Category Archives: Genome

What is Genome-Guided Medicine?
Dr. Deanna Church discusses the benefits of the Accuracy and Content Enhanced (ACE) technology by Personalis, Inc. - the provider of the most advanced genomi...

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What is Genome-Guided Medicine? - Video

The Human Race 3-5 Documentary
In the 1990s, the race to work out the structure of DNA 50 years ago was eclipsed by another race: to catalogue all the genes in the human genome. The rivalry became so bitter that presidents...

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The Human Race 3-5 Documentary - Video

[MINUSmin31] Sebastian Mullaert Patrick Siech - Genome I
Sebastian Mullaert Patrick Siech Announce Part One of Their Genome Trilogy Inspired in equal measure by analog synthesizer technology and the lush Swedish countryside, Genome marks the...

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[MINUSmin31] Sebastian Mullaert & Patrick Siech - Genome I - Video

Edico Genome Inc., a San Diego-based company that makes integrated circuits for processing genomic data, announced the broad commercial launch of its flagship Dragen processor.

Dragen is a chip that users can integrate into their servers or sequencing instruments to map sequencing reads, or DNA fragments, to a reference genome. The idea is that the chip can help companies piece short reads together to create a complete genome. This is a much faster approach than using a general purpose server, and it relieves one of the most time-consuming steps in working with genomic data.

Edico has recently grown from eight employees to 24, and made its first sale of the Dragen chip last month to San Diego-based Sequenom Inc., a prenatal testing company. Sequenom generated 20 million short reads on a sequencing machine to identify fetal chromosomal disorders from maternal blood samples. The reads were then mapped using both the Dragen chip and a standard pipeline that included Bowtie 2 as the mapping algorithm. Sequenom reported that the Dragen processor mapped the entire set of reads in nine seconds, roughly 30 times faster than the standard pipeline, with no significant difference in sensitivity or specificity in detecting the indicators that help determine fetal genetic disorders.

The impact of Dragens ability to rapidly and accurately analyze data in a cost-effective manner is greatly magnified when analyzing massive data sets, such as whole genomes, or large numbers of smaller tests such as RNA sequencing, said Pieter van Rooyen, chief executive officer of Edico Genome. Due to these advantages, weve already had a tremendous response to Dragens early access program, and now we are able to make our bio-IT processor broadly available to companies and academic institutions with low to very high-volume sequencing capacities.

The company sees particular benefits for using Dragen for cancer treatment, non-invasive prenatal testing and diagnosing rare disease, he added.

Edico has also announced that a Dragen processor is now deployed at the San Diego Supercomputer Center, which serves university and nonprofit labs across the city.

The company is headquartered at the EvoNexus incubator in La Jolla, and raised $10 million in venture capital earlier this year to commercialize the chip.

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Edico Genome Announces Launch of Dragen Processor

Scientists sequenced the genome of a man who lived 45,000 years ago
Scientists sequenced the genome of a man who lived 45000 years ago.

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Scientists sequenced the genome of a man who lived 45,000 years ago - Video

Customized genome editing -- the ability to edit desired DNA sequences to add, delete, activate or suppress specific genes -- has major potential for application in medicine, biotechnology, food and agriculture.

Now, in a paper published in Molecular Cell, North Carolina State University researchers and colleagues examine six key molecular elements that help drive this genome editing system, which is known as CRISPR-Cas.

NC State's Dr. Rodolphe Barrangou, an associate professor of food, bioprocessing and nutrition sciences, and Dr. Chase Beisel, an assistant professor of chemical and biomolecular engineering, use CRISPR-Cas to take aim at certain DNA sequences in bacteria and in human cells. CRISPR stands for "clustered regularly interspaced short palindromic repeats," and Cas is a family of genes and corresponding proteins associated with the CRISPR system that specifically target and cut DNA in a sequence-dependent manner.

Essentially, the authors say, bacteria use the system as a defense mechanism and immune system against unwanted invaders such as viruses. Now that same system is being harnessed by researchers to quickly and more precisely target certain genes for editing.

"This paper sheds light on how CRISPR-Cas works," Barrangou said. "If we liken this system to a puzzle, this paper shows what some of the system's pieces are and how they interlock with one another. More importantly, we find which pieces are important structurally or functionally -- and which ones are not."

The CRISPR-Cas system is spreading like wildfire among researchers across the globe who are searching for new ways to manipulate genes. Barrangou says that the paper's findings will allow researchers to increase the specificity and efficiency in targeting DNA, setting the stage for more precise genetic modifications.

The work by Barrangou and Beisel holds promise in manipulating relevant bacteria for use in food -- think of safer and more effective probiotics for your yogurt, for example -- and in model organisms used in agriculture, including gene editing in crops to make them less susceptible to disease.

The collaborative effort with Caribou Biosciences, a start-up biotechnology company in California, illustrates the focus of these two NC State laboratories on bridging the gap between industry and academia, and the commercial potential of CRISPR technologies, the researchers say.

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The above story is based on materials provided by North Carolina State University. Note: Materials may be edited for content and length.

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Genome editing technique advanced by researchers

A new comprehensive analysis of thyroid cancer from The Cancer Genome Atlas Research Network has identified markers of aggressive tumors, which could allow for better targeting of appropriate treatments to individual patients.

The finding suggests the potential to reclassify the disease based on genetic markers and moves thyroid cancer into a position to benefit more from precision medicine.

"This understanding of the genomic landscape of thyroid cancer will refine how it's classified and improve molecular diagnosis. This will help us separate those patients who need aggressive treatment from those whose tumor is never likely to grow or spread," says Thomas J. Giordano, M.D., Ph.D., professor of pathology at the University of Michigan Medical School.

Giordano is the project co-lead for TCGA thyroid cancer analysis along with Gad Getz, Ph.D., director of Cancer Genome Computational at the Broad Institute.

Thyroid cancer incidence has increased three-fold over the last 30 years and is the most rapidly increasing cancer in the United States. While the tumors are often slow-growing and easily treated with a combination of surgery, thyroid hormone and radioactive iodine, some patients will develop more aggressive and deadly thyroid cancers.

In this TCGA study, which is published in Cell, the researchers analyzed nearly 500 thyroid cancer samples to identify all genetic mutations that play a role. They found several new cancer genes as well as new variations of existing genes.

Overall, the thyroid cancer genome is relatively quiet, with fewer genetic mutations involved than in other common cancers, the researchers found. This may explain why the disease is often slow-growing.

Fewer mutations meant the researchers were able to look at the signaling pathways involved and understand what drives thyroid tumors. This approach helped them understand the genetic drivers of more of these cancers, reducing the percentage of "dark matter" cases -- those with unknown genetic drivers -- from 25 percent to 3.5 percent.

Those drivers can be broken down into two primary oncogenic groups: BRAF plus similar mutations and RAS plus similar mutations. But within these two primary groups, especially the BRAF group, several different subtypes of thyroid cancer exist. Currently, all thyroid cancers associated with BRAF, for example, had been considered essentially the same. That's not the case.

"This study integrated a wide variety of genomic data to not only identify cancer drivers, but to compare how these different drivers behave," said Getz, who is also director of the Bioinformatics Program at the Massachusetts General Hospital Cancer Center and an associate professor of pathology at Harvard Medical School. "Interestingly, we found that subsets of BRAF-mutated thyroid cancers are driving cancer through distinct mechanisms, and that some of these subsets are associated with higher risk and less differentiated cancers."

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Thyroid cancer genome analysis finds markers of aggressive tumors

An analysis of the oldest known DNA from a human reveals a mysterious group that roamed northern Asia

The Ust-Ishim femur. Credit:Bence Viola, MPI EVA

A 45,000-year-old leg bone from Siberia has yielded the oldest genome sequence forHomo sapienson record revealing a mysterious population that may once have spanned northern Asia. The DNA sequence from a male hunter-gatherer also offers tantalizing clues about modern humans journey from Africa to Europe, Asia and beyond, as well as their sexual encounters with Neanderthals.

His kind might have remained unknown were it not for Nikolai Peristov, a Russian artist who carves jewellery from ancient mammoth tusks. In 2008, Peristov was looking for ivory along Siberias Irtysh River when he noticed a bone jutting from the riverbank. He dug it out and showed it to a police forensic scientist, who identified it as probably human.

The bone turned out to be a human left femur, and eventually made it to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where researchers carbon-dated it. It was quite fossilized, and the hope was that it might turn out old. We hit the jackpot, says Bence Viola, a palaeoanthropologist who co-led the study of the remains. It was older than any other modern human yet dated. The luck continued when Violas colleagues found that the bone contained well-preserved DNA, and they sequenced its genome to the same accuracy as that achieved for contemporary human genomes (Q.Fuetal.Nature514,445449; 2014).

The researchers named their find Ust-Ishim, after the district where Peristov found the remains. They dated him to between 43,000 and 47,000 years old, nearly twice the age of the next-oldest known complete modern-human genome, although older, archaic-human genomes exist.

DNA may be the only chance to connect the remains to other humans. This guy came out of nowhere theres no archaeology site we could connect it to, says Viola, suggesting that his group roamed far and wide.

The Ust-Ishim man was probably descended from an extinct group that is closely related to humans who left Africa more than 50,000years ago to populate the rest of the world, but later went extinct, Viola says.

The most intriguing clue about his origin is that about 2% of his genome comes from Neanderthals. This is roughly the same level that lurks in the genomes of all of todays non-Africans, owing to ancient trysts between their ancestors and Neanderthals. The Ust-Ishim man probably got his Neanderthal DNA from these same matings, which, past studies suggest, happened after the common ancestor of Europeans and Asians left Africa and encountered Neanderthals in the Middle East.

Until now, the timing of this interbreeding was uncertain dated to between 37,000 and 86,000 years ago. But Neanderthal DNA in the Ust-Ishim genome pinpoints it to between 50,000 and 60,000 years ago on the basis of the long Neanderthal DNA segments in the Ust-Ishim mans genome. Paternal and maternal chromosomes are shuffled together in each generation, so that over time the DNA segments from any individual become shorter.

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45,000-Year-Old Man's Genome Sequenced

Bence Viola, MPI EVA

The Ust-Ishim femur.

A 45,000-year-old leg bone from Siberia has yielded the oldest genome sequence for Homo sapiens on record revealing a mysterious population that may once have spanned northern Asia. The DNA sequence from a male hunter-gatherer also offers tantalizing clues about modern humans journey from Africa to Europe, Asia and beyond, as well as their sexual encounters with Neanderthals.

His kind might have remained unknown were it not for Nikolai Peristov, a Russian artist who carves jewellery from ancient mammoth tusks. In 2008, Peristov was looking for ivory along Siberias Irtysh River when he noticed a bone jutting from the riverbank. He dug it out and showed it to a police forensic scientist, who identified it as probably human.

The bone turned out to be a human left femur, and eventually made it to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where researchers carbon-dated it. It was quite fossilized, and the hope was that it might turn out old. We hit the jackpot, says Bence Viola, a palaeoanthropologist who co-led the study of the remains. It was older than any other modern human yet dated. The luck continued when Violas colleagues found that the bone contained well-preserved DNA, and they sequenced its genome to the same accuracy as that achieved for contemporary human genomes (Q.Fu etal.Nature 514, 445449; 2014).

The researchers named their find Ust-Ishim, after the district where Peristov found the remains. They dated him to between 43,000 and 47,000 years old, nearly twice the age of the next-oldest known complete modern-human genome, although older, archaic-human genomes exist.

DNA may be the only chance to connect the remains to other humans. This guy came out of nowhere theres no archaeology site we could connect it to, says Viola, suggesting that his group roamed far and wide.

The Ust-Ishim man was probably descended from an extinct group that is closely related to humans who left Africa more than 50,000years ago to populate the rest of the world, but later went extinct, Viola says.

The most intriguing clue about his origin is that about 2% of his genome comes from Neanderthals. This is roughly the same level that lurks in the genomes of all of todays non-Africans, owing to ancient trysts between their ancestors and Neanderthals. The Ust-Ishim man probably got his Neanderthal DNA from these same matings, which, past studies suggest, happened after the common ancestor of Europeans and Asians left Africa and encountered Neanderthals in the Middle East.

Until now, the timing of this interbreeding was uncertain dated to between 37,000 and 86,000 years ago. But Neanderthal DNA in the Ust-Ishim genome pinpoints it to between 50,000 and 60,000 years ago on the basis of the long Neanderthal DNA segments in the Ust-Ishim mans genome. Paternal and maternal chromosomes are shuffled together in each generation, so that over time the DNA segments from any individual become shorter.

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Oldest-known human genome sequenced

Edico Genomes Dragen genome processor, mounted on a standard computer board.

A super-fast genome processor called the Dragen Bio-IT Processor is now on sale by San Diego's Edico Genome. The processor, which is sold on a standard PCIe computer board, is meant to relieve the bottleneck in analyzing the flood of genomic data.

The Dragen processor is a special-purpose microprocessor adapted to analyzing the human genome, said Pieter van Rooyen, Edico's chief executive. That enables the accelerator card to outperform general-purpose computer chips, such as those used in servers now used to characterize genomic data.

Gene sequencing technology cuts genetic material into fragments, determines the sequence of each fragment, then reassembles these fragments like an immensely complicated jigsaw puzzle.

Software algorithms and high-powered clusters of computers are now used to do that reassembling, but it takes many hours, van Rooyen said. A human genome has 3 billion base pairs, or DNA letters.

To produce a medical-grade genome, each genome is read and reassembled more than 30 times, and the results compared to reduce errors. Each genome is compared to a reference genome.

"What we've done is take that processing that needs to be done to reassemble that giant jigsaw puzzle, and put it in a chip," van Rooyen said.

"The chip does secondary processing. It does all the processing to map those reads, figure out where they came from, stack them up, compensate for the errors, and then identify how are you different from the reference (genome). Do you have a mutation in one of your genes that might cause cancer? Or if you have cancer, what type do you have?"

My teams use of the Dragen processor has enabled us to analyze our RNA-seq data more than 60 fold faster than a 16-core CPU," said Gene Yeo, of the Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California San Diego, in an Edico statement.

A video of Scripps Health geneticist/cardiologist Eric Topol discussing the Dragen processor can be viewed at http://www.youtube.com/watch?v=TXcrErjf3x8.

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Edico starts selling high-powered genome processor