Daily Archives: March 27, 2017

Where earlier approaches saw researchers using computers to stick small pieces of genetic code together, the new technique takes advantages of folding maps (which show how a 6.5ft long genome can cram into a cell's nucleus) to quickly build out a sequence. As you only need short reads of DNA to make this happen, the cost is much lower. You also don't need to know much about your sample organism going in.

As an example of what's possible, the team completely assembled the three chromosomes for the Aedes aegypti mosquito for the first time. More complex organisms would require more work, of course, but the dramatically lower cost makes that more practical than ever. Provided the approach finds widespread use, it could be incredibly valuable for both biology and medicine.

In the case of the mosquito, scientists hope the genomes will reveal the vulnerabilities that let the Zika virus spread. You could see gene-modified mosquitoes that resist the virus and stop it from spreading. Alternately, this could uncover patient-specific genetic changes that expose humans to certain diseases -- it wouldn't be a mystery why one person falls ill while another is healthy. And when it's relatively affordable to build a genome out of curiosity, biologists could catalog many species instead of the most vital examples.

Go here to see the original:
Scientists find a low-cost way to build genomes from scratch - Engadget

Subscribe on YouTube

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.

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

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 »

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

Scientists at Baylor College of Medicine, Rice University, Texas Children's Hospital, and the Broad Institute of MIT and Harvard say they have developed a new way to sequence genomes, which can assemble the genome of an organism entirely from scratch, much cheaper and faster.

The multi-institutional team reports a methodcalled 3D genome assemblythat can create a human reference genome, entirely from scratch, for less than $10,000. The ability to quickly and easily generate a reference genome from scratch would open the door to creating reference genomes for everything from patients to tumors to all species on earth. The group published their study ("De Novo Assembly of the Aedes aegypti Genome Using Hi-C Yields Chromosome-Length Scaffolds") in Science.

To illustrate the power of 3D genome assembly, the researchers have assembled the 1.2-billion-letter genome of the Aedes aegypti mosquito, which carries the Zika virus, producing the first end-to-end assembly of each of its three chromosomes. The new genome will enable scientists to better combat the Zika outbreak by identifying vulnerabilities in the mosquito that the virus uses to spread.

Despite the decline in the cost of DNA sequencing, determining the sequence of each chromosome from scratch via de novo genome assembly remains extremely expensive because chromosomes can be hundreds of millions of base pairs long. In contrast, today's inexpensive DNA sequencing technologies produce short reads, or hundred-base-pair-long snippets of DNA sequence, which are designed to be compared to an existing reference genome. Actually generating a reference genome and assembling all those long chromosomes involves combining many different technologies at a cost of hundreds of thousands of dollars. Unfortunately, because human genomes differ from one another, the use of a reference genome generated from one person in the process of diagnosing a different person can mask the true genetic changes responsible for a patient's condition.

"As physicians, we sometimes encounter patients who we know must carry some sort of genetic change, but we can't figure out what it is," said Aviva Presser Aiden, Ph.D., M.D., a physician-scientist in the Pediatric Global Health Program at Texas Children's Hospital and a co-author of the new study. "To figure out what's going on, we need technologies that can report a patient's entire genome. But, we also can't afford to spend millions of dollars on every patient's genome."

To tackle the challenge, the team developed a new approach, called 3D assembly, which determines the sequence of each chromosome by studying how the chromosomes fold inside the nucleus of a cell.

"Our method is quite different from traditional genome assembly," said Olga Dudchenko, Ph.D., postdoctoral fellow at the Center for Genome Architecture at Baylor College of Medicine, who led the research. "Several years ago, our team developed an experimental approach that allows us to determine how the 2-meter-long human genome folds up to fit inside the nucleus of a human cell. In this new study, we show that, just as these folding maps trace the contour of the genome as it folds inside the nucleus, they can also guide us through the sequence itself."

By carefully tracing the genome as it folds, the team found that they could stitch together hundreds of millions of short DNA reads into the sequences of entire chromosomes. Since the method only uses short reads, it reduces the cost of de novo genome assembly, which is likely to accelerate the use of de novo genomes in the clinic.

"Sequencing a patient's genome from scratch using 3D assembly is so inexpensive that it's comparable in cost to an MRI," said Dr. Dudchenko, who also is a fellow at Rice University's Center for Theoretical Biological Physics. "Generating a de novo genome for a sick patient has become realistic."

Unlike the genetic tests used in the clinic today, de novo assembly of a patient genome does not rely on the reference genome produced by the Human Genome Project. "Our new method doesn't depend on previous knowledge about the individual or the species that is being sequenced," Dr. Dudchenko noted. "It's like being able to perform a human genome project on whomever you want, whenever you want."

"Or whatever you want," added Erez Lieberman Aiden, Ph.D., director of the Center for Genome Architecture at Baylor and corresponding author on the new work. "Because the genome is generated from scratch, 3D assembly can be applied to a wide array of species, from grizzly bears to tomato plants. And it is pretty easy. A motivated high school student with access to a nearby biology lab can assemble a reference-quality genome of an actual species, like a butterfly, for the cost of a science fair project."

The effort took on added urgency with the outbreak of Zika virus, which is carried by the A. aegypti mosquito. Researchers hoped to use the mosquito's genome to identify a strategy to combat the disease, but the Aedes genome had not been well characterized, and its chromosomes are much longer than those of humans.

"We had been discussing these ideas for years, writing a chunk of code here, doing a proof-of-principle assembly there," explained Dr. Lieberman Aiden, also assistant professor of molecular and human genetics at Baylor, computer science at Rice and a senior investigator at the Center for Theoretical Biological Physics. "So we had assembly data for A. aegypti just sitting on our computers. Suddenly, there's an outbreak of Zika virus, and the genomics community was galvanized to get going on Aedes. That was a turning point."

"With the Zika outbreak, we knew that we needed to do everything in our power to share the Aedes genome assembly, and our methods, as soon as possible," according to Dr. Dudchenko."This de novo genome assembly is just a first step in the battle against Zika, but it's one that can help inform the community's broader effort."

The team also assembled the genome of the Culex quinquefasciatus mosquito, the principal vector for West Nile virus. "Culex is another important genome to have, since it is responsible for transmitting so many diseases," said Dr. Lieberman Aiden. "Still, trying to guess what genome is going to be critical ahead of time is not a good plan. Instead, we need to be able to respond quickly to unexpected events. Whether it is a patient with a medical emergency or the outbreak of an epidemic, these methods will allow us to assemble de novo genomes in days, instead of years."

Read more:
3D Assembly of Zika Genome Could Have Significant Impact on Human Reference Genome - Genetic Engineering & Biotechnology 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

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