statements. Therefore, you should not rely on any of these forward-looking statements. Important factors that could cause actual results, conditions and events to differ materially from those indicated in the forward-looking statements include, among others, the following: the ability of the parties to satisfy the remaining closing conditions in order to close the proposed merger with Exact Sciences Corporation and other risks as detailed from time to time in Genomic Health's reports filed with the SEC, including its annual report on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K and other documents filed with the SEC.

There can be no assurance that the merger or any other transaction described will in fact be completed in the manner described or at all. Any forward-looking statement speaks only as of the date on which it is made, and Genomic Health assumes no obligation to update or revise such statement, whether as a result of new information, future events or otherwise, except as required by applicable law. Readers are cautioned not to place undue reliance on any of these forward-looking statements.

GHDX-F

SOURCE Genomic Health, Inc.

http://www.GenomicHealth.com

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Genomic Health Stockholders Approve Proposed Acquisition by Exact Sciences - PRNewswire