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Announced on January 13th by President Obama in his eighth and final State of the Union Address, the multi-billion dollar project will be led by US Vice President, Joe Biden, who has a vested interest in seeing new cures for cancer. Using genomics to cure cancer is being held on par with JFK’s desire in 1961 to land men on the moon.

The post The Cancer Moonshot appeared first on OUPblog.

2016 is here. The New Year is a time for renewal and resolution. It is also a time for dieting. Peak enrolment and attendance times at gyms occur after sumptuous holiday indulgences in December and again when beach wear is cracked out of cold storage in summer. As the obesity epidemic reaches across the globe we need new solutions. We need better ways to live healthy lifestyles.

The post We should all eat more DNA appeared first on OUPblog.

It is hard to quantify the impact of ‘role-model’ celebrities on the acceptance and uptake of genetic testing and bio-literacy, but it is surely significant. Angelina Jolie is an Oscar-winning actress, Brad Pitt’s other half, mother, humanitarian, and now a “DNA celebrity”. She propelled the topic of familial breast cancer, female prophylactic surgery, and DNA testing to the fore.

The post The Angelina Jolie effect appeared first on OUPblog.

Society owes a debt to Henrietta Lacks. Modern life benefits from long-term access to a small sample of her cells that contained incredibly unusual DNA. As Rebecca Skloot reports in her best-selling book, “The Immortal Life of Henrietta Lacks”, the story that unfolded after Lacks died at the age of 31 is one of injustice, tragedy, bravery, innovation and scientific discovery.

The post The woman who changed the world appeared first on OUPblog.

Kuwait is changing the playing field. In early July, just days after the June 26th deadly Imam Sadiq mosque bombing claimed by ISIS, Kuwait ruled to instate mandatory DNA-testing for all permanent residents. This is the first use of DNA testing at the national-level for security reasons, specifically as a counter-terrorism measure. An initial $400 million dollars is set aside for collecting the DNA profiles of all 1.3 million citizens and 2.9 million foreign residents

The post Kuwait’s war on ISIS and DNA appeared first on OUPblog.

Another ‘Awareness Day’, International Kissing Day, is coming up on July 6. It might not seem obvious but kissing, like most subjects can now be easily linked to the science of DNA. Thus, there could be no more perfect opener for my Double Helix column, given the elegance and beauty of a kiss. To start, there is the obvious biological link between kissing and DNA: propagation of the species. Kissing is not only pleasurable but seems to be a solid way to assess the quality and suitability of a mate.

The post International Kissing Day and DNA appeared first on OUPblog.

One of the most fun and exciting sources of information available for free on the Internet are the videos found on the Technology, Entertainment and Design (TED) website. TED is a hub of stories about innovation, achievement and change, each artfully packaged into a short, highly accessible talk by an outstanding speaker. As of April 2015, the TED website boasts 1900+ videos from some of the most imminent individuals in the world. Selected speakers range from Bill Clinton and Al Gore to Bono and other global celebrities to a range of academics experts.

The post TED Talks and DNA appeared first on OUPblog.

DNA is the foundation of life. It codes the instructions for the creation of all life on Earth. Scientists are now reading the autobiographies of organisms across the Tree of Life and writing new words, paragraphs, chapters, and even books as synthetic genomics gains steam. Quite astonishingly, the beautiful design and special properties of DNA makes it capable of many other amazing feats. Here are five man-made functions of DNA, all of which are contributing to the growing “industrial-DNA” phenomenon.

The post DNA: The amazing molecule appeared first on OUPblog.

The news that Britain is set to become the first country to authorize IVF using genetic material from three people—the so-called ‘three-parent baby’—has given rise to (very predictable) divisions of opinion. On the one hand are those who celebrate a national ‘first’, just as happened when Louise Brown, the first ever ‘test-tube baby’, was born in Oldham in 1978. Just as with IVF more broadly, the possibility for people who otherwise couldn’t to be come parents of healthy children is something to be welcomed.

The post The third parent appeared first on OUPblog.

Watching the field of genomics evolve over the past 20 years, it is intriguing to notice the word ‘genome’ cozying up to the word ‘million’. Genomics is moving beyond 1k, 10k and 100k genome projects. A new courtship is blossoming.

The Obama Administration has just announced a Million Genomes Project – and it’s not even the first.

Now both Craig Venter and Francis Collins, leads of the private and public versions of the Human Genome Project, are working on their million-omes.

The company 23andMe might be the first ‘million-ome-aire’. By 2014, the company founded by Ann Wojcicki processed upwards of 800,000 customer samples. Pundit Eric Topol suggests in his article “Who Owns Your DNA” that without the skirmish with the FDA, 23andMe would already have millions.

In 2011, China’s BGI, the world’s largest genomics research company, boldly announced a million human genomes project. Building on projects like the panda genome and the 3000 Rice Genomes project, the BGI is building new next-generation sequencing technologies to support its flagship project.

Also in 2011, the United States Veterans Affairs (VA) Research and Development program launched its Million Veteran Program (MVP) aiming to build the world’s largest database of genetic, military exposure, lifestyle, and health information. The “large, diverse, and altruistic patient population” of the VA puts it ahead of the others in collecting samples.

Venter’s path will be through his non-profit Human Longevity, Inc (HLI), launched in San Diego, California in 2014 with $70 million in investor funding. To support the company’s tagline — “It’s not just a long life we’re striving for, but one which is worth living” — Venter aims to sequence a million genomes by 2020.

At a price tag of $1000 dollars per genome, one million genomes could cost a billion US dollars. The original human genome project cost $3 billion only 13 years ago, but produced 1 trillion US dollars in economic impact.

The Collins’ ‘million-ome’ will pull together new and existing genomes, with an initial budget of $215 million dollars. This includes genomes from the MVP, which has already enrolled 300,000 veterans and sequenced 200,000. The focus will initially be on cancer but subjects will be healthy and ill, men and women, old and young; it is the foundation of a Precision Medicine Initiative.

In addition to these projects we will have millions anyway. ARC Investment Analysis suggested we could see 4 to 34 billion human genomes by 2024 at historical rates of sequencing – if current trends in dropping costs and demand continue.

How could we have more genomes than humans living on earth? Cancer genomics is in ‘gold rush’ phase. Steve Jobs was famously one of the first 20 people to have his genome sequenced. He paid $100k but did so to also have the genome of the cancer that killed him sequenced. He left a personal genomics legacy to the world, but his investment in DNA sequencing also serves as a reminder that a genome is not the same as a cure. Hopes are high, though, especially for cancer diagnostics. The International Cancer Genomics Consortium is already backed with a billion dollar budget and the field continues to explode.

Further, an adult human body consists of 37 trillion genomes all working together (plus the 100 trillion genomes of the microbial cells in our microbiome). There is mounting evidence we are all genomic mosaics, meaning we all have more than one genome (e.g. from pre-cancerous cells, transplants, and mothers who carry the genomes of past live-born babies).

It is good to cultivate a healthy skepticism and not be drawn into the hype. Critics exist, as always. At the other end of the continuum, Ken Weiss of The Mermaid’s Tale blog, a geneticist himself, has outlined reasons to put valuable research dollars elsewhere than a million genomes project or precision medicine, but given than they will happen, he also contemplates what should be done with resulting data.

Eric Topol said in response to the rise of ‘million-ome’ projects, that there are now many 100k projects and he “might rather have 100,000 people with ‘pan-oromic definition’ than 1 million with just native DNA”. By high definition he means all the mapping (sensors, anatomy, environmental quantified, gut microbiome, etc.) that belongs to his vision of a “Google medical map”.

There are huge differences between “projections,” “announcements,” and “hard (published) data.” Big projects can fall by the way-side. 23andMe hit a barrier with the FDA decision. The BGI is still tooling up. Obama hasn’t yet secured a budget. Venter is giving himself time. Everyone is starting to think about genomes inside the systems in which they exist in (cells, organs, organisms, ecosystems).

Regardless of trajectory, it is a foregone conclusion that, counting all sources, the number of sequenced genomes will pass one million in 2015, if it hasn’t already.

Google is imagining the day when researchers compute over millions of genomes and is building the infrastructure to support it; Google Genomics has launched offering $25/year pricing to hold your genome in the Cloud.

Why stop at millions? Jong Bhak is calling for billions. He is suggesting that “the genomics era hasn’t even started.” Bhak, a leader of the Korean Personal Genomes Project, a project to sequence the genomes of all 50 million Koreans, has outlined a vision for a Billion Genome Project.

The first to talk of ‘a genome for everyone’ was perhaps George Church, technologist and founder of the Personal Genome Project. He wrote 2005 a paper entitled “The Personal Genome Project.” In it he recalled talking with Wally Gilbert that “Six billion base pairs for six billion people had a nice ring to it”—back in 1976, soon after Gilbert invented DNA sequencing, for which he won a Nobel Prize.

The fact that more voices in global science are debating the pros and cons of ‘millions and billions of genomes’ is evidence that 2015 marks a shift towards a Practical Genomics Revolution. It is becoming practical to think big(ger).

The post Did you say millions of genomes? appeared first on OUPblog.

        

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By Danielle Venton

For millions of years, the stout, muscular Przewalski’s horse freely roamed the high grasslands of Central Asia. By the mid-1960s, these, the last of the wild horses, were virtually extinct: a result of hunting, habitat loss, and cross breeding with domestic horses.

Recovering from a tiny population of 12 individuals and only four purebred females, there are now nearly 2,000 Przewalski’s horses around the world. Once again, the light-colored horses, standing about 13 hands, or 1.3 meters, tall, are beginning to graze on the Asian steppe, thanks to captive breeding and reintroduction programs.

Protecting Przewalski’s horses, listed as critically endangered by the International Union for Conservation of Nature, will require far more than protecting their habitat. Understanding and safeguarding their genetic diversity is key, said Kateryna Makova, an evolutionary genomicist at Pennsylvania State University. In a new study (Goto et al. 2011), Makova and her colleagues Hiroki Goto, Oliver Ryder, and others report on the most complete genetic analysis of Przewalski’s horses to date, clarifying previous genetic analyses that were inconclusive.

Because Przewalksi’s horses are the only remaining wild horses, many people have hypothesized that they gave rise to modern domestic horses. The Australian Brumbies or the American Mustangs, sometimes referred to as wild horses, are actually feral domestic horses, adapted to life in the wild. Przewalski’s horses are not the direct progenitors of modern domestic horses, Makova and her colleagues conclude, but split approximately 0.12 Ma. Horses were likely domesticated several times on the Eurasian steppes. It is not known where and when the first event took place. Recent excavations in Kazakhstan indicate humans were using domestic horses as early as 5,500 years ago.

Przewalski’s horse and offspring

The team base their findings on a complete sequencing of the mitochondrial genome and a partial sequencing, between 1% and 2%, of the nuclear genome. They used one horse from each of the historical matrilineal lines. After processing the DNA samples with massively parallel sequencing technology, they compared the Przewalski’s horses to each other, to domestic Thoroughbred horses, and to an outgroup, the Somali wild ass.

Their results carry several implications for breeding strategies. Przewalski’s horses and domestic horses come from different evolutionary gene pools, so breeders should avoid crosses with domestic horses, they advise. Przewalski’s horses and domestic horses have a different number of chromosomes (66 for the former, compared with 64); yet their offspring are fertile (with 65 chromosomes). The hybrids are viable because they differ only by a centric fusion translocation, also called a Robertsonian translocation. The process of pairing chromosomes during meiosis is not disrupted. Cross breeding should be a last resort, if too few Przewalski’s horses are available. Their analysis also suggests that, since diverging, Przewalski’s and domestic horses have both retained joint ancestral genes and swapped genes between populations. One of the two current major blood lines, the “Prague” line, is known to have a Mongol pony as one of its ancestors. The other primary line, the “Munich” line, is believed to be pure. However, because the two groups have historically mixed, keeping “pure” Przewalski’s horses from Przewalski’s horses with known domestic horse contributions might not be necessary, the authors write.

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This is the latest post in our regular OUPblog column SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: how do organisms evolve?

By Jonathan Crowe

The world around us has been in a state of constant change for millions of years: mountains have been thrust skywards as the plates that make up the Earth’s surface crash against each other; huge glaciers have sculpted valleys into the landscape; arid deserts have replaced fertile grasslands as rain patterns have changed. But the living organisms that populate this world are just as dynamic: as environments have changed, so too has the plethora of creatures inhabiting them. But how do creatures change to keep step with the world in which they live? The answer lies in the process of evolution.

Many organisms are uniquely suited to their environment: polar bears have layers of fur and fat to insulate them from the bitter Arctic cold; camels have hooves with broad leathery pads to enable them to walk on desert sand. These so-called adaptations – characteristics that tailor a creature to its environment – do not develop overnight: a giraffe that is moved to a savannah with unusually tall trees won’t suddenly grow a longer neck to be able to reach the far-away leaves. Instead, adaptations develop over many generations. This process of gradual change to make you better suited to your environment is called what’s called evolution.

So how does this change actually happen? In previous posts I’ve explored how the information in our genomes acts as the recipe for the cells, tissues and organs from which we’re constructed. If we are somehow changing to suit our environment, then our genes must be changing too. But there isn’t some mysterious process through which our genes ‘know’ how to change: if an organism finds its environment turning cold, its genome won’t magically change so that it now includes a new recipe for the growth of extra fur to keep it warm. Instead, the raw ‘fuel’ for genetic change is an entirely random process: the process of gene mutation.

In my last post, I considered how gene mutation alters the DNA sequence of a gene, and so alters the information stored by that gene. If you change a recipe when cooking, the end product will be different. And so it is with our genome: if the information stored in our genome – the recipe for our existence – changes, then we must change in some way too.

I mentioned above how the process of mutation is random. A mutation may be introduced when an incorrect DNA ‘letter’ is inserted into a growing chain as a chromosome is being copied: instead of manufacturing a stretch of DNA with the sequence ATTGCCT, an error may occur at the second position, to give AATGCCT. But it’s just as likely that an error could have been introduced at the sixth position instead of the second, with ATTGCCT becoming ATTGCGT. Such mutations are entirely down to chance.

And this is where we encounter something of a paradox. Though the mutations that occur in our genes to fuel the process of evolution do so at random, evolution itself is anything but random. So how can we reconcile this seeming conflict?

To answer this question, let’s imagine a population of sheep, all of whom have a woolly coat of similar thickness. Quite by chance, a gene in one of the sheep in the population picks up a mutation so that offspring of that sheep develop a slightly thicker coat. However, the thick-coated sheep is in a minority: most of the population carry the normal, non-mutated gene, and so have coats of normal thickness. Now, the sheep population live in a fairly tempera

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This is the second post in our latest regular OUPblog column: SciWhys. Every month OUP editor and author Jonathan Crowe will be answering your science questions. Got a burning question about science that you’d like answered? Just email it to us, and Jonathan will answer what he can. Today: What are genes and genomes?

By Jonathan Crowe

I described in my last blog post how DNA acts as a store of biological information – information that serves as a set of instructions that direct our growth and function. Indeed, we could consider DNA to be the biological equivalent of a library – another repository of information with which we’re all probably much more familiar. The information we find in a library isn’t present in one huge tome, however. Rather, it is divided into discrete packages of information – namely books. And so it is with DNA: the biological information it stores isn’t captured in a single, huge molecule, but is divided into separate entities called chromosomes – the biological equivalent of individual books in a library.

I commented previously that DNA is composed of a long chain of four building blocks, A, C, G, and T. Rather than existing as an extended chain (like a stretched out length of rope), the DNA in a chromosome is tightly packaged. In fact, if stretched out (like our piece of rope), the DNA in a single chromosome would be around 2-8 cm long. Yet a typical chromosome is just 0.00002–0.002 cm long: that’s between 1000 and 100,000 times shorter than the unpackaged DNA would be. This packaging is quite the feat of space-saving efficiency.

Let’s return to our imaginary library of books. The information in a book isn’t presented as one long uninterrupted sequence of words. Rather, the information is divided into chapters. When we want to find out something from a book – to extract some specific information from it – we don’t read the whole thing cover-to-cover. Instead, we may just read a single chapter. In a fortuitous extension of our analogy, the same is true of information retrieval from chromosomes. The information captured in a single chromosome is stored in discrete ‘chunks’ (just as a book is divided into chapters), and these chunks can be read separately from one another. These ‘chunks’ – these discrete units of information – are what we call ‘genes’. In essence, one gene contains one snippet of biological information.

I’ve just likened chromosomes to books in a library. But is there a biological equivalent of the library itself? Well, yes, there is. Virtually every cell in the human body (with specific exceptions) contains 46 chromosomes – 23 from each of its parents. All of the genes found in this ‘library’ of chromosomes are collectively termed the ‘genome’. Put another way, a genome is a collection of all the genes found in a particular organism.

Different organisms have different-sized genomes. For example, the human genome comprises around 20,000-25,000 genes; the mouse genome, with 40 chromosomes, comprises a similar number of individual genes. However, the bacterium H. influenzae has just a single chromosome, containing around 1700 genes.

It is not just the number of genes (and chromosomes) in the genome that varies between organisms: the long stretches of DNA making up the genomes of different organisms have different sequences (and so store different information). These differences make sense, particularly if we imagine the genome of an organism to represent the ‘recipe’ for that organism: a human is quite a different organism from a mouse, so we would expect the instructions that direct the growth and function of the two organisms to differ.

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