Category Archives: Genome

Faster, cheaper genome sequencing gives scientists new ways of ... Quartz In 2003, the US Department of Defense and the National Institutes of Health announced that13 years and $2.7 billion laterthey had finally finished mapping ... and more »

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Faster, cheaper genome sequencing gives scientists new ways of ... - Quartz

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Youve quite possibly heard of the Human Genome Project, the massive international science research project dedicated to sequencing the human DNA.A less well-known project called Genome 10K has a not-unrelated mission but instead of mapping just the human genome, its dedicated to sequencing the genome of thousands of animal species, including those most at risk of extinction.

The purpose of the Genome 10K project is to assemble a genomic zoo of DNA sequences representing the full diversity of vertebrate animals, including at least 10,000 different vertebrate species, David Haussler, the Genome 10K trustee and scientific director at theUniversity of California Santa Cruz Genomics Institute, told Digital Trends. Establishing the genetic diversity of vertebrate species would create a priceless resource for the life sciences and worldwide conservation efforts. We have only just begun to understand our natural environment. Because virtually all the biology of an animal is encoded in its genome, the Genome 10K project will provide a great leap forward.

More: Hybrid woolly mammoths could soon walk the Earth, thanks to Harvard scientists

A genome, Haussler said, can help us calculate how endangered a particular species is by the effects of population size reductions that lead to inbreeding. This information is vital for prioritizing conservation efforts and helping plan efforts to conserve, and, via outbreeding, increase diversity within a species.

Members of the Genome 10K Community of Scientists gathered at its first meeting in April 2009 at the Seymour Center in Santa Cruz, California.

The genomes of different vertebrates also tell us a great deal about ourselves: How we became human and what makes us uniquely human genetically, Haussler continued. By sequencing thousands of vertebrate genomes we will have an unprecedented evolutionary microscope for peering into our natural history, allowing us to understand our story over the last several hundred million years, and helping us better predict which genetic variations that are in our genomes today cause disease.

Scientists involved with Genome 10K have developed new methodologies for genome sequencing and analysis. These have been proved on hundreds of cases, including many endangered species.

Anyone can help assemble this genomic zoo by making a donation on our website, Haussler said. By donating now, you can help create a shared resource that will inform and guide our understanding of animal life for generations to come.

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Genome 10K wants to sequence the genes of endangered species - Yahoo News

ARMONK, NY, March 23,2017 A team led by researchers from The Center for Genome Architecture (TC4GA) at Baylor College of Medicine have used technologies from IBM, Mellanox and NVIDIA to assemble the 1.2 billion letter genome of the Culex quinquefasciatus mosquito, which carries West Nile virus. The new genome can help enable scientists to better combat West Nile virus by identifying vulnerabilities in the mosquito that the virus uses to spread.

The high performance computing (HPC) system dubbed VOLTRON, is based on the IBM Power Systems platform, which provides scalable HPC capabilities necessary to accommodate a broad spectrum of data-enabled research activities. Baylor College of Medicine joins leading supercomputing agencies globally the Department of Energys Oak Ridge and Lawrence Livermore National Labs and the U.K. governments Science and Technology Facilities Councils Hartree Centre that have recently selected IBMs Power Systems platform for cutting-edge HPC research.

VOLTRONs 3D assembly is changing the way in which researchers are able to sequence genomes, by using DNA folding patterns to trace the genome as it crisscrosses the nucleus. The resulting methodology is faster and less expensive. For example, while the original Human Genome Project took ten years and cost $4 billion, 3D assembly produces a comparable genome sequence in a few weeks and for less than $10,000.

Such efforts take on increased urgency when they are needed to combat disease outbreaks, like the West Nile virus.

Taking advantage of IBM POWER8 and Mellanox InfiniBand interconnect, we are now able to change the way we assemble a genome, said Olga Dudchenko, a postdoctoral fellow at The Center for Genome Architecture at Baylor College of Medicine. And while we originally created Voltron to sequence the human genome, the method can be applied to a dizzying array of species. This gives us an opportunity to explore mosquitoes, which carry diseases that impact many people around the globe.

3D assembly and IBM technology are a terrific combination: one requires extraordinary computational firepower, which the other provides, said Erez Lieberman Aiden, Director of The Center for Genome Architecture.

The Center for Genome Architecture is working closely with Mellanox to maximize their research capabilities with the VOLTRON high-performance computing system. By leveraging Mellanoxs intelligent interconnect technology and acceleration engines, TC4GA is able to provide its researchers with an efficient and scalable platform to enhance genome sequencing in order to find cures for the worlds life-threatening diseases.

Key to Baylors research breakthrough is a multi-year collaboration between IBM and NVIDIA to design systems capable of leveraging the POWER processors open architecture to take advantage of the NVIDIA Tesla accelerated computing platform.

Incorporated into the design of VOLTRON is POWER and Tesla technology combination that allows Baylor researchers to handle extreme amounts of data with incredible speed. Voltron consists of a cluster of four systems, each featuring a set of eight NVIDIA Tesla GPUs tuned by NVIDIA engineers to help Baylors researchers achieve optimum performance on their data-intensive genomic research computations.

Source: IBM

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Scientists Use IBM Power Systems to Assemble Genome of West Nile Mosquito - HPCwire (blog)

The mosquito-borne parasite Plasmodium vivax might have sparked the strongest evolutionary response in humans yet known.

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By Michael PriceMar. 23, 2017 , 8:00 AM

A genetic mutation that protects people from a common form of malaria spread like wildfire in sub-Saharan Africa about 42,000 years ago, according to a new study. Today, its nearly impossible to find somebody from this region who doesnt have it. That makes the mutation one of the swiftest, strongest changes to the human genome yet seenthough it remains a mystery why this particular disease sparked such a dramatic evolutionary response.

The worlds most widespread type of human malaria is caused by Plasmodium vivax, a single-celled parasite transmitted by mosquitoes. Although less deadly than other strains, P. vivax malaria remains a disruptive disease: It infected some 16 million people across the globe in 2013. Yet across much of sub-Saharan Africa, P. vivax accounts for fewer than 5% of all reported malaria cases. Thats because about 99% of Africans living here have a variant of a gene called DARC, which shuts off a particular protein receptor on the surface of red blood cells that the parasite needs to gain entry.

To learn more about how and when this mutation spread, Omar Cornejo, a population geneticist at Washington State University in Pullman, and colleagues analyzed full genome sequences from 1000 modern individuals from 21 population centers in Africa, Asia, and Europe. The researchers then employed a computer-based simulation that predicts how certain genetic variants spread throughout a population over time given the regions known demographics and various selective pressures.

Based on rates of genetic change, the simulation suggests the most recent common ancestor of living Africans who possessed the DARC mutation lived about 42,000 years ago, the team reports this month in PLOS Genetics. Back then, the mutation was likely just a random genetic variant possessed by a handful of people, not a functional evolutionary defense. Then something changedquite possibly the arrival of P. vivaxand some 8000 years later, more than 99% of people in the region had the mutation, according to the simulation.

Cornejo estimates that on average during that 8000-year period, for every 100 people born without the mutation, an additional 105 would have been born with it. Assuming that widespread exposure to P. vivax meant that people who had the mutation were more likely to survive than those without itthat would make this the strongest evolutionary response yet seen in the human genome, the researchers say.

Thats a bit mysterious because the disease caused by P. vixax is much less deadly than that caused by other Plasmodium strains, says David Serre, a microbiologist at the University of Marylands Institute for Genome Science in Baltimore who wasnt involved with this work. You get sick, you stay in bed for a few weeks, and most of the time you get better. One wouldnt expect such a powerful evolutionary response to a relatively benign disease, he notes.

One possibility is that the disease was much deadlier thousands of years ago, and that further adaptations in our immune system have rendered it less threatening, Serre says. Another is that evolution was acting against an entirely different, as-yet-unknown disease that used the same technique as P. vivax to enter red blood cells. The data are really good, the analysis is really good, but the story just doesnt quite make sense yet, he says.

Cornejo admits its a perplexing finding, and he agrees a heretofore unknown disease theoretically could be responsible.

Either way, he says the study should serve as a warning. Just as humans in Africa evolved to combat the parasite, the disease continues to evolve as well. Recent cases of P. vivax malaria have been reported in Madagascar, Ethiopia, and Sudan in people who possess the protective DARC mutation. Its not yet clear whether some other factor made them susceptible to the disease, or whether the parasite evolved to find another way into red blood cells. If its the latter, says Cornejo, millions of people who once didnt need to worry about P. vivax malaria might soon be at risk.

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Dramatic evolution within human genome may have been caused by malaria parasite - Science Magazine

Its a boy! or Its a girl! are pretty common pieces of information people expect to gather in a doctors office before their child is born. But what if in the near future those exclamations were followed by information that could impact that unborn childs lifelong health?

Genomic testing is ushering in that reality, revealing which gene-based issues could arise over a persons lifetime. This information could follow the soon-to-be newborn through his or her life, determining preventative care measures, identifying effective therapies and shaping their health all the way through to end-of-life care.

This technology is changing fast. As of right now, according to biotech analyst Jonathan Grobert, Less than 3 percent of the population knows anything about their genomic data. This opportunity is where the internet was in the 1970s. The Human Genome Project sequenced nearly all of the human genome by 2003, but this effort took 13 years and $1 billion to complete. By 2007, that effort had sped up 70 fold, and it now costs $1,500 and can be completed in about 15 minutes. Soon, according to Dr. Brendan Frey, getting a human genome sequenced will cost less than a trip to the grocery store.

Frey is the CEO of Deep Genomics, a company looking to improve the interpretation not just of genotype a persons genetic constitution but of phenotypes, which range from whether or not you're a redhead to whether or not you have cancer. His company wants to bridge this gap so doctors and patients can interpret and act on genetic information, despite the complex relationship between a persons genes and their phenotype, including health.

Theres a huge growth in data sets that allow us to literally peer inside of cells and measure at the single-molecule level what is happening in those cells, he says. So theres this explosion of data that connects genetics to the phenotypes. The best technology we have for making sense of large data sets is machine learning.

By applying machine learning to these large data sets, the genomics industry could change the current paradigm of medicine, which is hypothesis driven and tests for only a small number of pathologies while ignoring many others. Frey explains that switching to an information-based model could cut down on unnecessary invasive procedures, since it could do a better job at ruling out false positives.

For example, many women get mammograms. However, the efficacy of getting annual checkups for breast cancer has caused an unintended consequence. The odds a woman has a false positive after 10 years of annual mammograms is as high as 50 to 60 percent, according to the Susan G. Komen Foundation. Through an informatics-based approach, genomic machine learning could better determine which women actually need frequent imaging. Machine learning could parse through a large amount of relevant data to slice down that false positive rate.

An information science-based approach that leverages genotype information could also cut down on prescription rates for drugs. Instead of crudely prescribing the same drug to the masses, genomics could instead drive a precision medicine approach, where doctors understand which patients would most benefit from a drug before writing a script.

In spite of any hurdles, genomics is continuing to get cheaper, quicker and more accessible even outpacing Moores Law. Nine of the 10 leading causes of death, like Alzheimers, cancer and strokes, have a genetic factor. Linking this genome information with environmental factors and integrating across the board into the medical field is a big data problem. And its one machine learning is equipped to answer, says Frey.

When it comes to the health care industry, there are practices that will need to change to make that happen. I think the pressures are there, and the right forces are there to push the community and the industry in the right direction.

With this rapid pace of innovation in an increasingly crowded market, genomics companies must carve out their niche and differentiate against competitors with a messaging and positioning that sets them apart. In this rapid race for industry mindshare, genomics companies have a once-in-a-lifetime opportunity to make their mark. It makes for an exciting time for genomics companies to step out and become a thought leader in the field, contributing to the industry dialogue and shaping the market for generations to come.

Follow Alisa Valudes Whyte on Twitter: http://www.twitter.com/MerrittGroup

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Your Genome Holds the Key to a Healthier Life ... if Machine Learning has its Way - Huffington Post

The Scientist

Enzyme Required for Mitochondrial Genome Destruction The Scientist We suspect that this process of destroying genomes may be playing a role in disease and in aging, he said. We don't know at this point how far this is going to go, but we suspect strongly that the role in uniparental inheritance is going to be ...

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Enzyme Required for Mitochondrial Genome Destruction - The Scientist

News tagged with genome New software tools streamline DNA sequence design-and-build process

Synthetic DNA allows scientists to expand the breadth and depth of their genomic research. In this study researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization ...

A team of Hokkaido University researchers has discovered a hitherto-unknown mechanism that detains transposable elements or "mobile genes" - which can move and insert into new positions in plant genomes.

EPFL scientists have carried out a genomic and evolutionary study of a large and enigmatic family of human proteins, to demonstrate that it is responsible for harnessing the millions of transposable elements in the human ...

A new study by G. William Arends Professor of Microbiology at the University of Illinois Bill Metcalf with postdoctoral Fellow Dipti Nayak has documented the use of CRISPR-Cas9 mediated genome editing in the third domain ...

Meteorologists strive to predict the weather. Network scientists develop complex algorithms to predict the spread of disease. Might it also be possible to predict the emergence of scientific discoveries? If the answer is ...

Dwindling populations created a "mutational meltdown" in the genomes of the last wooly mammoths, which had survived on an isolated island until a few thousand years ago. Rebekah Rogers and Montgomery Slatkin of the University ...

In an age of booming biotechnology, it might be easy to forget how much we still rely on the bounty of the natural world. Some microbes make us sick, some keep us healthy, while others continue to give us some of our best ...

The National Academies of Science and Medicine (NASEM) released a report on Feb. 14 exploring the implications of new technologies that can alter the genome of living organisms, including humans.

Bioengineers at the University of California San Diego have developed a new tool to identify interactions between RNA and DNA molecules. The tool, called MARGI (Mapping RNA Genome Interactions), is the first technology that's ...

Gene transfers are particularly common in the antibiotic-resistance genes of Streptococcus pneumoniae bacteria.

In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes. In haploid organisms, including bacteria, archaea, viruses, and mitochondria, a cell contains only a single set of the genome, usually in a single circular or contiguous linear DNA (or RNA for retroviruses). In modern molecular biology the genome of an organism is its hereditary information encoded in DNA (or, for retroviruses, RNA).

The genome includes both the genes and the non-coding sequences of the DNA. The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a portmanteau of the words gene and chromosome; however, many related -ome words already existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically.

More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. Additionally, the genome can comprise nonchromosomal genetic elements such as viruses, plasmids, and transposable elements. When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Both the number of base pairs and the number of genes vary widely from one species to another, and there is little connection between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.

An analogy to the human genome stored on DNA is that of instructions stored in a book:

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Phys.org - genome

March 21, 2017

Einstein researchers have developed and validated a method for accurately identifying mutations in the genomes of single cells. The new method, which can help predict whether cancer will develop in seemingly healthy tissue, is described in a paper published in today's online edition of Nature Methods. The corresponding author is Jan Vijg, Ph.D., professor and chair of genetics and the Lola and Saul Kramer Chair in Molecular Genetics.

Before scientists can analyze the genome of a single cell, they must first obtain sufficient amounts of its DNAa process known as whole genome amplification (WGA). But WGA typically produces errors in nucleotide sequences that may falsely indicate the presence of mutations. In their Nature Methods paper, Dr. Vijg and colleagues describe a new method for accurately identifying the presence of mutations (technically referred to as single nucleotide variants) in the genomes of single cells.

The Einstein researchers' new method combines two techniques that they developed: an improved WGA method called single-cell multiple displacement amplification (SCMDA); and a single-cell variant "caller," which corrects for nucleotide-sequence errors that may be caused by gene amplification. Head-to-head comparisons showed that the Einstein method outperformed several methods now marketed for genome analysis.

"Being able to identify DNA mutations in single cells in the human body is important, since it can tell us who might be at risk for developing early-onset cancer," says Dr. Vijg. As an example, he cites women who develop breast cancer at a young age. For some of these women, breast cancer results from heritable mutations in the DNA repair genes BRCA1 or BRCA2. These defects in DNA repair permit increased numbers of mutations to develop in breast cells, resulting in cancer.

"But many women develop cancer early even without a BRCA1 or BRCA2 mutation," Dr. Vijg notes. "These women could also have a defect in DNA repairbut we don't know, because DNA repair is so complex. Our genome analysis method allows us, for the first time, to assess their breast-cancer risk directly. We can sequence several single cells to see how many mutations arose spontaneously in these cells and if the number of mutations is significantly higher than in the cells of women who did not develop early cancer."

In addition to assessing cancer risk in people, says Dr. Vijg, the new method for identifying mutations in single cells should help to reveal the role of mutations in human aging.

The paper is titled "Accurate identification of single nucleotide variants in whole genome amplified single cells."

Explore further: One in five breast cancer patients could benefit from existing treatment, genetic study reveals

More information: Xiao Dong et al. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells, Nature Methods (2017). DOI: 10.1038/nmeth.4227

Einstein researchers have developed and validated a method for accurately identifying mutations in the genomes of single cells. The new method, which can help predict whether cancer will develop in seemingly healthy tissue, ...

New genes which help prevent prostate, skin and breast cancer development in mice have been discovered by researchers at the Wellcome Trust Sanger Institute and their collaborators. The study identified genes that cooperate ...

Like almost all light-sensitive living beings, human beings follow biological rhythms set on a period of about 24 hours. The circadian clock (from Latin "circa" and "dies", which means "about a day") therefore describes the ...

The majority of genes associated with nephrotic syndrome (NS) in humans also play pivotal roles in Drosophila renal function, a conservation of function across species that validates transgenic flies as ideal pre-clinical ...

Britain's Newcastle University says its scientists have received a license to create babies using DNA from three people to prevent women from passing on potentially fatal genetic diseases to their childrenthe first time ...

Columbia University Medical Center (CUMC) researchers have discovered a common genetic variant that greatly impacts normal brain aging, starting at around age 65, and may modify the risk for neurodegenerative diseases. The ...

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Breakthrough in detecting mutations in genomes of single cells - Medical Xpress

The Scientist

Genome Digest The Scientist By sequencing and analyzing the quinoa genome, researchers uncovered a gene that regulates saponin production. The group reported its findings last month (February 8) in Nature. Their discoveries could help researchers create strains of quinoa without ...

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Genome Digest - The Scientist

The cells nucleus is like a densely packed but busy archive, one that resorts to the use of mobile shelving, which consists of wheeled shelving units that run along trackspushed together to save space, then separated to facilitate access, when needed. In the nucleus, where the mobile shelving units consist of chromosomal structures and genomic DNA domains, some order is maintained despite the constant shuttling of information, not to mention the occasional copying project, necessary for cell division. Characterizing this order is essential to understanding the cells normal function, as well as its dysfunction.

To get a feel for the usual disposition of the genomic shelving units in individual cells, scientists at the University of Cambridge and the MRC Laboratory of Molecular Biology calculated 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure. The new procedure, the scientists report, allowed them to first image and then process single cells.

Essentially, the scientist used a combination of imaging and up to 100,000 measurements of where different parts of the DNA are close to each other to examine the genome in a mouse embryonic stem cell. Ultimately, the scientists managed to determine the first 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei.

Details of this work appeared March 13 in the journal Nature, in an article entitled, 3D Structures of Individual Mammalian Genomes Studied by Single-Cell Hi-C. This article describes how the researchers were able to examine genome folding at a scale of less than 100kb. This resolution allowed the researchers to validate chromosome structures.

The structures of individual topological-associated domains and loops vary substantially from cell to cell, the articles authors wrote. By contrast, A and B compartments, lamina-associated domains and active enhancers and promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding.

Most people are familiar with the well-known "X" shape of chromosomes, but in fact chromosomes only take on this shape when the cell divides. Using their new approach, the researchers have now been able to determine the structures of active chromosomes inside the cell, and how they interact with each other to form an intact genome.

This is important because knowledge of the way DNA folds inside the cell allows scientists to study how specific genes, and the DNA regions that control them, interact with each other. The genome's structure controls when and how strongly genesparticular regions of the DNAare switched on or off. This plays a critical role in the development of organisms and also, when it goes awry, in disease.

The researchers found that the genome is arranged such that the most active genetic regions are on the interior and separated in space from the less active regions that associate with the nuclear lamina. The consistent segregation of these regions, in the same way in every cell, suggests that these processes could drive chromosome and genome folding and thus regulate important cellular events such as DNA replication and cell division.

"Knowing where all the genes and control elements are at a given moment will help us understand the molecular mechanisms that control and maintain their expression, commented Prof. Ernest Laue, whose group at Cambridge's Department of Biochemistry developed the new imaging approach. "In the future, we'll be able to study how this changes as stem cells differentiate and how decisions are made in individual developing stem cells."

Until now, we've only been able to look at groups, or 'populations', of these cells and so have been unable to see individual differences, at least from the outside. Currently, these mechanisms are poorly understood and understanding them may be key to realizing the potential of stem cells in medicine."

"Visualizing a genome in 3D at such an unprecedented level of detail is an exciting step forward in research and one that has been many years in the making, stated Tom Collins, Ph.D., from Wellcome's Genetics and Molecular Sciences team. This detail will reveal some of the underlying principles that govern the organization of our genomesfor example how chromosomes interact or how structure can influence whether genes are switched on or off. If we can apply this method to cells with abnormal genomes, such as cancer cells, we may be able to better understand what exactly goes wrong to cause disease, and how we could develop solutions to correct this."

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3D Single-Cell Genome Structures Compared, Contrasted - Genetic Engineering & Biotechnology News