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First spider genome sequenced, helping the quest to uncover arachnid secrets

First spider genome sequenced, helping the quest to uncover arachnid secrets | Amazing Science |

Scientists recently published the first spider genome, helping the quest to uncover secrets which could lead to smarter insecticides and man-made super-strong spider silk.

Bio-researchers led by Trine Bilde at Denmark's Aarhus University unravelled the DNA sequence of the tarantula and the African social velvet spider, each representing the two main groups of spiders. The tarantula—which is infamous despite having a bite that is only as painful as a bee sting—is a so-called mygalomorph, meaning a ground-dwelling spider that lurks in wait for its prey.

The social velvet spider is an araneomorph, part of a group of spiders that have diversified to exploit a wide range of habitats above ground, where they live in communities and weave sophisticated webs to snare flying insects.

Spiders are a source of fascination for biologists, as they combine survival skills with great efficiency. At a minimum cost in energy, they can catch prey as much as seven times their own body weight.

Chemists, though, see spiders somewhat differently. They hope to replicate spider silk, a complex protein many times stronger than steel or kevlar, and to use neurotoxins in spider venom, which kill specific insects, as the basis for greener, more selective pesticides.

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Genome Data Could Lead to Cancer Cures

Genome Data Could Lead to Cancer Cures | Amazing Science |

Scientists are cataloging the DNA of exceptional survivors for study,

Jan Crisitello, a 70-year-old grandmother of four, was diagnosed in 2002 with stage 4 melanoma, which kills the vast majority of its victims within five years. Although chemotherapy helped her make it past the five-year mark, by 2007 the cancer was growing again. Desperate, she joined a 29-patient trial of a drug being developed by Pfizer (PFE). The drug was a failure for almost all of the patients, and Pfizer spokeswoman Sally Beatty says it has been “deprioritized for further development.” For Crisitello, the drug worked, and her cancer is in full remission. Now oncologists are studying her DNA to determine how her genome may have made her unusually responsive to the drug. “I feel very fortunate,” she says. “It would make me feel good if they found out why and could replicate that for other people.”

So far, about 100 exceptional responders have been identified by researchers poring through roughly a decade’s worth of clinical trials, says Barbara Conley, associate director of the NCI’s cancer diagnosis program. Starting in June, she says, the institute will urge researchers and doctors nationwide to send in clinical data on these patients. “We want to cast a broad net,” Conley says. “The key is, can you find another patient with the same kind of abnormality, and will they respond?”

In a study presented in early April at the American Association for Cancer Research meeting in San Diego, researchers analyzed the case of a 57-year-old woman with advanced thyroid cancer whose tumor “melted away” during a drug trial and didn’t start growing again for 18 months, according to the study’s lead author, Dana-Farber instructor Nikhil Wagle. Although the rare, aggressive disease kills most victims within five months, an analysis of the patient’s genes showed that a mutation made her tumor responsive to Novartis’s (NVS) Afinitor, a drug typically used to treat kidney or breast cancer. Researchers plan to conduct further trials with thyroid cancer patients who have similar genetic mutations, Wagle says.

One of the first exceptional responders to have her genome sequenced has a similar mutation and saw her bladder cancer go into complete remission after she took Afinitor, says David Solit, director of the Center for Molecular Oncology at Memorial Sloan Kettering. He’s been seeking out surprising cases of cancer recovery ever since, trying to identify drugs that would be effective against diseases for which they weren’t intended. “I meet with clinical teams and often see these patients who have dramatic results to compounds not moving forward because they failed in a population,” Solit says. “These are mysteries we’ve always tried to solve, but we didn’t have the tools until now to figure out the variation of responses in patients.”

The challenge is to find a drug that even an ideal patient won’t develop a resistance to, says Lecia Sequist, an oncologist at Massachusetts General Hospital and associate professor of medicine at Harvard Medical School. People with advanced melanoma such as Crisitello are usually prescribed ipilimumab, a drug sold by Bristol-Myers Squibb (BMY) under the name Yervoy, but only 1 in 5 patients benefits from it, says Crisitello’s doctor, Lynn Schuchter. “While we’ve made huge advances in immunotherapy in recent years,” says Schuchter, the chief of hematology-oncology at the University of Pennsylvania’s Perelman School of Medicine, “we are still in the dark ages as to who should get the drug and why they are benefiting.”

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The challenge of cancer genomics: Embarking on CLARITY 2

The challenge of cancer genomics: Embarking on CLARITY 2 | Amazing Science |

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data.

DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data was donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.

Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization.

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First comprehensive atlas of human gene activity released

First comprehensive atlas of human gene activity released | Amazing Science |

A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

“Now, for the first time, we are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles,” said Winston Hide, associate professor of bioinformatics and computational biology at Harvard School of Public Health (HSPH) and one of the core authors of the main paper in Nature.

“This is a major advance that will greatly increase our ability to understand the causes of disease across the body.”

The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.

Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches” — called “promoters” and “enhancers” — are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.

“We now have the ability to narrow down the genes involved in particular diseases based on the tissue cell or organ in which they work,” said Hide. “This new atlas points us to the exact locations to look for the key genetic variants that might map to a disease.”

Eli Levine's curator insight, March 28, 2014 7:27 PM
There it is. As it is in our genes, so too is it in our individual psyches and societies. Check it out!
Martin Daumiller's curator insight, March 29, 2014 12:27 PM

original article:



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Craig Venter Wants to Build the World’s Biggest Database for Genome Information

Craig Venter Wants to Build the World’s Biggest Database for Genome Information | Amazing Science |
Craig Venter’s new company wants to improve human longevity by creating the world’s largest, most comprehensive database of genetic and physiological information.

Human Longevity, based in San Diego, says it will sequence some 40,000 human genomes per year to start, using Illumina’s new high-throughput sequencing machines (Illumina Has the First $1,000 Genome).

Eventually, it plans to work its way up to 100,000 genomes per year. The company will also sequence the genomes of the body’s multitudes of microbial inhabitants, called the microbiome, and analyze the thousands of metabolites that can be found in blood and other patient samples.

By combining these disparate types of data, the new company hopes to make inroads into the enigmatic process of aging and the many diseases, including cancer and heart disease, that are strongly associated with it. “Aging is exerting a force on humans that is exposing us to diseases, and the diseases are idiosyncratic, partly based on genetics, partly on environment,” says Leonard Guarente, who researches aging at MIT and is not involved in the company. “The hope for many of us who study aging is that by having interventions that hit key pathways in aging, we can affect disease.”

To that end, Human Longevity will collaborate with Metabolon, a company based in Durham, North Carolina, to profile the metabolites circulating in the bloodstreams of study participants. Metabolon was an early pioneer in the field of metabolomics, which catalogues the amino acids, fats, and other small molecules in a blood or other sample to develop more accurate diagnostic tests for diseases (Metabolomics).

Metabolon uses mass spectrometry to identify small molecules in a sample. In a human blood sample, there are around 1,200 different types; Metabolon’s process can also determine the amount of each one present. While genome sequencing can provide information about inherited risk of disease and some hints of the likelihood that a person will have a long life, metabolic data provides information on how environment, diet, and other features of an individual’s life affect health.

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Assembling a Colossus: Loblolly pine genome is largest ever sequenced - 7 times bigger than the human genome

Assembling a Colossus: Loblolly pine genome is largest ever sequenced - 7 times bigger than the human genome | Amazing Science |

The loblolly pine genome is big. Bloated with retrotransposons and other repetitive sequences, it is seven times larger than the human genome and easily big enough to overwhelm standard genome assembly methods.

This forced the loblolly pine genome sequencing team, led by David Neale at the University of California, Davis, to look for ways to reduce the enormous complexity of their task. The draft genome sequence, described in the latest issue of GENETICS and the journal Genome Biology, was pieced together from over 16 billion sequence reads. Spanning around 23 billion base pairs, it only just beats out the Norway spruce as the largest genome ever sequenced, but it is substantially more complete. For example, the N50 scaffold size of the current loblolly assembly is 66.9 Kbp, compared to 0.72 Kbp in the Norway spruce.

So how did they do it? One strategy was to generate most of the sequence from part of a single pine nut. This tiny source material was the mega-gametophyte, which is the haploid tissue that provides nutrients to the developing diploid embryo. Despite the limited amount of DNA that can be extracted from this source, the reduced complexity of a haploid genome makes it easier to assemble. To link up all the sequence fragments from the haploid genome, the team also created DNA libraries from diploid needles of the parent genotype.

But this still left the assembly team, led by Steven Salzberg at Johns Hopkins University and James Yorke at the University of Maryland, with more data than their computational methods could handle.

The solution was a method of pre-processing the data into “super reads”, or larger chunks of contiguous haploid sequence that condensed many individual reads. In essence, they were dealing with the unambiguous parts of the problem first, and getting rid a huge amount of overlapping and redundant data in the process.

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DNA Sequencing of IVF Embryos to screen out abnormalities

DNA Sequencing of IVF Embryos to screen out abnormalities | Amazing Science |

A reproductive clinic in New Jersey is testing whether DNA sequencing can help make in vitro fertilization less risky. In the trial, researchers will use DNA sequencing to count the number of chromosomes in each of the embryos they create by fertilizing a woman’s eggs in a dish. An abnormal number of chromosomes is the most common reason for IVF to fail, experts say, and as many as 30 percent of fertilized human eggshave such abnormalities. By selecting only those embryos with the normal number of chromosomes to transfer into the uterus, doctors hope to improve the success rate of IVF.

Traditionally in an IVF procedure, doctors visually inspect embryos and then transfer those that appear healthy after a few days of growth—often more than one at a time, because many of the embryos won’t result in a successful pregnancy. If multiple embryos do implant successfully, however, it can be risky for both them and the mother, saysRichard Scott, a reproductive endocrinologist and lead researcher in the trial, which is being conducted at Reproductive Medicine Associates of New Jersey.

To reduce such risks, some clinics, including Scott’s, are moving toward transferring only a single embryo, and new DNA analysis technologies are helping to ensure that they pick the most viable and healthy one. Researchers have already shown that other methods of chromosome screening can improve the success rate of IVF. DNA sequencing offers a more affordable way to do such tests because samples from multiple embryos can be analyzed simultaneously. That gain in efficiency lowers the cost of the procedure and could make chromosome screening feasible for more couples.

Lower-cost testing is especially important for IVF because it’s often necessary to screen many embryos for one couple, says Dagan Wells, an IVF researcher at the University of Oxford. “One patient does not equal one test,” he says. “Many patients who may want to use this kind of screening are denied because of the cost of the method.”

Last summer, Wells, who works with another New Jersey-based fertility clinic, called Reprogenetics, announced the birth of the first child whose chromosome content had been checked using next-generation sequencing during IVF embryo selection (see “Baby Born After Genome Analyzed in IVF Test”).

Several companies already sell prenatal blood tests that detect abnormalities such as Down syndrome by using sequencing to count chromosomes in a mother’s blood, which contains DNA from both mother and baby (see “A Brave New World of Prenatal DNA Sequencing”). Researchers have also shown that it is possible to determine the genome sequence of a fetus using DNA gathered from the mother’s blood and the father’s saliva (see “Using Parents’ Blood to Decode the Genome of a Fetus”). Scientists can even read the genome of a human egg before it is fertilized (see “Single-Cell Genomics Could Improve IVF Screening”).

Both New Jersey clinics are testing whether using DNA sequencing to count embryo chromosomes does indeed improve the success of IVF. The trial by Reproductive Medicine Associates will transfer two embryos into each participating mother, whereas the Reprogenetics trial will transfer just one.

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Genome Sequencing Identifies 1,300 Microbe Species In Beijing Smog

Genome Sequencing Identifies 1,300 Microbe Species In Beijing Smog | Amazing Science |
Metagenomic survey reveals traces of pathogens and allergens in the city’s air.

Chinese researchers have now used genome sequencing to identify about 1,300 different microbial species in an exceptionally soupy smog that hit Beijing in January 2013 (ref. 1). Reassuringly, most of the microbes they found are benign — but a few are responsible for allergies and respiratory disease in humans. And on days with heavier pollution, the proportion of DNA from these allergens and pathogens increased, suggesting that they might present an additional health threat to vulnerable groups, such as older people or those with weakened immune systems.

Surveys of airborne microbes have long relied on culturing samples in the lab, a method that can easily miss key species. In the past few years, researchers have looked at the microbial genomes found in air to identify broad families or genera of bacteria — an approach called metagenomics. But this is the first time that a survey has drilled down to pinpoint particular species of microbes in air, which is important for assessing their pathogenic potential, says Ting Zhu, a biologist at Tsinghua University, Beijing, who was part of the team that performed the latest study. “It’s a proof of principle that one can extract and identify these microbes at the species level,” says Zhu. “It adds to our understanding of what we inhale every day.”

The scientists took 14 air samples over 7 consecutive days and filtered out two types of particles: those measuring less than 2.5 micrometres across, and those up to 10 micrometres across, known as PM2.5 and PM10, respectively. On some days during the experiment, Beijing’s PM2.5 levels topped 500 micrograms per cubic metre — some 20 times the World Health Organization’s guideline limits.

The scientists extracted and sequenced DNA from the samples, and compared the results with a large gene database. The most abundant species identified was Geodermatophilus obscurus, a common soil bacterium. But they also found Streptococcus pneumoniae, which can cause pneumonia; Aspergillus fumigatus, a fungal allergen; and a range of other bacteria typically found in faeces. The proportion of DNA from these species increased by 2–4 times on the smoggiest days, although the samples probably included material from dead cells too, “so we don’t know if they are still viable”, says Zhu. The researchers suggest that clinical studies could look for the same microbes in the sputum of patients with respiratory tract infections, to assess whether smoggier days lead to more infections.

Andrea Franzetti, a microbiologist at the University of Milan–Bicocca, Italy, says that the make-up of the microbial community in Beijing's air is broadly in line with a similar survey of airborne bacteria that his team conducted in Milan2. “What’s new is the high number of sequences,” he says. That helps to quickly pinpoint bacteria that might have worrying health effects, allowing microbiologists to target them for further study. “There is increasing evidence that bacteria could play an important role in the health effects of airborne particles,” says Franzetti.

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Ancient Plague's DNA Recovered From A 1,500-Year-Old Tooth

Ancient Plague's DNA Recovered From A 1,500-Year-Old Tooth | Amazing Science |
Plague may have hastened the fall of the Roman Empire. Its DNA reveals ancient roots in China.

Scientists have reconstructed the genetic code of a strain of bacteria that caused one of the most deadly pandemics in history nearly 1,500 years ago. They did it by finding the skeletons of people killed by the plague and extracting DNA from traces of blood inside their teeth. This plague struck in the year 541, under the reign of the Roman emperor Justinian, so it's usually called the Justinian plague. The emperor actually got sick himself but recovered. He was one of the lucky ones.

"Some of the estimates are that up to 50 million people died," says evolutionary biologistDavid Wagner at Northern Arizona University. "It's thought that the Justinian plague actually led partially to the downfall of the Roman Empire." The plague swept through Europe, northern Africa and parts of Asia. Historians say that when it arrived in Constantinople, thousands of bodies piled up in mass graves. People started wearing name tags so they could be identified if they suddenly collapsed. Given the descriptions, scientists suspected that it was caused by the bacterium Yersinia pestis — the same kind of microbe that later caused Europe's Black Death in the 14th century.

The bacteria get spread by fleas. After someone gets infected from a flea bite, the microbes travel to the nearest lymph node and start multiplying. "And so you get this mass swelling in that lymph node, which is known as a buboe," says Wagner. "That's where the term bubonic plague comes from."

The Justinian plague has been hard to study scientifically. But recently, archaeologists stumbled upon a clue outside Munich.

Housing developers were digging up farmland when they uncovered a burial site with graves that dated as far back as the Justinian plague.

"They found some [graves] that had multiple individuals buried together, which is oftentimes indicative of an infectious disease," Wagner says. "And so in this particular case, we examined material from two different victims. One of those victims was buried together with another adult and a child, so it's presumed that they all may have died of the plague at the same time."

Skeletons were all that was left of the pair. But inside their teeth was dental pulp that still contained traces of blood — and the blood contained the DNA of plague bacteria.

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Researchers Develop DNA-based Method For Authenticating Premium Chocolate

Researchers Develop DNA-based Method For Authenticating Premium Chocolate | Amazing Science |
The taste of a rich, thick morsel of luxurious premium chocolate can be the ultimate experience for some people. But how do you know you are getting what you paid for? Until now, chocolate connoisseurs relied on just their taste buds.

A new study, published in the American Chemical Society’s (ACM) Journal of Agricultural and Food Chemistry, reports that a method to authenticate the varietal purity and origin of cacao beans — the source of chocolate’s main ingredient, cocoa—has been developed for the first time.

Lower-quality cacao beans often get mixed in with premium varieties on their way to becoming chocolate bars, truffles, sauces and liqueurs, said Dapeng Zhang, postdoctoral researcher at the National Center for Biotechnology Information. However, the stakes for policing the chocolate industry are high because it’s a multi-billion dollar global enterprise. In some areas, being a chocolatier is as much an art form as a business. Conservation also plays a role in knowing whether products are truly what the confectioners claim them to be in that the ability to authenticate rare varieties would encourage growers to maintain cacao biodiversity rather than depend on the most abundant and easiest to grow plants.

Using genetic testing, researchers have discovered ways to verify the authenticity of many other crops, such as cereals, fruits, olives, tea and coffee. However, these methods are not suitable for cacao beans, leading Zhang and his team to address the challenge of finding alternative methods.

The team applied the most recent developments in cacao genomics to identify a small set of DNA markers known as SNPs (pronounced “snips”). These SNPs make up unique fingerprints of different cacao species. The team found that the technique works on single cacao beans and can also be scaled up to handle large samples quickly.

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The Genographic Project -- National Geographic

The Genographic Project -- National Geographic | Amazing Science |

The Genographic Project is a multiyear research initiative led by National Geographic Explorer-in-Residence Dr. Spencer Wells. Dr. Wells and a team of renowned international scientists are using cutting-edge genetic and computational technologies to analyze historical patterns in DNA from participants around the world to better understand our human genetic roots.

The three components of the project are:

  • To gather and analyze research data in collaboration with indigenous and traditional peoples around the world
  • To invite the general public to join this real-time scientific project and to learn about their own deep ancestry by purchasing a Genographic Project Participation and DNA Ancestry Kit, Geno 2.0
  • To use a portion of the proceeds from Geno 2.0 kit sales to further research and the Genographic Legacy Fund, which in turn supports community-led indigenous conservation and revitalization projects

The Genographic Project is anonymous, nonmedical, and nonprofit, and all results are placed in the public domain following scientific peer publication.

Introducing Geno 2.0: Building on the science from the first phase of the Genographic Project, we have developed a cutting-edge new test kit, called Geno 2.0, that enables members of the public to participate in the Genographic Project while learning fascinating insights about their own ancestry. The Geno 2.0 test examines a unique collection of nearly 150,000 DNA identifiers, called “markers,” that have been specifically selected to provide unprecedented ancestry-relevant information.

With a simple and painless cheek swab, you submit a sample of your DNA to our lab. We then run a comprehensive analysis to identify thousands of genetic markers on your mitochondrial DNA, which is passed down each generation from mother to child, to reveal your direct maternal deep ancestry. In the case of men, we will also examine markers on the Y chromosome, which is passed down from father to son, to reveal your direct paternal deep ancestry. In addition, for all participants, we analyze a collection of more than 130,000 other ancestry-informative markers from across your entire genome to reveal the regional affiliations of your ancestry, offering insights into your ancestors who are not on a direct maternal or paternal line.

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Why hospitals will soon sequence the genes of every single patient

Why hospitals will soon sequence the genes of every single patient | Amazing Science |

We are now on the verge of a health data breakthrough, in which computers will be able to do similar diagnostic tasks, by analyzing massive amounts of data, including genome sequences, risk factors, medical histories, drug interactions, and more.

Looking at this trend last year, venture capitalist Vinod Khosla made the bold claim that technology will replace 80 percent of companies eventually. The reality is probably more nuanced: Far from threatening to put doctors out of jobs, the falling prices of data analysis and genome sequencing are enabling them with tools they could only dream of even a few years ago.

At the Mount Sinai Hospital in New York, Joel Dudley, Ph.D. uses Ayasdi’s products to discover how patients with certain genes are more likely to develop some diseases (diabetes, cardiovascular conditions…) as well as how genes influence the performance of a treatment, or may reveal risks of later relapses that can be prepared for.

Already 11,000 patients at Mount Sinai have had their genome sequenced, a pool large enough for meaningful analysis, although Ayasdi tells us “those are still early days for the industry. There are no plans to act on that data directly with individual patients just yet.”

Right now the Mount Sinai community is working at organizing itself to make the useful information available to the frontline staff. And another 30,000 patients may soon sign the consent form and opt in to participate in this new way to explore which care is best for them.

The exploration of big data by the enterprise is becoming less of a competitive edge and turning into more of a must-have. Similarly, hospitals may have to adopt genetic analysis as a rule of thumb sooner rather than later.  Mount Sinai is unusual today in pioneering regular genetic screenings, but it soon may become commonplace.

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Top Genomes of 2013

Top Genomes of 2013 | Amazing Science |

Comb jellies

A genomic analysis of comb jellies confirmed that the squishy marine predators are the new oldest animals, bumping the much simpler sea sponges from the base of the animal evolutionary tree (SN Online: 12/12/13SN: 5/18/13, p. 20).

Ancient horse

The oldest genome yet sequenced came from a horse’s foot bone dating to between 780,000 and 560,000 years ago that was excavated in Canada’s Yukon. The feat revealed that horse ancestors originated 2 million years earlier than previously thought (SN: 7/27/13, p. 5)

Big cats

Genome sequencing of a Siberian tiger, Bengal tiger, African lion, white African lion and snow leopard identified genes behind the carnivores’ ferocious metabolism and powerful pouncing skills (SN: 10/19/13, p. 6).


The mallard duck genome gave researchers clues about how flu viruses that can infect humans develop in waterfowl.


With nearly seven times the DNA of the human genome, the Norway spruce tree has the largest genome yet decoded (SN Online: 5/22/13).


The prehistoric-looking, lobe-finned fish’s genome revealed that it is not the closest living relative to land-traversing tetrapods — lungfish take that title (SN: 5/18/13, p. 18). 


The zebrafish (Danio rerio) is a widely used genetic, developmental, and disease model organism because of the near-effortlessness of imaging transparent zebrafish embryos and the variety of tools available to manipulate their genes. Plus, the small fish are relatively easy and inexpensive to keep in the lab (Nature, 496:498-503, 2013; Nature, 496:494-97, 2013).

Plant pest

The diamondback moth (Plutella xylostella) chows down on cruciferous vegetables—like cabbage and cauliflower—causing $4 billion to $5 billion dollars of damage a year and has been resistant to insecticides since the 1990s. Scientists sequenced the moth’s genome and published it in Nature Genetics in January. They found about 18,000 protein coding genes, including more than 1,400 unique to the diamondback moth. (Nature Genetics, 45:220-25, 2013).

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Broad Institute Gets Patent on Revolutionary Gene-Editing Method, CRISPR-Cas9

Broad Institute Gets Patent on Revolutionary Gene-Editing Method, CRISPR-Cas9 | Amazing Science |

One of the most important genetic technologies developed in recent years is now patented, and researchers are wondering what they will and won’t be allowed to do with the powerful method for editing the genome.

On Tuesday, the Broad Institute of MIT and Harvard announced that it had been granted a patent covering the components and methodology for CRISPR—a new way of making precise, targeted changes to the genome of a cell or an organism. CRISPR could revolutionize biomedical research by giving scientists a more efficient way of re-creating disease-related mutations in lab animals and cultured cells; it may also yield an unprecedented way of treating disease (see “Genome Surgery”). 

The patent, issued just six months after its application was filed, covers a modified version of the CRISPR-Cas9 system found naturally in bacteria, which microbes use to defend themselves against viruses. The patent also covers methods for designing and using CRISPR’s molecular components.

The inventor listed on the patent is Feng Zhang, an MIT researcher and core faculty member of the Broad. Zhang was an MIT Technology Review Innovator Under 35 in 2013.

The patent describes how the tools could be used to treat diseases, and lists many specific conditions from epilepsy, to Huntington’s, to autism, and macular degeneration. One of the most exciting possibilities for CRISPR is its potential to treat genetic disorders by directly correcting mutations on a patient’s chromosomes. That would enable doctors to treat diseases that cannot be addressed by more traditional methods, a goal already set by a startup cofounded by Zhang called Editas Medicine (further reading: “New Genome-Editing Method Could Make Gene Therapy More Precise and Effective”).

Another founder of Editas, Jennifer Doudna, and her institute, the University of California, have a pending patent application for CRISPR technology. How that west coast application will be affected is not yet clear. It’s also unclear what impact the Broad’s claims on the technology will have on its commercial use and on basic research.

Chelsea Loughran, an intellectual property litigation lawyer who has been following CRISPR over the last year, says that lots of people are already using CRISPR and it’s not clear if it will now become harder for them to do that. “All of that is in the hands of MIT and the Broad,” she says.

While MIT, Harvard, and the Broad all jointly own the CRISPR patents announced yesterday, the Broad’s technology licensing office is managing decisions about who will get licenses to use the technology, says Lita Nelsen, director of the MIT Technology Licensing Office. 

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Genetic 'App' Program Uses Genetic Markers To Pinpoint The Land Of Your Forebears

Genetic 'App' Program Uses Genetic Markers To Pinpoint The Land Of Your Forebears | Amazing Science |

Where are you from? Naming a childhood town is an easy reply for many, but for an adopted child or young refugees separated from their parents, the answer may never come. Now, a new app could help those who are unaware of their ancestral home. Using only DNA sequences, the program can trace how far away a person lives from the land of their forebears, according to a study published today in Nature Communications. The system relies on admixture—a genetic principle that argues that when a family migrates across a geographic barrier into a new location, they start mating with the locals; new traits start blending into their gene pool, and this genetic diversity provides a ruler for gauging the distance from home. The researchers started with a genome database of people from 54 worldwide regions (dots in map above). The subjects had historic ties to their regions dating back centuries. Using this info, the team built an admixture algorithm, dubbed Geographic Population Structure (GPS), which they tested with the genetic info from 600 DNA samples composed of 98 global subpopulations, such as Romanians or the Punjabis of northern India. Based solely on genetic markers, GPS could place individuals within their country of origin 83% of the time. Half of the subjects were pinpointed within 87 km of their reported point of origin. For instance, all female subjects from the mountain commune of San Basilio, Sardinia, were placed in their original village (inset). But the biggest claim made by the study is that humans are a highly mixed species with no evidence for races.

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Human evolution: The Neanderthal in every family

Human evolution: The Neanderthal in every family | Amazing Science |

Before ancient DNA exposed the sexual proclivities of Neanderthals or the ancestry of the first Americans, there was the quagga. An equine oddity with the head of a zebra and the rump of a donkey, the last quagga (Equus quagga quagga) died in 1883. A century later, researchers published1 around 200 nucleotides sequenced from a 140-year-old piece of quagga muscle. Those scraps of DNA — the first genetic secrets pulled from a long-dead organism — revealed that the quagga was distinct from the mountain zebra (Equus zebra).

A few years ago, David Reich discovered a ghost. Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts, and his team were reconstructing the history of Europe using genomes from modern people, when they found a connection between northern Europeans and Native Americans. They proposed that a now-extinct population in northern Eurasia had interbred with both the ancestors of Europeans and a Siberian group that later migrated to the Americas6.

Reich calls such groups ghost populations, because they are identified by the echoes that they leave in genomes — not by bones or ancient DNA.

Ghost populations are the product of statistical models, and as such should be handled with care when genetic data from fossils are lacking, says Carlos Bustamante, a population geneticist at Stanford University in California. “When are we reifying something that's a statistical artefact, versus when are we understanding something that's a true biological event?”

An international team had sequenced the genome of Ötzi, a 5,300-year-old frozen corpse found in the Tyrolean Alps of Italy in 1991. The researchers wondered if Bustamante could help them to make sense of the ice-man's ancestry. Together, they showed that Ötzi was more closely related to humans who now live in Sardinia and Corsica than those in central Europe, evidence that the population of Europe when he was alive looked very different to how it does today9.

Bustamante has since plunged into the world of ancient DNA. His team is sequencing samples that chart the arrival of farming in Bulgaria, the transatlantic slave trade in the Americas and dog domestication. The group is developing tools to make sequencing ancient DNA cheaper and easier. “We want to democratize the field,” says Bustamante.

These discoveries are only the beginning. The Akey and Reich teams found that the genomes of east Asians possess, on average, slightly more Neanderthal DNA than do people of European ancestry. Akey sees this as possible evidence that Neanderthals interbred with ancient humans on at least two separate occasions: once with the ancestors of all Eurasians, and later with a population ancestral only to east Asians. And Akey believes that humans are likely to bear genetic scraps from other extinct species, including some that interbred with the ancestors of humans in sub-Saharan Africa.

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Technology: With a unique program, the US government has managed to drive the cost of genome sequencing down to $1,000

Technology: With a unique program, the US government has managed to drive the cost of genome sequencing down to $1,000 | Amazing Science |

With a unique program, the US government has managed to drive the cost of genome sequencing down towards a much-anticipated target.

The quest to sequence the first human genome was a massive undertaking. Between 1990 and the publication of a working draft in 2001, more than 200 scientists joined forces in a $3-billion effort to read the roughly 3 billion bases of DNA that comprise our genetic material (International Human Genome Sequencing Consortium Nature 409860921; 2001).

It was a grand but sobering success. The project's advocates had said that it would reveal 'life's instruction book', but in fact it did not make it possible to interpret how the instructions encoded in DNA were transformed into biology. Understanding how DNA actually influences health and disease would require studying examples of the links between genes and biology in thousands, perhaps millions, more people. The dominant technology at the time was Sanger sequencing, an inherently slow, labour-intensive process that works by making copies of the DNA to be sequenced that include chemically modified and fluorescently tagged versions of the molecule's building blocks. One company, Applied Biosystems in Foster City, California, provided the vast majority of the sequencers to a limited number of customers — generally, large government-funded laboratories — and there was little incentive for it to reinvent its core technology.

A $7-million award from the NHGRI allowed the company to commercialize a technology called pyrosequencing, which was the first to begin chipping away at Applied Biosystems' monopoly. The funding commitments also ultimately helped to convince private investors to enter the market. Stephen Turner, founder and chief technology officer of Pacific Biosciences in Menlo Park, California, says that his company's 2005 NHGRI grant of $6.6 million helped to attract subsequent venture-capital funding.

The government program has invested $88 million in technologies based on nanopores and nanogaps. The form of this technology closest to the market involves reading bases as they are threaded through a pore (see Nature 456, 2325; 2008), a method that has long promised to save costs and time by reading DNA while it is processed. It would negate the need for expensive and slow reactions to make lots of copies of the molecule. But solving basic issues, including how to move the DNA through the pore slowly enough, has been a major challenge. The NHGRI has funded work to overcome these hurdles — including $9.3 million given to collaborators of the company now ushering the concept to market, UK-based Oxford Nanopore Technologies (Nature; 2014).

Sequencing still needs much improvement, especially in terms of quality. For all of Sanger sequencing's high cost, it remains the benchmark for accuracy. And sequencing costs are no longer dropping as quickly as they were a few years ago.

But researchers are optimistic that another technology will emerge to challenge Illumina. Most think, in fact, that the crucial questions for the field will shift away from technology. Now that sequencing is cheap enough to talk about scanning every patient's genome, or at least the protein-coding portion of it, it is still not clear how that information will translate into improved care (Nature; 2014). These more complex issues will require another great leap in genomic science — one that could make the trouncing of Moore's law seem easy

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Recreation of Species: How far back can we go?

Recreation of Species: How far back can we go? | Amazing Science |

The lesson of the Jurassic Park tragedy was clear — man and dinosaur were not meant to coexist. It’s lucky then that dinosaur fossils are far too old to contain any genetic material that could be used for cloning. DNA breaks down over time, even when kept in ideal conditions, and a study of extinct moa bones has revealed an estimate of the half-life for our genes.

It might be odd to think of DNA having a half-life, as it’s usually associated with radioactive material — but as it measures the time taken for half of something to decay, it makes sense to talk about old samples of DNA in the same way. For example, uranium-235, the fissile material that can be used in nuclear power plants (and nuclear weapons), has a half-life of 703.8 million years. DNA, by comparison, doesn’t fare so well — according to a study of 158 samples of moa bones between 500 and 6,000 years old, DNA appears to have a half-life of around 521 years.

A study in the Proceedings of the Royal Society B saw palaeogeneticists from the universities of Perth and Copenhagen drilling into the bones of 158 different moa, the largest of the flightless birds which used to dominated New Zealand’s odd and unique ecosystem before the arrival of humans. The bones had all been collected from within a five kilometre radius, and they were estimated to have been buried at an average temperature of 13 degrees Celsius since the birds died. Their similar preservation conditions were key to ensuring that a reliable figure for the DNA decomposition could be found.

Averaging out the results from the different bones gave the average half-life of 521 years. That result is caveated, of course, as there are many factors that can also affect the rate of decay — soil acidity, bone health, extreme temperature, humidity, and so on. However, it does provide a baseline against which to assess the viability of obtaining DNA samples from future finds.

If there is a lot of DNA, preserved in absolutely ideal conditions, then it might hang around for several thousand years. Samples of Neanderthal DNA have been found in ancient teeth as old as 100,000 years old, and New Scientist reports that there have also been tiny fragments of DNA from insects and plants hundreds of thousands of years old found in ice cores, but these are too decayed to be used for cloning.

The moa could theoretically be cloned, if a good enough DNA sample is found. The moa is generally thought to have been hunted to extinction by the Maori residents of New Zealand before the arrival of European settlers in the 1700s, which isn’t too long enough by DNA standards. Or, a better candidate might be the woolly mammoth — intact specimens have been found frozen into the permafrost (including very recently by a boy out walking his dog), and it is thought that it will eventually be possible to implant a mammoth embryo into an elephant’s uterus, which will grow into a full-on baby mammoth. We may even be able to reintroduce them into the wild, which is really the least we could do after driving them to extinction in the first place.

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Face-To-Face: Crude Mugshots built from DNA data alone

Face-To-Face: Crude Mugshots built from DNA data alone | Amazing Science |
Computer program crudely predicts a facial structure from genetic variations.

Researchers have now shown how 24 gene variants can be used to construct crude models of facial structure. Thus, leaving a hair at a crime scene could one day be as damning as leaving a photograph of your face. Researchers have developed a computer program that can create a crude three-dimensional (3D) model of a face from a DNA sample.

Using genes to predict eye and hair color is relatively easy. But the complex structure of the face makes it more valuable as a forensic tool — and more difficult to connect to genetic variation, says anthropologist Mark Shriver of Pennsylvania State University in University Park, who led the work, published today in PLOS Genetics1.

Shriver and his colleagues took high-resolution images of the faces of 592 people of mixed European and West African ancestry living in the United States, Brazil and Cape Verde. They used these images to create 3D models, laying a grid of more than 7,000 data points on the surface of the digital face and determining by how much particular points on a given face varied from the average: whether the nose was flatter, for instance, or the cheekbones wider. They had volunteers rate the faces on a scale of masculinity and femininity, as well as on perceived ethnicity.

Next, the authors compared the volunteers’ genomes to identify points at which the DNA differed by a single base, called a single nucleotide polymorphism (SNP). To narrow down the search, they focused on genes thought to be involved in facial development, such as those that shape the head in early embryonic development, and those that are mutated in disorders associated with features such as cleft palate. Then, taking into account the person’s sex and ancestry, they calculated the statistical likelihood that a given SNP was involved in determining a particular facial feature.

This pinpointed 24 SNPs across 20 genes that were significantly associated with facial shape. A computer program the team developed using the data can turn a DNA sequence from an unknown individual into a predictive 3D facial model (see 'Face to face'). Shriver says that the group is now trying to integrate more people and genes, and look at additional traits, such as hair texture and sex-specific differences.

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Advances in Next-Gen Sequencing and Bioinformatics Permit High-Res Single-Cell Genome Sequencing

Advances in Next-Gen Sequencing and Bioinformatics Permit High-Res Single-Cell Genome Sequencing | Amazing Science |

Single-cell Whole Genome Analysis (WGA) has recently been accomplished on a variety of high-throughput platforms, including DNA-microarrays, SNP-arrays, and NGS. A key difficulty in the interpretation of single-cell WGA data on any platform is the separation of the numerous WGA artifacts from the genuine genetic variants present in the template genome.

Standard DNA-microarrays can detect copy number variations (CNVs) larger than 2.5 Mb from a single-cell genome [Ref], while targeted array comparative genomic hybridizations can discover approximately 1 Mb-sized DNA imbalances [Ref], although remarkably, CNVs as small as 56 kb in single-cell PCR-based WGA products have been detected [Ref]. Similarly, SNP-arrays can find copy number aberrations encompassing millions of bases in a cell [Ref], but have the advantage of enabling the discovery of copy neutral DNA anomalies and regions of loss-of-heterozygosity (LOH), and allow inferring genome-wide haplotypes [Ref].

Next Generation Sequencing (NGS) has a number of advantages over microarrays enabling improved resolution and accuracy in variant calling [Ref]. First, NGS can examine every nucleotide amplified from the cell and allows genome-wide discovery of the full spectrum of DNA mutations, while microarrays only probe for certain CNV loci.

Secondly, sequencing provides digital precision, with one digital unit representing a mapped sequence read. Finally, paired-end sequencing and mapping discloses the linkage between both ends of each linear DNA-molecule in a sequencing library of a single-cell WGA product, allowing the identification of structural variations via read-pairs mapping discordantly to the reference genome.

Analytical challenges remain in interpreting single-cell NGS data for the full spectrum of genetic variants. Although WGA imperfections due to genome base composition (e.g. %GC-bias) can be computationally corrected for [Ref]. Allelic fractions of heterozygous SNPs [Ref] or aberrantly mapping read pairs following paired-end sequencing of the WGA product [Ref] can be used to increase confidence in CNV measurements. For instance, a real deletion of a diploid locus should show LOH and discordantly mapping read-pairs that explain the DNA loss. Furthermore, the cell cycle stage of the isolated cell must be considered, further complicating the analysis, as cells in S-phase demonstrate a dynamic copy number profile, leading to false structural DNA-imbalance discoveries [Ref].

The identification of the full spectrum of intra- and inter-chromosomal (un)balanced structural variants in a single-cell WGA product is still in its infancy—the main difficulty being to filter true structural variants from chimeric DNA generated during WGA, as well as issues with genome coverage. Although filters have been designed to permit the detection of the structural architecture of DNA copy number variation and even to detect L1-retro-transposition [Ref], many structural variants are still missed in single-cell analyses.

Despite these hurdles, several groups have proven the efficacy of single-cell NGS to detect multiple classes of mutation within a genome and even to detect sister chromatid exchanges following single-cell Strand-seq [Ref]. Step-by-step bioinformatics protocols for analyzing Strand-seq data as well as for copy number profiling single cells through NGS or microarray analysis and commercial solutions (e.g. platforms used within are surfacing.[Ref]

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Black Death Left a Mark on Human Genome

Black Death Left a Mark on Human Genome | Amazing Science |

There have been multiple plagues throughout history around the world, but none have been so deadly as the Black Death, which killed an estimated one in every four Europeans, and so exerted very strong selection. The Black Death didn’t just wipe out millions of Europeans during the 14th century. It left a mark on the human genome, favoring those who carried certain immune system genes, according to a new study. Those changes may help explain why Europeans respond differently from other people to some diseases and have different susceptibilities to autoimmune disorders.

Geneticists know that human populations evolve in the face of disease. Certain versions of our genes help us fight infections better than others, and people who carry those genes tend to have more children than those who don’t. So the beneficial genetic versions persist, while other versions tend to disappear as those carrying them die. This weeding-out of all but the best genes is called positive selection. But researchers have trouble pinpointing positively selected genes in humans, as many genes vary from one individual to the next.

Genetically, the Rroma gypsies in Romania are still quite similar to the northwestern Indians, even though they have lived side by side with the Romanians for a millennium, the team found. But there were 20 genes in the Rroma and the Romanians that had changes that were not seen in the Indians’ versions of those genes, Netea and his colleagues report online today in the Proceedings of the National Academy of Sciences. These genes “were positively selected for in the Romanians and in the gypsies but not in the Indians,” Netea explains. “It’s a very strong signal.”

Those genes included one for skin pigmentation, one involved in inflammation, and one associated with susceptibility to autoimmune diseases such as rheumatoid arthritis. But the ones Netea and Bertranpetit were most excited about were a cluster of three immune system genes found on chromosome 4. These genes code for toll-like receptors, proteins which latch on to harmful bacteria in the body and launch a defensive response. “We knew they must be important for host defense,” Netea says.

What events in history might have favored these versions of the genes in gypsies and Romanians, but not in Indians? Netea and his colleagues tested the ability of the toll-like receptors to react to Yersinia pestis, the bacterium that caused the Black Death. They found that the strength of the immune response varied depending on the exact sequence of the toll-like receptor genes.

Netea and Bertranpetit propose that the Rroma and European Romanians came to have the same versions of these immune system genes because of the evolutionary pressure exerted by Y. pestis. Other Europeans, whose ancestors also faced and survived the Black Death, carried similar changes in the toll-like receptor genes. But people from China and Africa—two other places the Black Death did not reach—did not have these changes. The similarities in the other genes were likely caused by other conditions experienced by Rroma and Europeans, but not Indians.

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Genome of 11,000-year-old living dog cancer determined, revealing cancer's origin and evolution

Genome of 11,000-year-old living dog cancer determined, revealing cancer's origin and evolution | Amazing Science |

A cancer normally lives and dies with a person, however this is not the case with a sexually transmitted cancer in dogs. In a study published in Science, researchers have described the genome and evolution of this cancer that has continued living within the dog population for the past 11,000 years.

Scientists have sequenced the genome of the world's oldest continuously surviving cancer, a transmissible genital cancer that affects dogs. This cancer, which causes grotesque genital tumors in dogs around the world, first arose in a single dog that lived about 11,000 years ago. The cancer survived after the death of this dog by the transfer of its cancer cells to other dogs during mating.

The genome of this 11,000-year-old cancer carries about two million mutations -- many more mutations than are found in most human cancers, the majority of which have between 1,000 and 5,000 mutations. The team used one type of mutation, known to accumulate steadily over time as a "molecular clock," to estimate that the cancer first arose 11,000 years ago.

"The genome of this remarkable long-lived cancer has demonstrated that, given the right conditions, cancers can continue to survive for more than 10,000 years despite the accumulation of millions of mutations," says Dr Elizabeth Murchison, first author from the Wellcome Trust Sanger Institute and the University of Cambridge.

The genome of the transmissible dog cancer still harbors the genetic variants of the individual dog that first gave rise to the cancer 11,000 years ago. Analysis of these genetic variants revealed that this dog may have resembled an Alaskan Malamute or Husky. It probably had a short, straight coat that was colored either grey/brown or black. Its genetic sequence could not determine if this dog was a male or a female, but did indicate that it was a relatively inbred individual.

"We do not know why this particular individual gave rise to a transmissible cancer," says Dr Murchison, "But it is fascinating to look back in time and reconstruct the identity of this ancient dog whose genome is still alive today in the cells of the cancer that it spawned."

Transmissible dog cancer is a common disease found in dogs around the world today. The genome sequence has helped scientists to further understand how this disease has spread.

"The patterns of genetic variants in tumors from different continents suggested that the cancer existed in one isolated population of dogs for most of its history," says Dr Murchison. "It spread around the world within the last 500 years, possibly carried by dogs accompanying seafarers on their global explorations during the dawn of the age of exploration."

Transmissible cancers are extremely rare in nature. Cancers, in humans and animals, arise when a single cell in the body acquires mutations that cause it to produce more copies of itself. Cancer cells often spread to different parts of the body in a process known as metastasis. However, it is very rare for cancer cells to leave the bodies of their original hosts and to spread to other individuals. Apart from the dog transmissible cancer, the only other known naturally occurring transmissible cancer is an aggressive transmissible facial cancer in Tasmanian devils that is spread by biting.

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World’s first $1,000 genome enables ‘factory’ scale sequencing for population and disease studies

World’s first $1,000 genome enables ‘factory’ scale sequencing for population and disease studies | Amazing Science |

Illumina, Inc. announced Tuesday that its new HiSeq X Ten Sequencing System has broken the “sound barrier” of human genomics by enabling the $1,000 genome. “This platform includes dramatic technology breakthroughs that enable researchers to undertake studies of unprecedented scale by providing the throughput to sequence tens of thousands of human whole genomes in a single year in a single lab,” Illumina stated.

Initial customers for the HiSeq X Ten System, which will ship in Q1 2014, include Macrogen, based in Seoul, South Korea and its CLIA laboratory in Rockville, Maryland, the Broad Institute in Cambridge, Massachusetts, and the Garvan Institute of Medical Research in Sydney, Australia.

“For the first time, it looks like it will be possible to deliver the $1,000 genome, which is tremendously exciting,” said Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. “The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”

“The HiSeq X Ten is an ideal platform for scientists and institutions focused on the discovery of genotypic variation to enable a deeper understanding of human biology and genetic disease,” Illumina stated. “It can sequence tens of thousands of samples annually with high-quality, high-coverage sequencing, delivering a comprehensive catalog of human variation within and outside coding regions.”

HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before — generating a 10x increase in daily throughput when compared to current HiSeq 2500 performance.

The HiSeq X Ten is sold as a set of 10 or more ultra-high throughput sequencing systems, each generating up to 1.8 terabases (Tb) of sequencing data in less than three days or up to 600 gigabases (Gb) per day, per system, providing the throughput to sequence tens of thousands of high-quality, high-coverage genomes per year.

Illumina Introduces the HiSeq X™ Ten Sequencing System

Nature: Is the $1000 Genome for real?

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Human Genome Shrinks To Only 19,000 genes, Less Than The C. elegans Worm

Human Genome Shrinks To Only 19,000 genes, Less Than The C. elegans Worm | Amazing Science |

Genes are the fundamental units of inheritance in living organisms. Together, they hold all the information necessary to reproduce a given organism and to pass on genetic traits to its offspring.


Biologists have long debated what constitutes a gene in molecular terms but one useful definition is a region of DNA that carries that code necessary to make a molecular chain called a polypeptide. These chains link together to form proteins and so are the bricks and mortar out of which all organism are constructed.


Given this crucial role, it is no surprise that an ongoing goal in biology is to work out the total number of protein-coding genes necessary to construct a given organism. Biologists think the yeast genome contains about 5300 coding genes and a nematode worm genome contains about 20,470.


Via Mariaschnee, Christian Allié
Christian Allié's curator insight, January 6, 2014 4:32 AM

"""""""""" Better beeing "Humble" """"""""""""""""

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NATURE: The Method of the Year for 2013 is… single-cell sequencing

NATURE: The Method of the Year for 2013 is… single-cell sequencing | Amazing Science |

Single-cell sequencing edged out other contenders as our choice of Method of the Year in 2013. These techniques really came into their own in 2013 and are fast providing new insights into the workings of single cells that ensemble methods are incapable of.

Back in 2008 we chose next-generation sequencing as our Method of the Year not only because of how the new techniques would improve performance in conventional sequencing applications, but also because they opened up whole new applications, unthinkable with traditional Sanger sequencing. Our choice of Method of the Year in 2013 bears this out, as none of these single-cell sequencing applications would be possible without next-generation sequencing. And in some applications the sequencing is used almost exclusively for identifying and counting tagged molecules.

Our choice likely comes as a surprise to all those who were certain that we would pick CRISPR/Cas9 technology for targeted genome modification. This is certainly an exciting technology, and not only for genome engineering, but also for epigenome editing as described in a Method to Watch. But genome editing with engineered nucleases was our pick for the 2011 Method of the Year and although CRISPR/Cas9 provides a huge practical improvement by largely dispensing with the need to engineer the nuclease and relying instead on a programmable guide RNA, the advance over 2011 is mostly one of ease-of-use.

Methods to investigate biology at the level of single cells have been of keen interest to Nature Methods since the journal started. Our first research article from Robert Singer described a paraffin-embedded tissue FISH (peT-FISH) method to simultaneously detect expression of several genes in situ in single cells while maintaining tissue morphology (Capodieci, P. 2005). This was followed by many other imaging-based methods for such things as measuring cell growth (Groisman, A. 2006), quantifying mRNA (Raj, A. 2008) and protein (Gordon, A. 2006) levels, profiling intracellular signaling (Krutzik, P.O. & Nolan, G.P. 2006) (Loo, L.-H. 2007) and DNA insertion-site analysis (Schmidt, M. 2008) in single cells.

The publication of M. Azim Surani’s article on mRNA-Seq whole-transcriptome analysis of a single cell (Tang, F. 2009) in 2009 helped signal the rise of sequencing-based methods for single-cell analysis. But even two years later the Reviews and Perspectives in our supplement on single-cell analysis were more focused on imaging-based than sequencing-based aproaches to single-cell analysis.

It was only in 2013 that we finally saw an explosion of original research articles using or reporting single-cell sequencing methods in Nature-family journals. Numerous studies reported new biological results that relied on sequencing of whole or partial genomes or transcriptomes from single cells.

Nature's Method of the Year special feature has three Commentaries by researchers in the field, including some of the earliest developers and users of methods for single-cell analysis. An Editorial, News Feature and Primer describe our choice and provide helpful background information. We hope you enjoy the selection of articles in our special feature.

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