Category Archives: Genome

all the genetic content contained within an organism. An organism's genome is made up of molecules of deoxyribonucleic acid (DNA) that form long strands that are tightly wound into chromosomes, which are found in the nucleus of eukaryotic organisms and in the cytoplasm of prokaryotic organisms. Chromosomes that are unique to certain organelles within a cell, such as mitochondria or chloroplasts, are also considered a part of an organism's genome. A genome includes all the coding regions (regions that are translated into molecules of protein) of DNA that form discrete genes, as well as all the noncoding stretches of DNA that are often found on the areas of chromosomes between genes. The sequence, structure, and chemical modifications of DNA not only provide the instructions needed to express the information held within the genome but also provide the genome with the capability to replicate, repair, package, and otherwise maintain itself. The human genome contains approximately 25,000 genes within its 3,000,000,000 base pairs of DNA, which form the 46 chromosomes found in a human cell. In contrast, Nanoarchaeum equitans, a parasitic prokaryote in the domain Archaea, has one of the smallest known genomes, consisting of 552 genes and 490,885 base pairs of DNA. The study of the structure, function, and inheritance of genomes is called genomics. Genomics is useful for identifying genes, determining gene function, and understanding the evolution of organisms.

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Genome - Definition and More from the Free Merriam-Webster ...

PUBLIC RELEASE DATE:

15-Jan-2014

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

January 14, 2014, Shenzhen, China - Researchers from Institute of Zoology, Chinese Academy of Sciences, BGI and other institutes have successfully decoded the whole genome sequence of Locust (Locusta migratoria), the most widespread locust species. The yielded genome is remarkably big- at 6.5 gigabytes, which is the largest animal genome sequenced so far. The latest study has been published online in the journal Nature Communications.

It surprises us that a single locust can eat its own bodyweight in food in a single day; this is, proportionately, 60 times a human's daily consumption. They are capable of inflicting famine and wiping out livelihoods when they swarms, which can cost countries billions of dollars in lost harvests and eradication efforts.

In this study, researchers sequenced Locusta migratoria using next-gen sequencing technology, totally yielding 721Gb of data, which covered 114 of the 6.3Gb locust genome size. They annotated and predicted about 17,307 gene models, and identified over 2,639 repeat gene families. Moreover, they discovered that the top ten repeat families only represented 10% of the total genome sequences, suggesting that there were no dominant families in the L. migratoria genome.

Compared with other reference insect genomes, researchers found the reason why locust has such large genome is transposable element proliferation combined with slow rates of loss for these elements. According to statistics, repetitive elements constituted 60% of the assembled genome. The transposable element in the Locust genome was expanded when comparing with the other insects. Besides, they also found that the locust genome exhibited the lowest rate of DNA deletions relative to the other insects.

To investigate the potential involvement of epigenetic regulation in locust phase change, researchers performed comparative methylome and transcriptome analysis. One interesting finding was that repetitive elements were highly methylated and introns had higher methylation levels than exons in locust genome. It was also noteworthy that there had changes in genes involved in the regulation of the cytoskeletal microtubular system and in neuronal activity during the onset of phase change in locusts from solitarious to swarm.

As we all know, locust has an most distinguishing feature- the long-distance flight- which enables them can fly at speed of hundreds of kilometers an hour, or even cross the ocean. In this study, researchers found that locust had developed a highly efficient energy supply system by expansion genes in lipid metabolism and detoxification to fulfill the intensive energy consumption during their long-distance flight. The expansion of its gustatory and olfactory receptor gene families is for its strong adaptation to host plant recognition.

To advance the development of new effective insecticides, researchers identified the gene targets for pest control and new insecticides, such as cys-loop ligand-gated ion channels and G-protein-coupled receptors, which are considered to be major traditional insecticide targets, and the repertoire of several biological processes that may serve as mechanistic targets and lead to the development of specific and sustainable pest control methods.

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World's largest animal genome belongs to locust

14 1 Human Genome
Video Notes for Section 14.1.

By: Jan Esmay

Original post:
14 1 Human Genome - Video

Business Wire

The HiSeq X Ten is composed of ten HiSeq X machines, and sells for at least $10 million.

The US$1,000 genome is here. Or so says sequencing-technology company Illumina, based in San Diego, California. At a healthcare investors' conference on 14 January, Illumina CEO Jay Flatley announced that his company will begin producing a new system this year called the HiSeq X Ten, one that can deliver full coverage human genomes for less than $1,000. Here Nature assesses the claim.

We've heard claims of the $1,000 genome before. Aren't we there already?

Other companies such as Life Technologies, in Carlsbad, California, maker of the Ion Torrent sequencing platforms, and UK-based Oxford Nanopore have said before that they will sell technologies capable of sequencing genomes for $1,000 or less. Neither technology is there yet, and pushing the cost of sequencing under $1,000 has proven to be a tough nut to crack.

Why do we care about a $1,000 genome?

The first sequenced human genome cost nearly $3 billion, but as sequencing costs have dropped substantially, doctors have begun using some patients' genome sequences to improve their care. But scientists think that they will need to sequence hundreds of thousands or even millions of people to truly understand how genes influence disease so that better drugs and treatments can be developed. They say that $1,000 genomes are needed to enable the huge sequencing studies that could lead to breakthroughs in personalized medicine.

What has Illumina said the HiSeq X Ten will do?

The HiSeq X is capable of producing up to 1.8 terabases of data 16 human genomes' worth per three-day run. Illumina says that each HiSeq X Ten will therefore be capable of sequencing 18,000 human genomes per year. Each genome will be sequenced to the gold standard of 30x, which means that each base will be read by the machine an average of thirty times. And these are whole human genomes we're talking about here not solely the protein-coding regions, or exomes.

How big a deal is this?

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Is the $1,000 genome for real?

Jan. 15 (UPI) -- San Diego-based genetic technology company Illumina has announced a machine that can sequence a human genome for $1,000.

The new product, called HiSeq X Ten Sequencing System, was launched at the annual JP Morgan Healthcare Conference in San Francisco. The $1 million sequencer comes in a set of 10 units and can generate 1.8 Tb of sequencing data in 3 days and up to 600 Gb in a single day at no more than $1,000 per genome.

"Breaking the sound barrier of human genetics not only pushes us through a psychological milestone, it enables projects of unprecedented scale," said Illumina CEO Jay Flatley.

This cost includes typical instrument depreciation, DNA extraction, library preparation, and estimated labor. A number of companies have placed orders for the product, including the Broad Institute, an independent biomedical research center affiliated with MIT and Harvard.

"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 Broad Institute founding Director Eric Lander.

The term "$1,000 genome" comes from the Archon X-prize that challenged teams to build machines that could sequence 100 genomes in 30 days or less, with minimal errors and at a cost of $1,000 per genome.

[Illumina]

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Illumina promises sequencing for $1000 per genome

BusinessWire

Yesterday, the company that leads the field in DNA sequencing machines announced that it was preparing to sell systems that would finally put a major milestone in reach: the $1,000 genome. This is a notable breakthrough as it's been less than a decade since a genome cost over a quarter-million dollars. While the price may be revolutionary, the system itself is an evolution of existing technology, built up to provide massive economies of scale.

The foundation of the new system is a sequencing machine that improves a bit on the company's existing hardware, providing more individual sequencing reactions at the same time in each machine (6-8 billion reactions in each machine) and speeding up the actual reactions so that more gets done within a 24-hour period. The system itself then clusters 10 of these sped-up machines. The cluster of 10, according to Matthew Herper at Forbes, will set you back $10 million.

Despite the high cost of entry, however, Illumina claims that the amortized price is included in their $1,000 figureas are the costs of preparing the DNA and consumables used during the reactions, even the labor needed to get it all to happen. In other words, a single genome will still cost a fortune; buying the system and cranking out genomes nonstop for a few years will mean that the average cost drops to near the $1,000 price tag.

The cluster itself will be impressive. Each machine will churn out 600 Gigabases each day. Each copy of the human genome is only about three billion base pairs, and sequencing each of those bases an average of 30 times is typical for a lot of genome work, which means that a single genome will only take up 15 percent of a single machine's daily capacity. Spread out over a year, Illumina estimates that the cluster can output about 18,000 genomes every year. Your mileage may vary.

A number of large genome sequencing centers have already signed up for delivery of these systems, so they'll have an almost immediate impact in the academic world. But the $1,000 genome is mostly a figure that will be appealing for consumers. Unfortunately, the enormous up-front costs of the system make it unlikely that anyone's going to be rushing out to buy one of these so that they can turn around and offer its benefits to consumers, given that the consumer market is essentially nonexistent right now.

For more details, you can read Illumina's description of the system.

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The $1,000 genome could be yours—if you spend $10 million on equipment

January 15, 2014

Brett Smith for redOrbit.com Your Universe Online

A thousand bucks can get you that new MacBook Air or serve as a sizeable down payment on a new car. But a longer-term investment might be to sequence your entire personal genome.

On Tuesday, Ilumina, the worlds leading seller of gene sequencing machines, unveiled HiSeq X Ten the first supercomputer made to process 20,000 human genomes annually at a cost of $1,000 each.

At a conference in San Francisco, Illuminas CEO Jay Flatleysaid customers will start to see the DNA-sequencing machine on the market in the first quarter of 2014.

This will be a blockbuster product, he told Bloomberg News.

The $1,000-mark is a major milestone for the genetic sequencing industry, which has been trying to hit that goal for years. Experts have predicted that this price point would allow for the mainstreaming of genetic sequencing and a resulting multiplication of genetic data that could lead to an explosion in medical breakthroughs.

To figure out cancer, we need to sequence hundreds of thousands of cancer genomes, and this is the way to do it, Flatley explained.

John Mattick, executive director of the Garvan Institute of Medical Research in Australia, said in an Illumina press release that his institution would seek to leverage this new technology in pursuit of its research goals.

The sequencing capacity and economies of scale of the HiSeq X Ten facility will also allow Garvan to accelerate the introduction of clinical genomics and next-generation medicine in Australia, Mattick said. We expect the HiSeq X Ten to underpin a new phase of collaboration between government, industry and other medical research stakeholders.

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Sequence Your Genome For $1,000?

Eric Green: Reading Cancer #39;s Genetic Signature
"Cancer death rates in the United States continue to decline." Despite this conclusion, from the recent Report to the Nation on the Status of Cancer, we are ...

By: Big Think

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Eric Green: Reading Cancer's Genetic Signature - Video

STi Genome Mufflers on Liberty/ Legacy 2.0GT tuned by STI twin scroll turbo
STi Genome mufflers fitted to AUDM MY06 Liberty GT tuned by STi. Exhaust setup: - HKS dump pipe - 3 inch centre w/ resonator to 2.5 inch Y pipe - STi Genome mufflers.

By: ynot87

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STi Genome Mufflers on Liberty/ Legacy 2.0GT tuned by STI twin scroll turbo - Video

European Genome-phenome Archive: Using the Secure Download client
This video shows users how to download datasets from the European Genome-phenome Archive (EGA). The EGA contains exclusive data collected from individuals wh...

By: EBImedia

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European Genome-phenome Archive: Using the Secure Download client - Video