Category Archives: Genome

Presentation from Large-Scale Genome Sequencing and Analysis Centers #39; Investigators - Richard Wilson
February 10, 2014 - National Advisory Council for Human Genome More: http://www.genome.gov/27556133.

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Presentation from Large-Scale Genome Sequencing and Analysis Centers' Investigators - Richard Wilson - Video

Richard III - The Whole Genome Sequence
The whole genome of King Richard III is to be sequenced in a project led by Dr Turi King of the Department of Genetics at the University of Leicester funded ...

By: UniversityLeicester

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Richard III - The Whole Genome Sequence - Video

Penn State University, The Genome Sciences Institute at the Huck - Pushing the Frontier
Understanding the function and evolution of genomes and the implications on how organisms live in their environments and thrive or get sick, requires a combi...

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Coding the Snail Genome: What little critters are teaching us about reproduction

By: Melissa Dawkins

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Coding the Snail Genome: What little critters are teaching us about reproduction - Video

Almost 25 years after the Human Genome Project launched, and a little over a decade after it reached its goal of reading all three billion base pairs in human DNA, genome sequencing for the masses is finally arriving. It will no longer be just a research tool; reading all of your DNA (rather than looking at just certain genes) will soon be cheap enough to be used regularly for pinpointing medical problems and identifying treatments. This will be an enormous business, and one company dominates it: Illumina. The San Diegobased company sells everything from sequencing machines that identify each nucleotide in DNA to software and services that analyze the data. In the coming age of genomic medicine, Illumina is poised to be what Intel was to the PC erathe dominant supplier of the fundamental technology.

Illumina already held 70 percent of the market for genome-sequencing machines when it made a landmark announcement in January: using 10 of its latest machines in parallel makes it feasible to read a persons genome for $1,000, long considered a crucial threshold for moving sequencing into clinical applications. Medical research stands to benefit as well. More researchers will have the ability to do large-scale studies that could lead to more precise understanding of diseases and help usher in truly personalized medicine.

Illumina was relentless in getting to this point. When CEO Jay Flatley joined the company in 1999, it was a 25person startup that sold microarray chips, which were useful in examining specific spots on the genome for important variations. But while the market grew relatively fast, competition was tough. In 2003, for example, Illumina had $28 million in revenue and a net loss of $27 million. Making matters tougher, the potential for microarrays seemed limited once more comprehensive sequencing technology began to improve quickly. In 2006, when a company called 454 Life Sciences was months away from the first rapid readout of an individual human genome (that of DNA scientist James D. Watson), Flatley knew Illumina had to have a sequencing technology of its own, and he had a choice: build it or buy it. We had an internal development program, but we were also looking at anyone in the market that already had a sequencing technology, he says now. Ultimately he settled on buying a company called Solexa.

Solexa took advantage of a novel way of sequencing, known as sequencing by synthesis, that was 100 times faster than other technologies and correspondingly cheaper, says -Flatley. But it was a small business, with just $2.5 million in revenue in 2006. After -Illumina provided the global distribution Solexa needed, we built it into a $100 million business in one year, he says. It was an inflection point for us. We began this super-rapid growth.

The deal also turned out to be a turning point for Illuminas competitors, which quickly fell behind technologically. Roche, which bought 454 Life Sciences in 2007, announced last October that it would shutter the company and phase out its sequencers. Complete Genomics, another competitor, cut jobs and began looking for a buyer in 2012; last year the Chinese company BGI-Shenzhen bought it, although Illumina made a failed bid for it as well.

The Solexa deal was far from the last time that Flatley transformed Illumina by buying the technology he thought it needed. Another pivotal point came last year, when the company bought Verinata Health, maker of a noninvasive prenatal sequencing test to identify fetal abnormalities. That gave Illumina a service that consumers can buy (through their doctors), in a market that could be worth billions of dollars in revenue.

Since 2005 Illumina has spent more than $1.2 billion on acquisitions. But it would be a mistake to dismiss the company as just a deep pocket. Illumina has a knack for improving the technology of companies it buys, says Doug Schenkel, managing director for medical technology equity research at Cowen and Company. When Illumina bought Solexas sequencing technology, Schenkel says, it was considered inflexible and was thought likely to hit a ceilingafter which it could probably not be improved furtherwithin three years. Illumina took that technology and, with innovation and investment, has made it flexible enough to not only dominate existing markets but open up multiple new opportunities, he adds. Even todaysix years laterthe ceiling is still at least three years away.

Illuminas soup-to-nuts strategyof providing fundamental sequencing technologies as well as services that mine genomic insightsappears to be a winner as genomic information begins to touch the practice of medicine and enter everyday life. Illumina already has an iPad app that lets you review your genome if it has been analyzed. One of the biggest challenges now is increasing the clinical knowledge of what the genome means, Flatley says. Its one thing to say, Heres the genetic variation. Its another to say, Heres what the variation means. Demand for that understanding will only increase as millions of people get sequenced. We want to be at the apex of that effort, he says.

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Why Illumina is No. 1

Discovery of skeleton lets scientists plan to sequence Richard IIIs genome

A year after they revealed that a twisted skeleton found under a parking lot was the remains of King Richard III, scientists in Britain plan to grind samples of his ancient bones and use them to map his genome.

(University of Leicester/AP) - The remains of Englands King Richard III, which were found in a dig in Leicester, England, in Sept. 2012.

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Scientists to map the genome of medieval English king Richard III

Now that genomes can be sequenced for $1,000, more patients can benefit, says Howard Jacob.

Howard Jacob

The quest for the $1,000 genome sequence began in December 2001 at the National Human Genome Research Institutes scientific retreat. That quest appears to have been completed with Illuminas January announcement of the HiSeqX Ten machine (see Illumina). Fifteen years after the first human genome was sequenced at a cost of $2.7 billion, we are at the dawn of a new era in medicine.

Many more genomes will now be sequenced, and they will be sequenced in much more detail. Today, because examining the whole genome has been so costly, most clinical and research labs look only at the exome, the roughly 1.5 percent of the genome associated with known functions. You might say that we are only looking where we understand. The ability to sequence the whole genome affordably will now generate an abundance of data and an opportunity to understand the importance of many more genetic variants. Sequencing the entire genome typically finds hundreds of times as much variation between any two individuals as just sequencing their exomes, most of it in regions of the genome that are poorly understood.

Learning the functions of those regions will help scientists better understand diseases, drug side effects, and the mechanisms by which the genome functions. Early efforts to use whole-genome sequencing in health care have produced promising results. In our clinic at the Medical College of Wisconsin and Childrens Hospital of Wisconsin, we have already used whole-genome sequencing to identify the causative variant, or mutation, in 26 percent of unexplained diseases we have taken on. The national rate of success without sequencing the genome is between 5 and 10 percent.

Being able to routinely use genome-wide sequencing in the clinic should make it possible to treat patients with an eye to their genetic predisposition toward specific diseases and their responsiveness to particular treatments. We already have evidence that this can improve success rates and reduce costs, which should make these technologies appealing to health insurers.

However, we arent there yet. More genomic data must be gathered and shared if we are to understand it well enough to affect clinical outcomes on a large scale. We must also remember that a genome sequence is only the first step; it must be followed up with genetic counseling and evidence-based care. Ethics must also be part of the discussion, because decisions about genomic screening affect generations to come. Now that the technology needed to deliver the $1,000 genome has arrived, we must determine the best way to use this information to save lives.

Howard Jacob is director of the Human and Molecular Genetics Center at the Medical College of Wisconsin.

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The $1,000 Genome Is Here

Finding Hope in Whole Genome Sequencing: Retta Beery at TEDxYouth@SanDiego 2013
Retta Beery #39;s twins, Noah and Alexis, were born with a neurologic disorder. Through research and advocacy, Retta discovered that her twins were misdiagnosed ...

By: TEDxYouth

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Finding Hope in Whole Genome Sequencing: Retta Beery at TEDxYouth@SanDiego 2013 - Video

2 hours ago by Bob Yirka This diagram shows a protein nanopore set in an electrically resistant membrane bilayer. An ionic current is passed through the nanopore by setting a voltage across this membrane. Credit: Oxford Nanopore Technologies

(Phys.org) U.K. based Oxford Nanopore Technologies has made good on a promise made two years ago to produce an inexpensive genome sequencer that is based on nanopore technology. David Jaffe, with the Broad Institute reported to an audience at the Advances in Genome Biology and Technology meeting in Florida last week that he has been asked by Oxford Nanopore to try out the new the device, called the MinION, and has found it to be promising.

Oxford Nanopore Technologies created a stir in the biological sciences world in 2012 when representatives for the company announced that its research team had successfully created a sequencing device based on nanopore technology and that an inexpensive prototype would be delivered to researchers outside the company soon thereafter. The company apparently ran into difficulty ramping up its pore technology and had to find some alternative materialsthus the two year delay.

Nanopore sequencing is where single strands of DNA are pulled through a poreas each base pair passes through the pore its conductivity is measuredinformation that can be used for identification by a computer. The advantage of this approach is that at least in principle, any strand length can be sequenced.

The MinION isn't for sale yetat this time the company is making prototypes available to a select few notables in the genome sequencing fieldeach will have to pony up $1000 as a down-payment for the honor. The device plugs into a port on a computer, which does the processing. Along with the device, which has been compared to the size of a pack of gum, Oxford Nanopore Technologies will send along DNA samples that researchers can use to learn how to use the new deviceafter that, they can sequence anything they want. In testing strands of two types of bacterial DNA sent to him, Jaffe reports having mixed results long stretches of data were obtained correctly in some cases, but in others there were some errors. In order to assemble the entire genome of a type of bacteria, for example, he had to also use a sequencing device made by another company. He noted that he is optimistic about the device, however, as reps from Oxford Nanopore have assured him that error rates can be reduced using certain techniques even as improvements to the device are being worked out back at the lab.

If the error rates using the MinION can be reduced to a practical level, the device could mark a turning point in gemone sequencing as it would be a device that could be carried and used for fieldwork. And though the cost of such a device has not been announced, Oxford Nanopore has repeatedly used terms such as inexpensive and affordable to describe it, indicating it will cost much less than other sequencing devices currently on the marker, once it's ready for sale.

Explore further: The gene sequencing that everyone can afford in future

More information: http://www.nanoporetech.com

2014 Phys.org

(PhysOrg.com) -- Oxford University spinoff company, Oxford Nonopore has announced at this years Advances in Genome Biology and Technology conference in Florida, two new machines for sequencing genes. ...

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Oxford Nanopore unveils portable genome sequencer MinION

How to sequence the human genome
BioTechGuru.in is a blog that provides information about the Indian Biotechnology Sector to the students, so that they can achieve their best place in the in...

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How to sequence the human genome - Video