Category Archives: Genome

"This landmark FDA approval codifies the need to determine whether cancer patients potentially eligible for immuno-oncology therapy have microsatellite instability present in their tumors," said Doug Ward, CEO of PGDx. "It is particularly fitting that the approval involves MSI, a genomic condition whose relevance to cancer therapy was first uncovered by researchers at Johns Hopkins, with assistance from researchers at PGDx. We were thrilled to license rights to the patent-pending MSI measurement technology for immuno-oncology applications developed at Johns Hopkins, and are proud to be the first to offer it in both tissue and liquid biopsy formats. PGDx is also planning to submit a tissue-based MSI assay for FDA review later this year."

PGDx's MSI testing is incorporated in the company's tissue-based CancerSELECT 125 pan cancer genomic profiling assay and its non-invasive PlasmaSELECT 64 pan cancer assay that analyzes circulating tumor DNA in patient plasma. The company also recently received grant funding from the National Cancer Institute to advance liquid biopsy tests for determining a related biomarker known as tumor mutational burden.

PGDx was an early leader in identifying the importance of MSI, contributing to a study on MMR and immune checkpoint blockade presented at the 2015 ASCO Annual Meeting. In that study, researchers found that colorectal cancer patients who had tumors with MSI/MMR deficiency had a much greater therapeutic response to pembrolizumab. The analysis showed that cancer patients with MSI/MMR deficiency on average had more than 20 times the number of mutations in their tumors as similar patients who were not mismatch repair deficient. This finding is consistent with other studies showing that PD-1/PD-L1 checkpoint blockers are most effective against tumors containing many mutations. The study was published in the New England Journal of Medicine.

"We established PGDx to advance technology invented at Johns Hopkins based on our belief that greater understanding of tumor genomics would ultimately enable more effective and less toxic treatments for cancer," noted Victor E. Velculescu, MD, PhD, a co-founder of PGDx. Dr. Velculescu also is Professor of Oncology at the Johns Hopkins University School of Medicine. "This breakthrough approval from the FDA is an important milestone in the realization of that vision. I am proud that PGDx has played a significant role in this advance and that the company will help many more patients realize the benefits of immuno-oncology approaches for cancer treatment."

PGDx representatives will be attending the 2017 ASCO Annual Meeting and are available at Booth #2078 to discuss the company's MSI testing and its complete range of cancer genome analysis tools for researchers and clinicians. Research services include exome and targeted approaches for tissue specimens, targeted approaches for plasma samples and a variety of custom tissue and plasma-based options designed to address the specific research needs of cancer researchers and drug developers. PGDx's service offerings for researchers and testing labs are complemented by the clinical services it provides to patients and physicians through its CLIA-certified laboratory, including its CancerSELECT 125 pan cancer genomic profiling assay and the non-invasive PlasmaSELECT 64 pan cancer profiling assay, both of which include MSI testing.

About Personal Genome DiagnosticsPersonal Genome Diagnostics (PGDx) is empowering the fight against cancer by unlocking actionable information from the genome for oncology researchers, drug developers, clinicians and patients. The expert team at PGDx draws on a deep understanding of cancer biology, extensive experience in cancer genomics and clinical oncology, and the company's distinctive technologies that precisely identify and characterize unique genomic alterations in tumors. PGDx is working toward broad patient access to its genomic technologies and products, through a CLIA-certified facility providing comprehensive genomic services, as well as a portfolio of tissue-based and liquid biopsy genomic testing products for laboratories worldwide. Privately-held PGDx is headquartered in Baltimore, MD. For additional information, visit PersonalGenome.com.

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Personal Genome Diagnostics Highlights its Patent-Pending Microsatellite Instability Testing Technology as FDA ... - PR Newswire (press release)

The mummified body of Minirdis, a 14-year-old Egyptian boy, and his burial mask, pictured at the Field Museum in Chicago in 2014 after researchers opened the coffin for the first time.

AP

Modern Egyptians have more DNA from sub-Saharan Africa than mummies entombed in their country, according to the first genome data on mummies.

The findings are helping researchers gauge the impact of history on Egyptians' genetics.

The international team of researchers analyzed DNA from 151 mummies from the archaeological site of Abusir el-Meleq. The site is along the Nile River in Middle Egypt. The mummies date from about 1400 B.C. to 400 A.D.

Genetic studies of ancient Egyptian mummies are rare due to a number of issues.

"The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques contribute to DNA degradation and are thought to make the long-term survival of DNA in Egyptian mummies unlikely," said study senior author Johannes Krause. He is director at the Max Planck Institute for the Science of Human History in Germany.

13 Photos

California museum exhibit displays pets preserved for all time in ancient Egypt

This team's success in extracting and analyzing nuclear DNA from mummies is a breakthrough that opens the door to further direct study of mummified remains in order to get a better understanding of Egypt's population history, the study authors explained in an institute news release.

The researchers' goal was to find out if ancient Egyptian populations were affected at the genetic level by foreign conquest and domination during the time period in the study.

According to study co-lead author Verena Schuenemann, of the University of Tuebingen, Germany, the research team "wanted to test if the conquest of Alexander the Great and other foreign powers has left a genetic imprint on the ancient Egyptian population."

Wolfgang Haak, group leader at the Max Planck Institute, said, "The genetics of the Abusir el-Meleq community did not undergo any major shifts during the 1,300-year timespan we studied, suggesting that the population remained genetically relatively unaffected by foreign conquest and rule."

Modern Egyptians share about eight percent more ancestry on the nuclear level with sub-Saharan African populations than with ancient Egyptians, the investigators found.

Stephan Schiffels, also at the Max Planck Institute, concluded that the finding "suggests that an increase in sub-Saharan African gene flow into Egypt occurred within the last 1,500 years."

The study was published May 30 in the journalNature Communications.

2017 HealthDay. All rights reserved. This material may not be published, broadcast, rewritten, or redistributed.

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The first genome data from ancient Egyptian mummies is in - CBS News

Researchers have finished the first full genome map of the threatened Mojave desert tortoise (Gopherus agassizii), also known as Agassizs desert tortoise.

Kenro Kusumi with Arizona State Universitys School of Life Sciences said the team hopes the data will aid conservation efforts, fill in blanks in the reptiles evolutionary history and perhaps offer clues to improving human health and longevity.

For diseases, were certainly interested in what makes them susceptible, the connection we study this in humans, too between their diet and their environment and their stresses, and their ability to fight off diseases," said Kusumi.

The research was published May 31 in PLOS ONE.

Mojave desert tortoises face threats from various quarters. Invasive grasses like red brome can stunt their early growth and may reduce their resistance to illnesses including upper respiratory tract disease (URTD), which afflicts the nose, nasal sinuses and trachea of some of the creatures. Humans threaten their survival by destroying habitat and building power lines, which provide new perches for predatory ravens.

Its a new habitat for the ravens. Its great for them, but its bad for baby tortoises, which they like to look at and then swoop down and eat, said Kusumi.

Based on comparisons with other existing reptile genomes, the study found changes in Mojave desert tortoise genes that regulate shell development, longevity and water conservation.

They also found that, among three desert tortoises (Mojave desert tortoise, Sonoran desert tortoise and Goodes Thornscrub tortoise), evolutionary forces seem to have differentiated protein sequences related to circadian rhythm the daily cycle of physiological and behavioral processes and the innate immune system.

The U.S. Fish and Wildlife Service listed the Mojave population that is located north and west of the Colorado River as threatened in 1990. Nevertheless, its numbers declined by about 50 percent from 2004 to 2013.

Understanding genetic variation and responses could help wildlife managers better grasp how disease and inbreeding affect the reptiles. Kusumi said it could also help scientist understand how the creatures adapt to their environs by isolating genes related to withstanding ultraviolet radiation and controlling urine volume.

We dont really know where the genetic treasure in the gold mine is. Where is the diversity that would allow the tortoise, as a species, to survive changes? said Kusumi.

A clearer picture of Mojave desert tortoises genetics and biodiversity could also improve management of reproduction and maintenance of habitat corridors, particularly under conditions of climate change. It would also help nail down the species geographical range, which overlaps with the Sonoran desert tortoise, aka Morafka's desert tortoise (Gopherus morafkai). The two desert tortoises sometimes mix boundaries and interbreed.

Were trying to answer, based on using the genome, where is the Mojave desert tortoise? Because we actually dont know exactly where that boundary is right now, said Kusumi.

Mojave desert tortoises live 40-50 years in the wild and more than 100 years in captivity. Dark green, with brown and yellow accents, they have rounded shells, stubby hind legs and flat front limbs built for digging. They occur in western Arizona, southern Nevada, Southern California and southwestern Utah. Kusumi said genetics could also offer clues as to how the species can live in such a diverse range of environments.

If you moved one from, say, Las Vegas to Southern California, it probably wouldnt do very well, because thats not the environment that its genome is making it suited for," he said. "So, within that species, wed love to know the genetic instructions that make a tortoise better suited for one place versus another.

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Team Maps Genome of Mojave Desert Tortoise - AZPM - Arizona Public Media

Jennifer A. Doudna & Samuel H. Sternberg Houghton Mifflin: 2017. ISBN: 9780544716940

Buy this book: US UK Japan

Graeme Mitchell/Redux/Eyevine

Jennifer Doudna helped to uncover the CRISPRCas gene-editing system.

The prospect of a memoir from Jennifer Doudna, a key player in the CRISPR story, quickens the pulse. And A Crack in Creation does indeed deliver a welcome perspective on the revolutionary genome-editing technique that puts the power of evolution into human hands, with many anecdotes and details that only those close to her may have known. Yet it does not provide the probing introspection, the nuanced ethical analysis, the moral counterpoint that we CRISPR junkies crave.

After the race for discovery comes the battle for control of the discovery narrative. The stakes for the CRISPRCas system are extraordinarily high. In February, the US Patent and Trademark Office ruled against Doudna and the University of California, Berkeley. It found that a patent on the application of CRISPR to eukaryotic cells filed by Feng Zhang of the Broad Institute of MIT and Harvard in Cambridge, Massachusetts did not interfere with Berkeley's more sweeping patent on genetic engineering with CRISPR.

Although that battle is over, the war rages on. Berkeley has already appealed against the decision; meanwhile, the European Patent Office has ruled in favour of Doudna and Berkeley. Doubtless there are many more patents to milk out of this versatile system. And then there's the fistful of 66-millimetre gold medals they give out in Stockholm each year.

So far, the Broad Institute has controlled the CRISPR narrative. Rich in funds and talent, the Broad melds sleek, high-tech sexiness with a sense of East Coast, old-money privilege. Last year, institute director Eric Lander published a now-infamous piece entitled 'The heroes of CRISPR' (E.Lander Cell 164, 1828; 2016). It adopted a tone of magnanimity, crediting Lithuanian biochemist Virginijus Siksnys with observing early on that his findings pave the way for engineering of universal programmable RNA-guided DNA endonucleases, and Doudna and her CRISPR co-discoverer Emmanuelle Charpentier with noting the potential to exploit the system for RNA-programmable genome editing.

Lander's clear implication was that they were laying the groundwork; Zhang's group got CRISPR over the finish line. To many of us, such tactics made Team Broad look like the villains of CRISPR.

Doudna's book was a chance to deliver a righteous knockout blow. Instead, we get a counter-narrative just as constructed as Lander's article. It is written entirely in the first person; co-author Samuel Sternberg, a former student in the Doudna lab, barely surfaces.

In that counter-narrative, Doudna had always been interested in gene editing. Her early work was on RNA enzymes, or ribozymes. She developed an impeccable pedigree, doing her PhD with Jack Szostak at Harvard and a postdoc with Tom Cech at the University of Colorado Boulder, before joining the faculty at Yale University in New Haven, Connecticut. From the mid-1990s, she writes, she was exploring the basic molecular mechanisms that would be able to unlock the full potential of gene editing.

Her work on CRISPR dates to 2006 six years before the key papers were published and a call from Berkeley geomicrobiologist Jillian Banfield. Over coffee, Banfield described the clustered, regularly interspaced, short palindromic repeats that kept popping up in her DNA databases of bacteria and archaea. The sequences were ubiquitous among these prokaryotes, but unique to each species. This realization sent a little shiver of intrigue down my spine, Doudna writes. If CRISPR was so widespread, there was a good chance that nature was using it to do something important. By 2012, she and her co-workers had characterized the natural CRISPR system, harnessed it as a laboratory tool and developed a modified system that was programmable, cheap and easy to use.

The middle of the book reels off the obligatory breathless list of potential uses, generating everything from malaria-free mosquitoes and police dogs with muscles like Vin Diesel to the canonical cure for cancer. Thankfully, Doudna counterweights sensationalism with a sober accounting of the risks and responsibilities of applications such as altering the genomes of entire populations of organisms with 'gene drives'. In 2015, she sustained doubts about CRISPR ever being safe enough for clinical trials, but she has come to embrace editing of the human germ line inheritable DNA modification once it is proved safe.

But the discussion is ultimately unsatisfying. When it is time to grapple with tricky ethical issues, such as human experimentation, she baulks, unspooling instead a series of rhetorical questions. Rather than guiding us through the ethical thickets of precision genetic engineering, or providing a candid, warts-and-all look at one of the great scientists of our time, the book mainly polishes her 'good scientist' image and rationalizes the unfettered self-direction of human evolution, within liberal bounds of safety, efficacy and individual choice.

Rather than dispel the cartoon-character feel of this epic battle, Doudna elaborates on it. She presents us with a persona so flawless that it seems more concealing than revealing. She waves away the bloody patent fight as a disheartening twist in the story, but the entire biomedical world knows that it was much more. As I read A Crack in Creation, I was reminded of Benjamin Franklin's benevolent man, who, he wrote, should allow a few faults in himself, to keep his friends in countenance and, I would add, to give him- or herself more depth.

The narrative often substitutes melodrama for dramatic tension. A conference in Puerto Rico sees Charpentier and Doudna strolling the cobbles of Old San Juan, with Charpentier saying earnestly, I'm sure that by working together we can figure out the activity of what became the Cas enzyme. I felt a shiver of excitement as I contemplated the possibilities of this project, Doudna writes. When first wrestling with the ethical dilemmas of gene editing, she dreams of meeting Adolf Hitler, who demands to know the secrets of her technique. She wakes, of course, freshly determined to ensure that CRISPR is not put to nefarious use.

The larger purpose of A Crack in Creation, clearly, is to show that Doudna is the true hero of CRISPR. And ultimately, despite the book's flaws, I'm convinced. Nominators and the Nobel Committee will need to read this book. But CRISPR binge-watchers like me still await a truly satisfying account one that is insightful, candid and contextualized.

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That's the way the CRISPR crumbles - Nature.com

The Memorial Sloan Kettering Cancer Center (MSK) and Philips will exploit the latters IntelliSpace Genomics platform through their research collaboration to develop new genome analysis methods and informatics approaches for diagnosing pancreatic cancer and aiding personalized therapeutics. The collaboration will employ large-scale next-generation sequencing to generate new insights into the drivers of pancreatic cancer at the single-cell level, with the goal of enabling more precise diagnosis so that patients can be prescribed optimum treatments that target the cause of their disease.

Philips' IntelliSpace Genomics platform has been developed to support the implementation and scaling of informatics-heavy precision medicine research. "Collaborating with MSK and its experts will allow us to take a unique approach to diagnosing and treating this devastating disease, commented Henk van Houten, Ph.D., CTO at Philips. Leveraging the advanced capabilities of the Philips IntelliSpace Genomics solution we can gain new insights into the origin, development, and optimal treatment of pancreatic cancer and share these insights broadly with care providers to help improve outcomes for patients. Our ultimate goal is to translate these findings into more precise diagnostics and therapeutics to battle this devastating disease."

Philips and MSK have previously established a research collaboration in the field of radiation oncology. Just yesterday, MSK and Mabvax Therapeutics signed a research agreement to develop chimeric antigen receptor (CAR) T-cellimmunotherapies for pancreatic and small-cell lung cancer.

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Philips, MSK Partner on Genome Analytics for Prostate Cancer Precision Medicine - Genetic Engineering & Biotechnology News

By Ian Haydon 3 minute Read

A new research paper is stirring up controversy among scientists interested in using DNA editing to treat disease.

In a two-page article published in the journal Nature Methods on May 30, a group of six scientists report an alarming number of so-called off-target mutations in mice that underwent an experimental gene repair therapy.

CRISPR, the hot new gene-editing technique thats taken biology by storm, is no stranger to headlines. What is unusual, however, is a scientific article so clearly describing a potentially fatal shortcoming of this promising technology.

The research community is digesting this newswith many experts suggesting flaws with the experiment, not the revolutionary technique.

The research team sought to repair a genetic mutation known to cause a form of blindness in mice. This could be accomplished, they showed, by changing just one DNA letter in the mouse genome.

They were able to successfully correct the targeted mutation in each of the two mice they treated. But they also observed an alarming number of additional DNA changesmore than 1,600 per mousein areas of the genome they did not intend to modify.

The authors attribute these unintended mutations to the experimental CRISPR-based gene-editing therapy they used.

Cas9, the CRISPR enzyme that snips DNA, in contact with its target. [Graph: via rcsb.org]A central promise of CRISPR-based gene editing is its ability to pinpoint particular genes. But if this technology produces dangerous side effects by creating unexpected and unwanted mutations across the genome, that could hamper or even derail many of its applications.Several previous research articles have reported off-target effects of CRISPR, but far fewer than this group found.

The publicly traded biotech companies seeking to commercialize CRISPR-based gene therapiesEditas Medicine, Intellia Therapeutics, and Crispr Therapeuticsall took immediate stock market hits based on the news.

Experts in the field quickly responded.

Either the enzyme is acting at near optimal efficiency or something fishy is going on here, tweeted Matthew Taliaferro, a postdoctoral fellow at MIT who studies gene expression and genetic disease.

The Cas9 enzyme in the CRISPR system is what actually cuts DNA, leading to genetic changes. Unusually high levels of enzyme activity could account for the observed off-target mutationsmore cutting equals more chances for the cell to mutate its DNA. Different labs use slightly different methods to try to ensure the right amount of cuts happen only where intended.

Gatan Burgio, whose laboratory at the Australian National University is working to understand the role that cellular context plays on CRISPR efficiency, believes the papers central claim that CRISPR caused such an alarming number of off-target mutations is not substantiated.

Burgio says there could be a range of reasons for seeing so many unexpected changes in the mice, including problems with accurately detecting DNA variation, the extremely small number of mice used, random events happening after Cas9 acted, or, he concedes, problems with CRISPR itself.

Burgio has been editing the DNA of mice using CRISPR since 2014 and has never seen a comparable level of off-target mutation. He says hes confident that additional research will refute these recent findings.

Although the news of this two-mouse experiment fired up the science-focused parts of the Twittersphere, the issue it raises is not new to the field.

Researchers have known for a few years now that off-target mutations are likely given certain CRISPR protocols. More precise variants of the Cas9 enzyme have been shown to improve targeting in human tissue in the lab.

Researchers have also focused on developing methods to more efficiently locate off-target mutations in the animals they study.

As scientists continue to hone the gene-editing technique, we recognize theres still a way to go before CRISPR will be ready for safe and effective gene therapy in humans.

Ian Haydon is a doctoral student in Biochemistry at the University of Washington. This story originally appeared at The Conversation.

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Unraveling The Controversy Over The CRISPR Mutations Study - Fast Company

Ness Ziona, Israel May 30, 2017NRGene, the worldwide leader in genomic mapping, assembly, and referencing, has assembled 300 genomes of major crop plants in less than two years, enabling the highly accurate genome comparisons required to breed better seeds.

Before NRGenes technology, individual genomes took years to produce and then many more years to improve genome accuracy. With NRGenesDeNovoMAGICTM, the highest level of genome completeness and accuracy is achieved with a single assembly.

Over the past two years, assemblies have been created in cooperation with many of the worlds leading universities, government research institutes and non-for-profit organizations, as well as global companies like Syngenta and Monsanto.

DeNovoMAGIC 3.0delivers reference genomes quickly, accurately, and cost effectively, without requiring external data. It accelerates downstream analysis and reduces unnecessary technical work. DeNovoMAGIC assembles Illumina reads into long, phased sequences, delivering accurate assembly results, even from complex genomes, no matter the size, ploidy, or zygosity, for high quality genome mapping and productive breeding.

For crops with an existing reference genome, theDeNovoMAGICassemblies enable researchers to elucidate the vast genomic diversity that exists within the crop species. Scientists are using this critical information to breed more productive new varieties with the highest nutritional values.

Many full genomes now exist in most of the key crops, and NRGenesPanMAGICTMcombines the initial assemblies into an accurate genome-to-genome mapping to capture the full diversity of the crop varieties, including all types of sequence differences within the studied population, e.g. SNPs, InDels of any size, inversions, translocations, gene PAVs, and gene CNVs.

Breeding is all about making the most of a given genomic diversity in a given crop. If your goal is to make genomics applicable for breeding you must describe crop diversity accurately and affordably, says NRGene CEO Gil Ronen. Based on the feedback we get from our customers, were doing that and more allowing them to make major breakthroughs in the quest to increase the worlds food supply with more productive, hardier seeds.

About NRGene

NRGeneis a genomic big data company developing cutting-edge software and algorithms to reveal the complexity and diversity of crop plants, animals, and aquatic organisms for supporting the most advanced and sophisticated breeding programs. NRGene tools have already been employed by some of the leading seed companies worldwide as well as the most influential research teams in academia.www.nrgene.com.

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NRGene Assembles its 300th Crop Genome - DirectionsMag.com

May 30, 2017 Map of Egypt, showing the archaeological site of Abusir-el Meleq (orange X), and the location of the modern Egyptian samples used in the study (orange circles). Credit: Graphic: Annette Guenzel. Credit: Nature Communications, DOI: 10.1038/NCOMMS15694

An international team of scientists, led by researchers from the University of Tuebingen and the Max Planck Institute for the Science of Human History in Jena, successfully recovered and analyzed ancient DNA from Egyptian mummies dating from approximately 1400 BCE to 400 CE, including the first genome-wide nuclear data from three individuals, establishing ancient Egyptian mummies as a reliable source for genetic material to study the ancient past. The study, published today in Nature Communications, found that modern Egyptians share more ancestry with Sub-Saharan Africans than ancient Egyptians did, whereas ancient Egyptians were found to be most closely related to ancient people from the Near East.

Egypt is a promising location for the study of ancient populations. It has a rich and well-documented history, and its geographic location and many interactions with populations from surrounding areas, in Africa, Asia and Europe, make it a dynamic region. Recent advances in the study of ancient DNA present an intriguing opportunity to test existing understandings of Egyptian history using ancient genetic data.

However, genetic studies of ancient Egyptian mummies are rare due to methodological and contamination issues. Although some of the first extractions of ancient DNA were from mummified remains, scientists have raised doubts as to whether genetic data, especially nuclear genome data, from mummies would be reliable, even if it could be recovered. "The potential preservation of DNA has to be regarded with skepticism," confirms Johannes Krause, Director at the Max Planck Institute for the Science of Human History in Jena and senior author of the study. "The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques, contribute to DNA degradation and are thought to make the long-term survival of DNA in Egyptian mummies unlikely." The ability of the authors of this study to extract nuclear DNA from such mummies and to show its reliability using robust authentication methods is a breakthrough that opens the door to further direct study of mummified remains.

For this study, an international team of researchers from the University of Tuebingen, the Max Planck Institute for the Science of Human History in Jena, the University of Cambridge, the Polish Academy of Sciences, and the Berlin Society of Anthropology, Ethnology and Prehistory, looked at genetic differentiation and population continuity over a 1,300 year timespan, and compared these results to modern populations. The team sampled 151 mummified individuals from the archaeological site of Abusir el-Meleq, along the Nile River in Middle Egypt, from two anthropological collections hosted and curated at the University of Tuebingen and the Felix von Luschan Skull Collection at the Museum of Prehistory of the Staatliche Museen zu Berlin, Stiftung Preussicher Kulturbesitz.

In total, the authors recovered mitochondrial genomes from 90 individuals, and genome-wide datasets from three individuals. They were able to use the data gathered to test previous hypotheses drawn from archaeological and historical data, and from studies of modern DNA. "In particular, we were interested in looking at changes and continuities in the genetic makeup of the ancient inhabitants of Abusir el-Meleq," said Alexander Peltzer, one of the lead authors of the study from the University of Tuebingen. The team wanted to determine if the investigated ancient populations were affected at the genetic level by foreign conquest and domination during the time period under study, and compared these populations to modern Egyptian comparative populations. "We wanted to test if the conquest of Alexander the Great and other foreign powers has left a genetic imprint on the ancient Egyptian population," explains Verena Schuenemann, group leader at the University of Tuebingen and one of the lead authors of this study.

Close genetic relationship between ancient Egyptians and ancient populations in the Near East

The study found that ancient Egyptians were most closely related to ancient populations in the Levant, and were also closely related to Neolithic populations from the Anatolian Peninsula and Europe. "The genetics of the Abusir el-Meleq community did not undergo any major shifts during the 1,300 year timespan we studied, suggesting that the population remained genetically relatively unaffected by foreign conquest and rule," says Wolfgang Haak, group leader at the Max Planck Institute for the Science of Human History in Jena. The data shows that modern Egyptians share approximately 8% more ancestry on the nuclear level with Sub-Saharan African populations than with ancient Egyptians. "This suggests that an increase in Sub-Saharan African gene flow into Egypt occurred within the last 1,500 years," explains Stephan Schiffels, group leader at the Max Planck Institute for the Science of Human History in Jena. Possible causal factors may have been improved mobility down the Nile River, increased long-distance trade between Sub-Saharan Africa and Egypt, and the trans-Saharan slave trade that began approximately 1,300 years ago.

This study counters prior skepticism about the possibility of recovering reliable ancient DNA from Egyptian mummies. Despite the potential issues of degradation and contamination caused by climate and mummification methods, the authors were able to use high-throughput DNA sequencing and robust authentication methods to ensure the ancient origin and reliability of the data. The study thus shows that Egyptian mummies can be a reliable source of ancient DNA, and can greatly contribute to a more accurate and refined understanding of Egypt's population history.

Explore further: 17 mummies discovered in central Egypt

More information: Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods, Nature Communications (2017). nature.com/articles/doi:10.1038/ncomms15694

Egyptian archaeologists have discovered 17 mummies in desert catacombs in Minya province, an "unprecedented" find for the area south of Cairo, the antiquities ministry announced Saturday.

New research published in Global Heart (the journal of the World Heart Federation) shows that there are no significant differences in the incidence or severity of atherosclerotic disease (narrowing of the arteries with fatty ...

(AP) -- Archeologists have unearthed 57 ancient Egyptian tombs, most of which hold an ornately painted wooden sarcophagus with a mummy inside, Egypt's Supreme Council of Antiquities said Sunday.

(Phys.org) The study and popular perception of Egyptian antiquities focuses too much on the unwrapping of mummies and the use of technologies such as scanning, according to an academic from the University of East Anglia.

As silent witnesses to the past, ancient Egyptian mummies can add to our knowledge of their society well beyond what we can learn from the study of texts, art and funerary rituals.

Egyptian archaeologists have unearthed several mummies, colourful wooden sarcophagi and more than 1,000 funerary statues in a 3,500-year-old tomb near the city of Luxor, hailing an "important discovery".

An international team of scientists, led by researchers from the University of Tuebingen and the Max Planck Institute for the Science of Human History in Jena, successfully recovered and analyzed ancient DNA from Egyptian ...

About 1 to 2 million years ago, early humans in East Africa periodically faced very dry conditions, with little or no water in sight. But they likely had access to hundreds of springs that lingered despite long dry spells, ...

The origin of animals was one of the most important events in the history of Earth. Beautifully preserved fossil embryos suggest that our oldest ancestors might have existed a little more than half a billion years ago.

In human history, the transition from hunting and gathering to farming is a significant one. As such, hunter-gatherers and farmers are usually thought about as two entirely different sets of people. But researchers reporting ...

A new species of a fossil pliosaur (large predatory marine reptile from the 'age of dinosaur') has been found in Russia and profoundly change how we understand the evolution of the group, says an international team of scientists.

People using smartphones are more likely to make rational and unemotional decisions compared to PC users when presented with a moral dilemma on their device, according to a new study from City, University of London.

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The first genome data from ancient Egyptian mummies - Phys.Org

New York, May 30 (IANS) The CRISPR-Cas9 gene-editing technology can introduce hundreds of unintended mutations into the genome, warns a new study.

"We feel it's critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR, including single nucleotide mutations and mutations in non-coding regions of the genome," said co-author Stephen Tsang, Associate Professor at Columbia University Medical Centre in the US.

CRISPR-Cas9 editing technology -- by virtue of its speed and unprecedented precision -- has been a boon for scientists trying to understand the role of genes in disease.

The technique has also raised hope for more powerful gene therapies that can delete or repair flawed genes, not just add new genes.

The first clinical trial to deploy CRISPR is now underway in China, and a US trial is slated to start next year.

But even though CRISPR can precisely target specific stretches of DNA, it sometimes hits other parts of the genome.

Most studies that search for these off-target mutations use computer algorithms to identify areas most likely to be affected and then examine those areas for deletions and insertions.

"These predictive algorithms seem to do a good job when CRISPR is performed in cells or tissues in a dish, but whole genome sequencing has not been employed to look for all off-target effects in living animals," co-author Alexander Bassuk, Professor at the University of Iowa, said.

In the new study, published in the journal Nature Methods, the researchers sequenced the entire genome of mice that had undergone CRISPR gene editing in the team's previous study and looked for all mutations, including those that only altered a single nucleotide.

The researchers determined that CRISPR had successfully corrected a gene that causes blindness, but they also found that the genomes of two independent gene therapy recipients had sustained more than 1,500 single-nucleotide mutations and more than 100 larger deletions and insertions.

None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.

"We're still upbeat about CRISPR," co-author of the study Vinit Mahajan, Associate Professor at Stanford University, said.

"We're physicians, and we know that every new therapy has some potential side effects - but we need to be aware of what they are," Mahajan added.

--IANS

gb/dg

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CRISPR gene tool can cause unintended flaws in genome - The ... - Economic Times

Local diagnostics company One BioMed Pte Ltd and A*STARs Genome Institute of Singapore (GIS) have established a joint laboratory to develop molecular diagnostic assays for the Asian clinical infectious disease testing market.

The joint laboratory will focus on the full development and integration of the initial assays for the One BioMed platform. Each panel will be multiplexed and syndromic, and is expected to address clinically important infectious diseases in Asia, including pediatric respiratory infections, drug resistant tuberculosis and mosquito-borne illnesses. The laboratory will be located in the Genome building at Biopolis and will leverage the genomic expertise of GIS to improve the delivery of clinical medicine.

One BioMed recently spun-out of A*STARs Institute of Microelectronics (IME) is developing a point-of-care diagnostic platform deploying two proprietary technologies: a chemistry-based nucleic acid extraction and a silicon biophotonics dual-ring sensor. Integrated into a consumable cartridge design and run on a portable instrument, these approaches are expected to enable simple, cost-effective, rapid and highly multiplexed molecular testing outside of a central laboratory setting.

Dr Alexander Lezhava, Group Leader, Translational Research will lead the lab for GIS, and Dr Park Mi Kyoung, founder and Chief Technology Officer of One BioMed, will lead the lab for the company. We allied with the GIS Translational Research group because they combine extensive molecular diagnostics assay development expertise with regulatory and commercialisation experience, said Dr Park.

Prof Ng Huck Hui, Executive Director of GIS said, Our collaboration with One BioMed helps us address one of the most difficult problems facing patients and healthcare providers across the region poor access to accurate testing for infectious diseases like influenza, dengue and tuberculosis.

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One BioMed and A*STAR's Genome Institute of Singapore establish joint lab - Enterprise Innovation