Category Archives: Genome

Types of genome sequencing
This video will explain different types of genome sequencing process in understanding human genome. For more information, log on to- http://shomusbiology.wee...

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Types of genome sequencing - Video

The $1,000 human genome is here. For real this time.

Illumina (ILMN), the worlds leading seller of gene sequencing machines, unveiled its HiSeq X (pronounced High Seek 10) on Tuesday. The system is the worlds first DNA-crunching supercomputer designed to process 20,000 genomes per year at a cost of $1,000 each. Currently it costs about $10,000 to sequence a human genome. Jay Flatley, Illuminas chief executive officer, introduced the machine at an investors conference in San Francisco, saying customers will begin receiving the machine this quarter. This will be a blockbuster product, he said in an interview.

The biotech industry has been trying to reach the $1,000 genome mark for years. Its a figure that should make full genome sequencing much more mainstream. As more people get sequenced, researchers get more data to use in their analysis of how DNA variations manifest themselves in diseases. The high-speed, low-cost sequencing system arrives at a crucial time, with a number of biotech companies, research centers, and hospitals starting to show real clinical breakthroughs. To figure out cancer, we need to sequence hundreds of thousands of cancer genomes, and this is the way to do it, Flatley said.

About a decade ago it cost much more than $1 billion to sequence a human genome, and the process took months. Illuminas new machine can knock out dozens of genomes in about a day. The HiSeq X systems, which cost $1 million each, should end up at large research centers and will be sold in groups of 10. Illumina has unveiled a smaller, $250,000 system called the NextSeq 500, which can fit on a laboratory counter and handle one genome at a time. The first customers for the HiSeq X include Macrogen, the Broad Institute in Cambridge, Mass., and the Garvan Institute of Medical Research in Sydney.

If it feels like weve been through this whole $1,000 genome thing before, its because we have. In early 2012, Ion Torrent, which was acquired by Life Technologies (LIFE), declared victory, saying it had a machine capable of the $1,000 genome in hand. The celebration, however, was premature. Glitches have prevented the company from actually selling such a machine. We expect it to be out in 2014, says Ron Andrews, the president of genetic and medical sciences at Life. We still have a team working on it, but it is not the ultimate goal. I think the reality is there are bigger and more urgent business opportunities than the $1,000 genome.

Illumina, based in San Diego, has fended off dozens of startups that were meant to upend the sequencing market and make its machines obsolete. In 2011, for example, Pacific Biosciences (PACB) began selling a machine (that cost $600million to design) with the promise to sequence genomes faster and more accurately than ever before. The system has not lived up to its billing, as its mostly been used for highly specialized botanical sequencing and for some cancer genomes that have repetitive sequences which are tough for other machines to decipher. According to a recent survey by industry trade publication In Sequence, Illumina increased its market share to 71 percent during 2013, followed by Life at 16percent, Roche (RHO:GR) at 10percent, and PacBio at 3percent. Wall Street analysts expect Illumina to report revenue of about $1.6billion this year, according to data compiled by Bloomberg.

Along with holding off startups, Illumina has had to contend with a hostile takeover attempt from Roche and Chinas recent entry into the sequencing-machine market. From late 2011 through the early part of 2012, Roche tried to acquire Illumina, topping out its bids at $51 per share. According to Flatley, Illuminas board was reluctant to sell, knowing it had these new machines and the potential for growth on the way. Illumina went so far as to prepare a roadshow in which it would show off its upcoming systems to convince investors about the possibility of a bright future. It was our responsibility to let the shareholders know what was in the kitchen being cooked, Flatley says. Ultimately, Illumina fended off the bid and kept the systems secret. Its share price has since surged, trading today at $117 per share.

Flatley says Illumina will continue to reduce the cost of sequencing hardware, as well as diversify into services. Last year, for example, it acquired Verinata Health for about $350 million. Verinata performs tests for expecting parents to see if their children have any chromosomal abnormalities; it does so via a blood test rather than the dreaded amniocentesis procedure. Illumina also offers a human genome sequencing service, which comes with a complimentary MyGenome app for the iPad, and has moved into cancer diagnostics.

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Illumina's DNA Supercomputer Heralds the $1,000 Human Genome

Illumina announces a new high-end sequencer made for factory-scale sequencing of human genomes.

Humans only: A new high-throughput sequencing machine from Illumina is optimized to sequence thousands of human genomes in a year.

The $1,000 genome has been a catchphrase of the sequencing industry for years, but despite bold promises from different companies, this benchmark hasnt been met. Now, thanks to a new sequencing machine from Illumina, it may finally be within reach.

At the J.P. Morgan Healthcare Conference on Tuesday, Illumina CEO Jay Flatley announced a new high-end sequencing machine that could accurately sequence whole human genomes at a cost of less than $1,000 each. Competitor Ion Torrent (later bought by Life Technologies) announced in 2012 that it had developed a machine capable of doing so (see Device Brings $1,000 Genome Within Reach), but capability has yet to materialize. Illuminas new machine is scheduled to reach its first customers in March. Faster chemistry and better opticsIlluminas machines read DNA sequences by analyzing patterns of fluorescent nucleotideshave allowed costs to come down.

The $1,000 price tag is often seen as vital to making whole-genome sequencing cost-effective for medical testing and personalized medicine. At this price, it might become reasonable for well-off patients to have their genomes sequenced for potential medical information.

Still, Illuminas new machines will be out of reach for most labs. The ultrahigh-throughput sequencers will be sold in systems of at least 10 machines each, at a starting price of $10 million. According to Flatley, the $1,000 price tag does take into account the cost of the machines, chemicals to do each run of sequencing, sample prep, and more. But these are machines intended to sequence tens of thousands of genomes each year.

Illumina emphasizes that the new machines will speed population-level genome sequencing for large projects aimed at understanding human disease and natural genetic variation. In his presentation, Flatley predicted an explosion of demand for factory-scale sequencing of human genomes. He pointed to a few large-scale projects already in the works, including the U.S. Veterans Affairs project to sequence the genomes of thousands of former soldiers and the U.K.s 100K Genomes project, which will sequence the genomes of National Health Service patients to help guide their care and to study genetic disease (see Why the U.K. Wants a Genomic National Health Service).

Researchers still struggle to understand how changes in DNA sequence cause disease and influence health. Large-scale sequencing projects can help reveal associations between a particular DNA variant and a disease or a healthy outcome. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine, said Eric Lander, founding director of the MIT and Harvard genomics center the Broad Institute, in a released statement.

The Illumina machine was built specifically for human genomes, says Flatley, and it can sequence human genomes accurately enough to reliably identify DNA variants 10 times faster than its predecessor, another high-end Illumina machine. While other machines may sequence human genomes more quickly, they cannot produce the same quality of sequence data at that speed, says Joel Fellis, a senior manager of product marketing at Illumina.

Flatley says the new machine can partially sequence five human genomes in a day. A complete run takes three days, during which time it can produce 16 human genomes at a quality level widely accepted by the sequencing community.

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Does Illumina Have the First $1,000 Genome?

SAN FRANCISCO The cost of sequencing a human genome has been brought below $1,000, San Diego DNA sequencing giant Illumina said Tuesday, opening the door to bringing the full benefit of 21st-century genomic medicine to the public.

The lower cost is made possible by the new HiSeq X Ten Sequencing System, announced by Illumina chief executive Jay Flatley at the JP Morgan Healthcare Conference in San Francisco.

Bringing the price below $1,000 is like breaking the sound barrier, Flatley said. That cost level long has been considered the price below which mass adoption of genome sequencing becomes feasible.

There was a collective gasp that went across the room, said Joe Panetta, chief executive of Biocom, the San Diego-based life science trade group.

Illuminas announcement was a big surprise, said Dr. Eric Topol, a pioneer in health care genomics and chief academic officer of Scripps Health in San Diego. Topol said genome sequencing costs appeared to have been stuck around the $3,000 to $5,000 range for a couple of years.

Knowledge of a persons individual genetic makeup helps doctors find out which drugs work best and what diseases they may be predisposed to get. Studying many genomes helps advance research by allowing individual variations to be linked to health. On a larger scale, more efficient treatment holds the promise of reining in rising health care costs by making medicine more effective.

Genome sequencing costs have been plummeting since the first genome was sequenced about 13 years ago, for a price in the hundreds of millions. Lower costs have allowed more exploration of the differences between individuals. These differences are the key to the goal of providing individualized health care.

But while the cost of genome sequencing has fallen to mass-market levels, the machines that perform them are far most costly. So these machines will mostly appeal to research laboratories and large health systems that can use them on a big scale.

The $1,000 cost takes into account the cost of the machines and the chemicals needed to do the sequencing, but not overhead, Flatley said. Interpreting the genome readout is not part of the process; trained scientists and clinicians must determine what the sequence means.

Illuminas new system consists of 10 HiSeq X sequencing machines, which sell for $1 million each, bringing the total system cost to $10 million. The new system will start shipping in March, Flatley said.

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Illumina breaks genome cost barrier

Photo by DOE Joint Genome Institute

Above: Older Illumina machines put the price of sequencing a genome around $10,000.

Sequencing an entire genome for $1,000 or less has long been seen as a tipping point in the field of genetics. At $1,000 a pop, sequencing would be within reach for many patients. And scientists studying the roll of genes in cancer and other diseases could greatly expand their research.

One San Diego company says they've now succeeded in bringing prices down that low.

Illumina CEO Jay Flatley announced the price cut today at the JP Morgan Healthcare Conference in San Francisco. The San Diego-based leader in gene sequencing claims to be the first company to reach this major milestone.

"It has come as a surprise," said Kelly Frazer, director of the Institute of Genomic Medicine at UC San Diego. She says researchers in her field knew the thousand-dollar genome was coming soonbut maybe not this soon.

Describing Illumina's new sequencers as "breakout technology," Frazer said, "It's going to mean a lot for basic researchers doing human disease work. And there's a potential for it to mean a lot for the clinic also."

The system itself is fairly expensive. At $10 million, the machines included in Illumina's HiSeq X Ten package are targeted towards large research institutions for now.

Though it could be awhile before typical patients see the benefits of a $1,000 genome, Frazer said the impact on her own research could be great. Her lab has been studying genetic risk factors for venous thromboembolism (VTE), a disease that causes potentially deadly blood clots.

To stay within budget, Frazer currently relies on incomplete genetic snapshots of her 1,2000 subjects. She says a $1,000 genome would allow her to order full sequencing for an even larger cohort, giving her a better idea of who might be at risk for VTE.

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San Diego Company Claims Major Milestone In Gene Sequencing

Startup Genome Highlights: Crdoba, Argentina

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Startup Genome Highlights: Córdoba, Argentina - Video

Subaru Legacy STI Genome exhaust

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Subaru Legacy STI Genome exhaust - Video

Subaru Liberty 3RB with STI Genome #39;s
05 Subaru Liberty 3RB 6MT Wagon with stock exhaust and STI Genome mufflers.

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Subaru Liberty 3RB with STI Genome's - Video

Jan. 12, 2014 Variations in non-coding sections of the genome might be important contributors to type 2 diabetes risk, according to a new study.

DNA sequences that don't encode proteins were once dismissed as "junk DNA," but scientists are increasingly discovering that some regions are important for controlling which genes are switched on.

The new study, published in Nature Genetics, is one of the first to show how such regions, called regulatory elements, can influence people's risk of disease.

Type 2 diabetes affects over 300 million people worldwide. Genetic factors have long been known to have an important role in determining a person's risk of type 2 diabetes, alongside other factors such as body weight, diet and age.

Many studies have identified regions of the genome where variations are linked to diabetes risk, but the function of many of these regions is unknown, making it difficult for scientists to glean insights into how and why the disease develops. Only around two per cent of the genome is made up of genes: the sequences that contain code for making proteins. Most of the remainder is shrouded in mystery.

"Non-coding DNA, or junk DNA as it is sometimes known, is the dark matter of the genome. We're only just beginning to unravel what it does," said leading author Professor Jorge Ferrer, a Wellcome Trust Senior Investigator from the Department of Medicine at Imperial College London.

In the new study scientists mapped the regulatory elements that orchestrate gene activity in the cells of the pancreas that produce insulin, a hormone that regulates blood sugar.

In type 2 diabetes, the tissues become less responsive to insulin, resulting in blood sugar levels being too high. Most people can compensate when this happens by producing more insulin, but in people with type 2 diabetes, the pancreas cannot cope with this increased demand.

"The cells that produce insulin appear to be programmed to behave differently in people with type 2 diabetes," said co-author Mark McCarthy, a Wellcome Trust Senior Investigator at the University of Oxford. "This study provides some important clues to the mechanisms which are disturbed in the earliest stages of the development of type 2 diabetes, and may point the way to novel ways of treating and preventing the disease."

The team identified genome sequences that drive gene activity in insulin-producing cells specifically. They found that these sequences are located in clusters, and that genetic variants known to be linked to diabetes risk are also found in these clusters.

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Non-coding DNA implicated in type 2 diabetes

Scientists from The Genome Analysis Centre (TGAC) in Norwich UK have developed a new bioinformatics tool to boost complex genome analysis.

The tool supports Illuminas recently released Nextera LMP kit, which enables the production of jumping libraries of up to 12kb. These Long Mate Pair libraries are an invaluable resource for analysing large areas of the genome, carrying out complex assemblies and other downstream bioinformatics analytics.

However, LMP libraries are intrinsically noisy and to maximise their value, post-sequencing data analysis is required.

Richard Leggett, at TGAC, said: Regulating laboratory protocols and selection of sequenced data for downstream analysis are vital in making effective use of mate pair libraries.

However, quality control of the libraries can require significant bioinformatics analysis. Further processing is also required to extract true mate pair reads, remove fragment junction adaptors and clip reads.

For this reason we developed NextClip, a tool for comprehensive quality analysis of Nextera LMP libraries and preparation of reads for scaffolding.

Mate pair libraries are formed by making large fragments of DNA (5-12 kb in length for Nextera) and are sequenced from either end of the fragment to produce two sequences of DNA that are separated by a known distance.

Sequence reads from Long Mate Pair libraries are an important tool in the construction of complex genome assemblies because they connect large repeat regions.

Grouping the data generated from mate pair library sequencing with shorter insert paired-end reads provide a powerful combination, allowing the joining together of longer DNA sequences, with higher certainty.

The Genome Analysis Centre is a research institute focused on the development of genomics and computational biology. Based at Norwich Research Park, it receives strategic funding from the Biotechnology and Biological Science Research Council - 9.2 million in 2012-2013 - as well as support from other research funders.

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New bioinformatics tool for complex genome analysis