Category Archives: Genome

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Genome analysis of ancient people from Africa reveals a complicated migration history for the human species.

Ignored for too long by researchers, ancient humans who lived in Africa thousands of years ago are finally having their genomes studied. Two projects released results this week on the genomes of around 20 individuals, which together reveal that the history of our species on the continent was far more complex than previously thought.

Africas neglect until now by ancient-DNA researchers was largely down to the continents scorching climate. Because heat speeds the deterioration of DNA, scientists have focused on sequencing remains from cooler European sites and Siberian permafrost. The first success in Africa came in 2015 when researchers sequenced the genome of a 4,500-year-old man from Ethiopia who was preserved in a relatively chilly mountainous cave.

But advances in removing contamination and the discovery that a tinyinner ear bone is chock full ofancient DNA has convincedresearchers that the technology is finally ready to grapple withAfricas past.

Stephan Schiffels, a population geneticist at the Max Planck Institute for the Science of Human History, in Jena, Germany, says gaps in the knowledge of sub-Saharan African history are embarrassing especially in light of how much researchers know about ancient peoples in Eurasia. This makes it all the more important to use DNA to uncover Africa's hidden history of human migration, he says.

That is what a team led by Pontus Skoglund and David Reich, population geneticists at Harvard Medical School in Boston, Massachusetts, have now done. In a talk on 3 July at the Society for Molecular Biologys annual meeting in Austin, Texas, Skoglund said his team had examined the genomes of 15 ancient individuals and described detailed analysis of 11 of them who lived as long as 6,000 years ago in eastern and southern Africa.

They showed ancient humans moved around on the continent far more than was appreciated. The genome of a 3,000-year-old individual from Tanzania bore the ancestry of both ancient East African hunter-gatherers and early farmers from the Middle East. That supports past studies that documented a back to Africa migration several thousand years ago: these migrants were closely related to early farmers from the Levant region in the Middle East.

The Tanzanian fossil was found at an archaeological site linked to animal herding, or pastoralism, and some of its genetic signatures have also been found in present-day pastoralists in southern Africa, Skoglund said. This suggests that east Africans brought herding to southern Africa.

The unpublished study from Skoglunds team revealed additional movement. The genome of a 2,000-year-old individual from southern Africa was related to contemporary southern African hunter-gatherers known as the San, as well as to ancient hunter-gatherers the team sequenced from Malawi and Tanzania but not to the current inhabitants of eastern Africa.

The reason for this, Skoglund suggested, is a well-documented migration of Bantu groups from Western Africa, who brought agriculture and distinct language to eastern and southern Africa around 1,000-2,000 years ago. This Bantu expansion seems to have completely replaced local hunter-gatherers. An individual who lived on Tanzanias Zanzibar peninsula 750 year ago, after the migration, shared no ancestry with earlier hunter-gatherers from southern or east Africa.

A separate team, led by Mattias Jakobsson at Uppsala University in Sweden, found evidence for the same migrations in the genome of a boy who lived 2,000 years ago near Balito Bay in South Africa and 6 other ancient southern Africans. Their study1 was posted to the bioRxiv preprint server last month.

Proof of migrations such as the Bantu expansion have been found at archaeological sites, as well as in the DNA of contemporary Africans, says Schiffels. But it is still nice to have direct evidence of these movements, he notes.

Ancient African genomes also have the potential to illuminate much earlier events. Jakobssons team used the Ballito Bay boys genome to infer that Homo sapiens emerged at least 260,000 years ago far earlier than previous genetic studies have suggested. Skoglunds team, meanwhile, used their ancient genomes to help uncover a possible ghost population that diverged from the founding population of H. sapiens before any other African group and later contributed to the genetic make-up of some present-day West Africans.

IainMathieson, a population geneticist at the University of Pennsylvania in Philadelphia,hopes that ancient African DNA can explain our species migration out of Africa, some 50,000-100,000 years ago, by painting a genetic picture of the continents inhabitants around this time.

This might require DNA far older than several thousand years which could mandateanother major technical advance. Analysis of bones thought to be about 300,000 years old from Morocco, attributed to the earliest-known H. sapiens, has so far yielded no usable DNA. "It's early days," for ancient African genomics, says Mathieson, "it really is."

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Ancient-genome studies grapple with Africa's past - Nature.com

July 6, 2017 Wild Emmer wheat. Credit: Energin .R Technologies 2009 LTD.

A global team of researchers has published the first-ever Wild Emmer wheat genome sequence in Science magazine. Wild Emmer wheat is the original form of nearly all the domesticated wheat in the world, including durum (pasta) and bread wheat. Wild emmer is too low-yielding to be of use to farmers today, but it contains many attractive characteristics that are being used by plant breeders to improve wheat.

The study was led by Dr. Assaf Distelfeld of Tel Aviv University's School of Plant Sciences and Food Security and Institute for Cereal Crops Improvement, in collaboration with several dozen scientists from institutions around the world and an Israel-based company - NRGene, which developed the bioinformatics technology that accelerated the research.

"This research is a synergistic partnership among public and private entities," said Dr. Daniel Chamovitz, Dean of Tel Aviv University's George S. Wise Faculty of Life Sciences, who was also involved in the research. "Ultimately, this research will have a significant impact on global food safety and security."

"Our ability to generate the Wild Emmer wheat genome sequence so rapidly is a huge step forward in genomic research," said Dr. Curtis Pozniak from the University of Saskatchewan, a project team member and Chair of the Canadian Ministry of Agriculture Strategic Research Program. "Wheat accounts for almost 20% of the calories humans consume worldwide, so a strong focus on improving the yield and quality of wheat is essential for our future food supply."

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"From a biological and historical viewpoint, we have created a 'time tunnel' we can use to examine wheat from before the origins of agriculture," said Dr. Distelfeld. "Our comparison to modern wheat has enabled us to identify the genes involved in domestication - the transition from wheat grown in the wild to modern day varieties. While the seeds of wild wheat readily fall off the plant and scatter, a change in two genes meant that in domesticated wheat, the seeds remained attached to the stalk; it is this trait that enabled humans to harvest wheat."

"This new resource allowed us to identify a number of other genes controlling main traits that were selected by early humans during wheat domestication and that served as foundation for developing modern wheat cultivars," said Dr. Eduard Akhunov of Kansas State University. "These genes provide an invaluable resource for empowering future breeding efforts. Wild Emmer is known as a source of novel variation that can help to improve the nutritional quality of grain as well as tolerance to diseases and water-limiting conditions."

"New genomic tools are already being implemented to identify novel genes for wheat production improvement under changing environment," explains Dr. Zvi Peleg of the Hebrew University of Jerusalem, Israel. "While many modern wheat cultivars are susceptible to water stress, Wild Emmer has undergone a long evolutionary history under the drought-prone Mediterranean climate. Thus, utilization of the wild genes in wheat breeding programs promotes producing more yield for less water." "The wheat genome is much more complex than most of the other crops and has agenome four times the size of a human genome." said Dr. Gil Ronen, NRGene's CEO. "Still, the computational technology we developed has allowed us to quickly assemble the very large and complex genome found in Wild Emmer's 14 chromosomes to a standard never achieved before in genomic studies."

For the first time, the sequences of the 14 chromosomes of Wild Emmer wheat are collapsed into a refined order, thanks to additional technology that utilizes DNA and protein links. "It was originally tested in humans and recently demonstrated in barley, both of which have smaller genomes than Wild Emmer wheat," says Dr. Nils Stein, the Head of Genomics of Genetic Resources at Leibniz Institute of Plant Genetics and Crop Plant Research in Germany. "These innovative technologies have changed the game in assembling the large cereal genomes."

"This sequencing approach used for Wild Emmer wheat is unprecedented and has paved the way to sequence durum wheat (the domesticated form of Wild Emmer). Now we can better understand how humanity transformed this wild plant into a modern, high-yielding and high-quality crop," said Dr. Luigi Cattivelli, Head of the CREA Research Centre for Genomics and Bioinformatics (Italy) and coordinator of the International Durum Wheat Genome Sequencing Consortium. "This Wild Emmer wheat sequencing and approach is an invaluable contribution to the entire wheat community to improve and better understand nutritional mechanisms," said Dr. Hikmet Budak, Montana Plant Science Endowed Chair at Montana State University.

"We now have the tools to study crops directly and to make and apply our discoveries more efficiently than ever before," concluded Dr. Distelfeld.

Explore further: A lesson from wheat evolution: From the wild to our spaghetti dish

More information: R. Avni el al., "Wild emmer genome architecture and diversity elucidate wheat evolution and domestication," Science (2017). science.sciencemag.org/cgi/doi 1126/science.aan0032

Journal reference: Science

Provided by: Tel Aviv University

While wheat has been much maligned recently for it's gluten content, and new suspicions casted about as to its nutritional value, scientists have been eager to trace the evolutionary history of wheat to better understand ...

Kansas State University wheat scientists have completed the first study of a chromosome in a tertiary gene pool and have called it a breakthrough in exploring wheat wild relatives for future crop improvement.

Increases in climate variability have placed new emphasis on the need for resilient wheat varieties. Alongside demands for increased resiliency, consumer interest in healthier, more functional foods is growing. Therefore, ...

The German Federal Ministry of Food and Agriculture announced today that it would award 1.5 million Euros to a project aimed at providing a reference sequence for two wheat chromosomes, part of the international effort to ...

A team of Spanish scientists, with the participation of the University of Granada, has carried out the first durum wheat genetic, phenotypic and geographic adaptation study to date. Durum wheat is mostly used for the production ...

The International Wheat Genome Sequencing Consortium (IWGSC) announced today the production of a whole genome assembly of bread wheat, the most widely grown cereal in the world, significantly accelerating global research ...

In butterflies, sex is determined by chromosome differences between males and females. But unlike in humans with the familiar X and Y, in butterflies, it is the females that determine the sex of offspring.

A University of Kentucky plant pathologist is part of an international team of researchers who have uncovered an important link to a disease which left unchecked could prove devastating to wheat. UK College of Agriculture, ...

A global team of researchers has published the first-ever Wild Emmer wheat genome sequence in Science magazine. Wild Emmer wheat is the original form of nearly all the domesticated wheat in the world, including durum (pasta) ...

After observing the mating habits of chacma baboons living in the wild over a four-year period, researchers have found that males of the species often use long-term sexual intimidation to control their mates. The findings ...

Bacteria of the Spiroplasma genus produce toxic, ribosome-inactivating proteins (RIPs) that appear to protect their symbiotic host flies against parasitic wasps, according to new research published in PLOS Pathogens.

Plants and brains are more alike than you might think: Salk scientists discovered that the mathematical rules governing how plants grow are similar to how brain cells sprout connections. The new work, published in Current ...

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Wild wheat genome sequencing provides 'time tunnel' capable of ... - Phys.Org

A new era of genome-based personalised medicine could open up for cancer patients within five years under new plans unveiled by the Government's chief medical adviser.

The "genomics dream" outlined by Professor Dame Sally Davies would see millions of patients having all their DNA tested as genome sequencing becomes as routine as MRI or CT scans.

Ultimately, the future goal is for every cancer patient to have his or her whole genome sequenced, making the procedure as standard as blood tests and biopsies.

People with rare diseases are also expected to benefit from having greater access to the technology, ending the years long "diagnostic odyssey" of multiple tests and visits to different specialists.

Whole genome sequencing involves unscrambling the entire book of genetic instructions that make us what we are, encompassing 3.2 billion "letters" of code.

Research suggests that in 60 per centof cases, the genomes of cancer patients reveal "actionable" data - personal mutations that can shape future treatment.

Tens of thousands of NHS patients have already had their DNA mapped, but the new recommendations set out in Chief Medical Officer Dame Sally's "Generation Genome" report aim to multiply the numbers many times over.

Dame Sally said: "The age of precision medicine is now and the NHS must act fast to keep its place at the forefront of global science .

"This technology has the potential to change medicine forever - but we need all NHS staff, patients and the public to recognise and embrace its huge potential.

"Genomic medicine has huge implications for the understanding and treatment of rare diseases, cancer and infections."

Currently, genetic testing of NHS patients in England is conducted via 25 regional laboratories and a plethora of smaller ones operating along the lines of a "cottage industry", said Dame Sally.

Her chief recommendation is to centralise all the labs and establish a national network providing equal access to the tests across the country.

Within government, a new National Genomics Board would be set up, chaired by a minister, to oversee the expansion and development of genomic services taking into account new advances within the rapidly evolving technology.

Other proposals include offering every existing clinician training in genomics and ensuring their descendants are equipped to practise genomic medicine.

The report also recommends setting up a standing committee of experts to advise on the availability of genetic tests and indications for their use.

Lessons could be learned from the highly successful 100,000 Genomes Project, which has now sequenced more than 31,000 genomes from patients with cancer and rare diseases, said Dame Sally.

Her report calls for a simplified two-stage consent system that draws on the Genomes Project model and makes it easier for patients to get involved in research studies and clinical trials.

Speaking at a news briefing in London, Dame Sally said she hoped to see the new system fully operational within five years.

Part of what made greater access to whole genome sequencing feasible was the rapidly reducing cost of the tests, which has fallen from several thousand pounds to an average 680, she pointed out.

Results from analysis of cancer samples could now be delivered in as little as four weeks.

In the short term, she wanted to see "all appropriate patients" given the opportunity to have their genomes sequenced under the guidance of experts.

Wearable device could help fight brain cancer

Further down the line, she hoped the tests would become routine for every cancer patient.

Dame Sally said: "Yes, my dream is that, in the end, every patient gets their genome done if they've got cancer.

"It's not just their genome but its the cancer itself, and as the cancer changes over time and with treatment it will need redoing.

"But you go at it through what will give a worthwhile actionable result for the patients, and the experts will tell us."

Health Secretary Jeremy Hunt said he welcomed the report, pointing out that the UK had established itself as a world leader in genomics medicine.

He added: "Tens of thousands of patients across the country have already benefited from quicker diagnosis, precise treatment and care, and we will support the NHS to continue its relentless drive to push the boundaries of modern science to benefit even more people."

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Every cancer patient could have DNA tested under five-year government plan to cut deaths - The Independent

Mike Liskay

Biotechnologist Andrew Adey developed a high-throughput method for mapping the genomes of single cells. The advance, reported in January, allows for the identification of diverse cell populations in tumours, and so paves a path towards precision medicine. To develop it, Adey, now at Oregon Health & Science University in Portland, relied on HeLa cells, a prolific cancer-cell line biopsied in the 1950s from Henrietta Lacks, who had cervical cancer, and used widely in biomedical research without her consent.

How has single-cell biology advanced?

In the mid-2000s, next-generation sequencing was just starting, so today's version of single-cell biology was non-existent. Today, researchers can look at genome-wide properties or other aspects of single cells.

How did you use HeLa cells?

I knew nothing about the history of HeLa, just that it was a cancer-cell control line that grew really well. We wanted to understand how different copies of chromosomes influence cells. Once we developed technology to do this in normal cells, we set out to see how those copies act in cancer cells, and so applied it to HeLa. We learned more about HeLa notably, that multiple copies of a genome can act differently and worked out the genomic changes that enable an aggressive cancer to reproduce so readily.

What was your role in the privacy debate over publishing HeLa sequence information?

As we were readying a paper in 2013 (A. Adey et al. Nature 500, 207211; 2013), we didn't know how we were going to publish genetic information that could have consequences for Lacks's descendants. Ultimately, the US National Institutes of Health reached an agreement with the Lacks family that accompanied our paper, and that granted researchers access to the cells while maintaining the Lacks's privacy. HeLa is a unique case one not only at the forefront of medical advances but also about the ethical informed consent that is crucial to medical practice.

Can you explain the technique put forth in your January paper?

Initially, our platform could fully sequence only the portion of the genome that regulates gene expression in single cells (S. A. Vitak et al. Nature Meth. 14, 302308; 2017). We wanted to progress to whole-genome sequencing from single cells. But when you target regulatory elements, you typically have access to only 14% of the genome. We had to work out how to free up the DNA to convert the entire genome into sequenceable molecules.

What were the main obstacles?

At one point, it seemed like we were playing 'whack-a-mole'. Every time we altered one fixed property of the protocol, something else that had been working fine would stop. It was challenging, because the genome is packed nicely into nuclei. We needed to destroy the proteins that packaged the DNA inside the nucleus, without destroying everything else. Most of the time, everything would just explode and we'd lose the ability to look at single cells.

What's next?

We've already improved our method from what we published in January. It's even more reproducible, and we can get more data from single cells. Half of my lab does technology development; the other half applies those methods to answer questions of interest. This method was the first step to examining other aspects at the single-cell level. We're now using these technologies to explore cell identity. For example, how does a cell respond when treated by a cancer drug?

How will your method affect cancer treatment?

With a single-cell focus, we can start to profile an individual's tumour and identify molecularly distinct subpopulations in a tumour. If we can then profile large cohorts and tumours at the single-cell level, we can learn how certain subpopulations will respond to specific drugs to better home in on effective treatments.

This interview has been edited for length and clarity.

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Turning point: Single-cell mapper - Nature.com

July 5, 2017 All flowers share a history of genome duplication, which may have contributed to their spectacular diversity. Credit: James Clark, University of Bristol

Scientists at the University of Bristol have shed new light on the evolution of flowers in research published today in the Royal Society journal Proceedings of the Royal Society B.

The evolution of plants has been punctuated by major innovations, none more striking among living plants than the flower.

Flowering plants account for the vast majority of living plant diversity and include all major crops.

The discovery that all flowering plants underwent a doubling of their genome at some point during their evolution has led to speculation that this duplication event triggered the diversification of this spectacular lineage, but the timing of this event has remained difficult to pin down.

Genome duplications provide a second copy of every single gene on which selection can act, potentially leading to new forms and greater diversity.

This process leads to the formation of large families of genes - we can examine the history of duplication in gene families in the genomes of all major groups of plants and then look to the rate of change in their DNA sequences in relation to the evidence presented by the plant fossil record. This provides us with a 'molecular clock', with which we can date evolutionary events.

James Clark from the University of Bristol's School of Earth Sciences, led the research.

He said: "We have found that, based on the signal of these gene families, the timing of this duplication does not support a direct role as a 'trigger' for flowering plant evolution.

"Rather, the duplication seems to have occurred at least 50 million years prior to the diversification of flowering plants.

"These results suggest that if the duplication had any impact on flowering plant evolution, then it may have been more of a 'long fuse' that may have paved the way for later innovations and diversification, rather than directly causing them."

Genome duplication undoubtedly had some role to play in the evolution of plants, and these findings highlight the need to carefully consider exactly when each duplication occurred.

Professor Philip Donoghue, also from the University of Bristol's School of Earth Sciences, co-authored the research.

He said: "Genome duplications are rare events, but they have often occurred at major turning points in evolutionary history, including in our own deep evolutionary history.

"Our approach will allow us and other scientists to get to the bottom of the relationship between genome duplication and evolutionary success."

Explore further: Researchers find size isn't everything in the world of plant evolution

More information: Constraining the timing of whole genome duplication in plant evolutionary history, Proceedings of the Royal Society B, rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2017.0912

Researchers from the University of Bristol have uncovered one of the reasons for the evolutionary success of flowering plants.

U.S. scientists may have solved Charles Darwin's "abominable mystery" of flowering plants' rapid evolution after they appeared 140 million years ago.

(PhysOrg.com) -- Researchers from the University of Florida and six other institutions have unlocked some of the key foundations for the evolution of seed and flowering plants.

(Phys.org)A team of researchers from several academic institutions in the U.S. has found that contrary to popular belief, conifers have experienced at least two complete genome duplication events over the course of their ...

(PhysOrg.com) -- The evolution and diversification of the more than 300,000 living species of flowering plants may have been "jump started" much earlier than previously calculated, a new study indicates. According to Claude ...

In a step that advances our ability to discern the ancient evolutionary relationships between different genes and their biological functions, researchers have provided insight into the present-day outcome of a single gene ...

Researchers at the University of Manchester have discovered a new species of yeast that could help brewers create better lager.

A study of burrowing bettongs in the Australian desert has shown for the first time that exposing threatened native animals to small numbers of predators in the wild teaches them how to avoid their enemies.

Scientists at the University of Bristol have shed new light on the evolution of flowers in research published today in the Royal Society journal Proceedings of the Royal Society B.

Maligned as a bee-killer and possibly cancer-causing, a common herbicide has turned out to be a boon for tadpoles making them more toxic to predators, researchers said Wednesday.

A wealth of previously undescribed plant enzymes have been discovered by scientists at the John Innes Centre. The team who uncovered the compounds hope that harnessing the power of these enzymes will unlock a rich new vein ...

For the first time, researchers have succeeded in establishing the relationships between 200-million-year-old plants based on chemical fingerprints. Using infrared spectroscopy and statistical analysis of organic molecules ...

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Flowers' genome duplication contributes to their spectacular diversity - Phys.Org

Getty Images / Pacific Press / Contributor

The NHS should embrace genomic testing for cancer patients and those with rare diseases, the UK's chief medical officer has said.

In her annual report, Dame Sally Davies, says that the ability to create personalised prevention methods is "now with us" and the health service should attempt to make the most of genomics and predictive algorithms.

"The importance of moving from a generalised top down model of health promotion to a more specific and personalised model is predicated on the reality that societal changes now pay much greater importance to individual autonomy," the annual report says.

Davies, who spoke at this year's WIRED Health conference, says health systems in the future must have a greater deal of individual autonomy.

In part, this can be achieved by genomic sequencing. The genome is the collection of a person's 20,000 genes and includes 3.2 billion letters of DNA. By sequencing the genome, it is possible to read every letter of a person's DNA and it is hoped doing so will allows clinicians to understand the origins of diseases.

The first complete human genome was sequenced in 2006 and since then the cost to do so has rapidly decreased. Genomics England, which is running a project to sequence 100,000 genomes, says sequencing now costs 1,000 to read every letter and takes two days.

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So far, proving its worth, the 100,000 genomes project has diagnosed three British men and two children with rare diseases based on their genomes. Davies says this approach should be expanded within the NHS going forward. Around 30,000 genomes have been sequenced so far.

"Personalised prevention must take place through the agency of the individual," the annual report says. "He or she is expected to change behaviour, or undergo screening, or in some other way to respond behaviourally to information".

Davies told The Guardian this approach has the potential to change the NHS and "has the potential to change medicine forever".

Davies says that rare inherited disorders should be tackled using a "combination of genomic, environmental and other biological markers". These could be inserted into a "risk prediction algorithm". When this can be achieved, it will be possible to enhance public health at a large scale, the report says.

There are obvious data protection considerations that need to be completed for the development of health tools that use a large number of people's data. A pioneering trial to create a prediction app between the NHS' Royal Free Trust and Google's DeepMind was found to have unlawfully used patient data. The test, which has since been altered, saw 1.6 million patients' data being used without proper authorisation.

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NHS should use genome testing and predictive algorithms for personalised prevention - Wired.co.uk

By Michael Le Page

The thought of shaping future generations to fit some pre-imagined ideal of strength and beauty is one that should make us uncomfortable. Once a fashionable field of enquiry, the study of eugenics remains associated with some of the worst excesses of the 20th century, from forced sterilisation to genocide. The lesson we might be tempted to draw from this is to let nature proceed unchecked, free from human meddling, and embrace the diversity it engenders.

But as ethically comforting as that sounds, deciding to do nothing is a decision in itself. We may like to think of humans as perfect, finished natural products that should not be interfered with, but natures creations are botch jobs, full of mindless mistakes. And evolutions way of getting rid of the worst mistakes is to let children suffer horribly and die young.

In the interests of human well-being, then, should we head back down the slippery slope?

Actually, we already have. In most countries, it is already legal to shape the genomes of our children in various ways, from the abortion of fetuses with Downs syndrome to the screening of embryos during IVF. Last year, the thin end of the wedge got that little bit thicker when the UK gave the go-ahead for what have been called three-parent babies, whose mitochondrial DNA is supplied by a third-party donor.

And now, thanks to the revolutionary genome-editing method known as CRISPR, we can directly edit the main genome of cells. In theory, CRISPR could be used to weed out the hundreds of mutations that make us more likely

Read more here:
The ethics issue: Should we edit our children's genomes? - New Scientist

Achieving the genomics dream could make a huge difference to the 3.5 million adults and children with one of the 7,000 recognised rare diseases that could be treated far more quickly and more effective with genome testing.

Every persons genome contains 3.2 billion letters of genetic code, amounting to two terabytes of data. If it was printed your genome would fill a stack of books 61 metres high. Although officials now talk about personalised medicine, what they are trying to deliver is diagnosis and treatment related to the genomic signature of a particular patient.

It would be a disservice to patients if the UK were slow to respond to innovations in this area.

Sir Harpal Kumar, Chief Executive, Cancer Research UK

This means giving the most effective drugs against cancer, using drugs which will cause fewer side effects, seeking new drugs and treatments and moving to personalised prevention. There will also be other applications, many of which we are not yet aware of, the report says.

In the case of cancer, tumour cells develop a different genome to normal cells. Comparing a patients normal and cancerous DNA can provide valuable clues about the best form of treatment, although this information is not set in stone. Cancers evolve rapidly and alter their DNA, which can make them resistant to treatments.

This is still much more to learn about genomes and their relation with treatment response, but once that knowledge base expands there should be much faster diagnosis of rare diseases which currently take on average four years to diagnose.

The average patient sees five different doctors and is misdiagnosed three times before the nature of his or her illness is finally known.

As Dame Sally Davies the nations top doctor pointed out when launching her Generation Genome report, the true benefits of genomic medicine will only be realised if all clinical staff, managers and the Government work together to make wider use of revolutionary genetics techniques in the battle to improve cancer survival rates and identify rare diseases faster so patients can get the right care at the earliest opportunity.

Sir Harpal Kumar, Cancer Research UKs chief executive, said: It would be a disservice to patients if the UK were slow to respond to innovations in this area.

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How your genome could make cancer treatment more effective - iNews

Genomic medicine has great potential and could revolutionise treatments on NHS. Photograph: AFP/Getty Images

Genomic testing should become a normal part of NHS care, beginning with cancer patients and those with rare diseases, says the chief medical officer, Dame Sally Davies.

In her annual report, Davies stresses her enthusiasm for the genomic revolution which could transform the treatment that NHS patients receive. Drugs can be matched to the disease and to the patient to maximise the benefit and reduce side-effects.

The genome is the collection of 20,000 genes, including 3.2 billion letters of DNA, that make up any individual. We all share about 99.8% of the genome. The secrets of our individuality and also of the diseases we are prone to lie in the other 0.2%, which is about 3 or 4 billion letters of DNA.

Davies says that individual patients have everything to gain from the pooling of data which allows scientists to compare hundreds of thousands of genomes, to find out why some have small mutations or errors in the code that lead to illness. She talked of a new social contract, in which the public recognises that they and everybody else will benefit if they allow data about their own genome to be studied.

The age of precision medicine is now and the NHS must act fast to keep its place at the forefront of global science, said Davies. This technology has the potential to change medicine forever but we need all NHS staff, patients and the public to recognise and embrace its huge potential. Genomic medicine has huge implications for the understanding and treatment of rare diseases, cancer and infections.

Cancer and rare diseases are the first targets for genomic medicine. More than 30,000 people have had their genomes sequenced so far. Within five years, she would like to see genomic testing to be as normal as blood tests and biopsies for cancer patients, leading to the most appropriate treatment for the individual. Davies said she wanted to democratise genomics medicine so that it would be available to every patient for whom it was appropriate.

That means we have got to change the NHS system, she said. Genomics is at present a cottage industry which needed to be centralised and extended across the country. We need to take the science to the patients and not the patients to the science, she said.

There are great potential benefits for patients with rare diseases, defined as those affecting fewer than one in 2,000 patients. But there are at least 6,000 rare diseases worldwide and at least three million people often children in the UK suffer from them. Genome sequencing is also very useful in infectious diseases, allowing doctors to find out whether antibiotic and antiviral drugs will work in a patient.

Amongst her recommendations, Davies calls for a National Genomics Board to be set up, chaired by a government minister. All genomic laboratories should be centralised and a national network established to provide equal access across the country, she says.

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Make DNA tests routine, says UK's chief medical officer - The Guardian

Our genomes are minefields, studded with potentially damaging DNA sequences over which hundreds of thousands of sentries stand guard. These sentries, called epigenetic marks, attach to the double helix at such spots and prevent the underlying DNA sequences from springing into destructive action.

About half the human genome is composed of these damaging sequences. They are places where ancient viruses and parasitic elements called transposons and retrotransposons have incorporated themselves over the long course of evolution. It's astonishing, then, to consider that during two of the most crucial processes in the life cycle, the sentries are removed, leaving the genome naked. The defenders are quickly welcomed back, but only after an interval in which the epigenetic slate is wiped clean.

Today in Cell, a team from Cold Spring Harbor Laboratory (CSHL) describes its discovery of what might be considered emergency replacements for the sentries, shock troops pressed into service across the genome only during these curiously undefended moments. Specifically, these defenders are protecting the genome in mammalian embryos, at the very early point in their development before they are implanted in the wall of the maternal uterus.

The preimplantation embryo is one of two normal settings in which epigenetic marks are wiped clean before being reinscribed. The other setting is a step in the formation of germline cells - sperm and eggs -- which have temporary defenders already known to biology, so-called piwi-interacting RNAs (piRNAs). The research published today, led by first author Andrea Schorn, a postdoctoral investigator in the lab of Rob Martienssen, demonstrates that another species of small RNA performs an analogous genome-defending role in preimplantation embryos during an interval of epigenetic reprogramming. Dr. Martienssen is a CSHL Professor and HHMI-Gordon and Betty Moore Foundation investigator.

The newly identified defenders come in two varieties - RNA fragments consisting of 18 and 22 nucleotides. These RNA fragments, Dr. Schorn discovered, are perfect complements of sequences in retrotransposons that must be engaged in order for the genomic parasites to be activated.

This fact led to the discovery. Schorn scrutinized the contents of mouse embryonic stem cells and found many free-floating RNA fragments 18 nucleotides in length. Computer analysis revealed that their sequences perfectly matched sequences within transfer RNAs. tRNAs are ubiquitous, and are involved in the synthesis of proteins. It has been known for decades that tRNAs are hijacked by long terminal repeat (LTR)-retrotransposons, a portion of their sequence docking at a primer binding site (PBS) and initiating a process that activates the genomic parasite.

"Knowing that LTR retrotransposons need tRNAs to replicate, it was very tempting to believe that these 18-nucleotide tRNA fragments we were seeing in preimplantation embryonic stem cells could interfere with that process," says Schorn. "We think the cell is deliberately chopping up full-length tRNAs into smaller fragments precisely because both tRNAs and the fragments cut from them recognize the PBS. This means the small, tRNA-derived fragments would be able to occupy that site and inhibit retrotransposon replication and mobility," Martienssen explains.

The implications, Martienssen says, are potentially profound. This appears to tell us one way in which the genomes of mammals have tolerated vast numbers of transposons and other parasitic elements, even during periods when the genome is wiped clean of repressive epigenetic marks. "It's plausible that this is a very ancient mechanism that cells have found to not only inhibit retrotransposons but help in protection against viruses as well," Martienssen says.

Read more from the original source:
Newly Identified Small RNA Fragments Defend the Genome When It's 'Naked' - Bioscience Technology