Category Archives: Genome

Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features.[1] The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.

The Human Genome Project was a landmark genome project that is already having a major impact on research across the life sciences, with potential for spurring numerous medical and commercial developments.[2]

Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. These pieces are then "read" by automated sequencing machines, which can read up to 1000 nucleotides or bases at a time. (The four bases are adenine, guanine, cytosine, and thymine, represented as AGCT.) A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. These overlapping reads can be merged, and the process continues.

Genome assembly is a very difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as repeats. These repeats can be thousands of nucleotides long, and some occur in thousands of different locations, especially in the large genomes of plants and animals.

The resulting (draft) genome sequence is produced by combining the information sequenced contigs and then employing linking information to create scaffolds. Scaffolds are positioned along the physical map of the chromosomes creating a "golden path".

Originally, most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced. However, this has changed as the software has grown more complex and as the number of sequencing centers has increased. An example of such assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis.[3][4][5]

Genome annotation is the process of attaching biological information to sequences.[6] It consists of three main steps:

Automatic annotation tools try to perform all this by computer analysis, as opposed to manual annotation (a.k.a. curation) which involves human expertise. Ideally, these approaches co-exist and complement each other in the same annotation pipeline.

The basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on that.[1] However, nowadays more and more additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl) rely on both curated data sources as well as a range of different software tools in their automated genome annotation pipeline.[7]

Structural annotation consists of the identification of genomic elements.

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Genome project - Wikipedia, the free encyclopedia

Scientists from the University of Liverpool have sequenced the mitochondrial genome in glaucoma patients to help further understanding into the genetic basis for the disease.

Glaucoma is a major cause of irreversible blindness, affecting more than 60 million people worldwide, increasing to an estimated 79.6 million people by 2020. It is thought that the condition has genetic origins and many experiments have shown that new sequencing approaches could help understand how the condition develops.

Studies on primary open-angle glaucoma -- the most common form of glaucoma -- have shown that mutations in mitochondria, the energy generating structures in all cells, could give valuable insight into how to prevent the disease.

Using new gene sequencing techniques, called massively parallel sequencing, the Liverpool team have produced data on the mitochondrial genome taken from glaucoma patients from around the world.

The impact that mitochondrial gene change has on disease progression has been difficult to fully determine as cells in the human body can contain mixtures of healthy and mutated mitochondrial genes. Using this new technology, however, the researchers aim to support the delivery of personalised medicines to identify drugs that will target mutated mitochondria.

Professor Colin Willoughby, from the University's Institute of Ageing and Chronic Disease, explains: "Understanding the genetic basis of glaucoma can direct care by helping to determine the patient's clinical risk of disease progression and visual loss.

"Increasing evidence suggests that mitochondrial dysfunction results in glaucoma and drugs that target mitochondria may emerge as future therapeutic interventions.

"Further studies on larger glaucoma numbers of patients are required to firmly establish the link between genetic defects in the mitochondrial genome and glaucoma development.

"Our research, however, has demonstrated that massively parallel sequencing is a cost-effective approach to detect a wide spectrum of mitochondrial mutations and will improve our ability to understand glaucoma, identify patients at risk of the disease or visual loss and support the development of new treatments."

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DNA sequencing helps identify genetic defects in glaucoma

The Human Genome Project - Genome Libraries Part 2
In this video we begin our discussion of the human genome project, by discussing how and why we need to produce a genome library.

By: Ben Garside

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The Human Genome Project - Genome Libraries Part 2 - Video

How We Proved There Was No Contamination in the Sasquatch Genome Project Samples
This video shows how, as scientists, we can determine whether contamination is present in a DNA sample. It also addresses how peer reviewers failed to ask to see the raw data to determine whether...

By: Dr. Melba Ketchum

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How We Proved There Was No Contamination in the Sasquatch Genome Project Samples - Video

It may not surprise the average cat owner, but a team of researchers has discovered that the genome of domestic mousers differs only slightly from that of wildcats.

In other words, after 9,000-odd years of living alongside humans, the house cat remains only semi-domesticated, according to a report published this week in the Proceedings of the National Academy of Sciences.

After comparing the genome of an Abyssinian cat named Cinnamon with those of humans, tigers, cows, dogs and another cat breed known as the Birman, the scientists found that cats retain many of the hunting, sensory and digestive traits of their wild kin.

Researchers did find a signal for human influence on cat evolution, however, in fur color and pattern, as well as a set of genes that are thought to be associated with tameness.

We believe we have created the first preliminary evidence that depicts domestic cats as not that far removed from wildcat populations, said senior author Wes Warren, an associate professor of genomics at the Genome Institute at Washington University in St. Louis.

The discovery that as few as 13 genes may separate domestic cats from their wild ancestors was a genuinely important advance, according to John Bradshaw, an anthrozoologist at the University of Bristol School of Veterinary Sciences in Britain, who was not involved in the research.

This can only be the beginning of what will surely lead to a revolution in cat breeding, Bradshaw wrote.

By pinpointing genes responsible for cat behavior and temperament, humans could more easily guide more changes in the animal.

The potential is there to finally guide the cat through the remaining stage of domestication, not only producing cats that are better adapted to the demands of 21st century living, but at the same time enhancing their well being, Bradshaw wrote.

Unlike dogs, which some researchers say began their association with humans roughly 30,000 years ago, archaeological evidence suggests that cats first entered our living space when we began to grow crops, about 10,000 years ago.

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Semi-domesticated? House cats not far removed from wild, genome shows

November 12, 2014

Chuck Bednar for redOrbit.com Your Universe Online

In news unlikely to surprise most cat owners, an analysis of the feline genome reveals that the DNA of the typical housecat differs only slightly from those living in the wild when compared to their canine counterparts.

Researchers from the Washington University School of Medicine in St. Louis, who published their findings earlier this week in the journal Proceedings of the National Academy of Sciences, found that unlike dogs, which arose from wolves over 30,000 years ago, the separation between domestic felines and wild cats occurred far more recently, when people began growing crops.

Cats, unlike dogs, are really only semidomesticated, senior author Wes Warren, associate professor of genetics at The Genome Institute at Washington University, explained in a statement Monday. They only recently split off from wild cats, and some even still breed with their wild relatives. So we were surprised to find DNA evidence of their domestication.

The research is part of the cat genome sequencing project, a National Human Genome Research Institute-funded project that began in 2007, and initially set out to study hereditary diseases in domestic cats. However, while comparing the genomes of domestic and wild cats, the authors found significant differences in specific regions of the domestic cat genome in particular, those linked with memory, fear and reward-seeking behavior.

Those behaviors, especially when it comes to animals seeking rewards, are believed to play an important role in the domestication process, the researchers found. When people began growing food, they likely offered some of it to cats in order to keep them around to keep the rodent population under control and away from grain harvests. As a result, cats that normally preferred to live solitary lives in the wild had additional incentive to stick around humans.

While cat domestication is believed to have begun about 9,000 years ago, Bloomberg News reporter Megan Scudellari explained that the majority of the 30-40 modern cat breeds originated just 150 years ago. In order to investigate the domestication process, Warren and his colleagues sequenced the genome of a female Abyssinian cat and compared her DNA to six other domestic cat breeds, two wild cat species and several other creatures.

Compared to omnivorous humans and herbivorous cows, carnivorous cats appear to have more quickly evolved genes that bestow an enhanced ability to digest heavy fats found in meat, Scudellari said. In addition, by comparing cat and dog genomes, the researchers found a unique evolutionary trade-off between the two groups: While dogs evolved an unsurpassed sense of smell, cats traded in those smell receptor genes for genes that enhanced their ability to sense pheromones, odorless substances that enable animals of the same species to communicate.

Warren told the Los Angeles Times that he believed he and his colleagues have created the first preliminary evidence that depicts domestic cats as not that far removed from wildcat populations, and the study authors wrote that their findings suggest that selection for docility, as a result of becoming accustomed to humans for food rewards, was most likely the major force that altered the first domesticated cat genomes.

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Feline Genome Project Reveals That Cats Are Only 'Semidomesticated'

This is made possible through a cartridge (that uses microscopic plumbing to separate DNA molecules) created by Fluidigm, and a touchscreen created by fuseproject. Courtesy of fuseproject

This is made possible through a cartridge (that uses microscopic plumbing to separate DNA molecules) created by Fluidigm, and a touchscreen created by fuseproject.

Prior to Juno, it could take several days and manual steps to prep and analyze genomic material. This machine automates everything, and goes from prep to results in three hours. Courtesy of fuseproject

Prior to Juno, it could take several days and manual steps to prep and analyze genomic material. This machine automates everything, and goes from prep to results in three hours.

Juno, a slick new machine designed by Yves Bhar for biotech startup Fluidigm, makes it easier than ever for lab technicians to analyze DNA molecules. Courtesy of fuseproject

Juno, a slick new machine designed by Yves Bhar for biotech startup Fluidigm, makes it easier than ever for lab technicians to analyze DNA molecules.

The pattern on the casing, designed by fuseproject, shows the grooves created during CNC milling. This kind of manufacturing, that shows the roughness of the process, makes it cheaper and easier to build Junos. Courtesy of fuseproject

The pattern on the casing, designed by fuseproject, shows the grooves created during CNC milling. This kind of manufacturing, that shows the roughness of the process, makes it cheaper and easier to build Junos.

This is made possible through a cartridge (that uses microscopic plumbing to separate DNA molecules) created by Fluidigm, and a touchscreen created by fuseproject. Courtesy of fuseproject

This is made possible through a cartridge (that uses microscopic plumbing to separate DNA molecules) created by Fluidigm, and a touchscreen created by fuseproject.

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A Genome Testing Device That Looks as Cool as a Jambox

Genome Browser In A Box
Create your own personal installation of the UCSC Genome Browser on your computer with the Genome Browser in a Box (GBIB). For data that is subject to privac...

By: Trey Lathe

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Genome Browser In A Box - Video

Googles push into the genome storage and research market seems like a natural move to make personalized medicine a mainstream treatment option. And the price for storing genomic data has plummeted to a consumer friendly $25 per month. But comments in response to a recent article from MIT Technology Review illustrate the mixed feelings we have about the potential benefits and potential for abuse these businesses pose.

So far 3,500 genomes are stored on Googles servers, according to the article. David Glazer, the software engineer who led the development of Google Genome, also led platform engineering for Google+.

Google has developed an interface for its genome business that lets it move DNA data into its servers and do experiments using the same database technology that indexes the Web and tracks billions of Internet users, according to the article. We saw biologists moving from studying one genome at a time to studying millions, Glazer told MIT Technology Review. The opportunity is how to apply breakthroughs in data technology to help with this transition.

Other groups are taking different approaches to storing DNA and research. StoreMyTumor holds onto customers tumors that have been removed in surgery so they can be screened to gain admittance into clinical trials as well as determining their best cancer treatment options. Though the global directory of biobank and tissue bank websites on Speciman Central illustrates is extensive, most of these are run by institutes and educational institutions, not corporations. Some of the comments left on the article suggest Google has a lot to prove to ease peoples instinct to distrust what a company will do with this sensitive data.

Here are some of the comments:

Xomami 1 day ago With extremely low sequencing costs almost anyone may have access to your genome. In fact, your full genome is not even necessary. Just the critical parts detailing the major diseases susceptibilities (think 23andme profile) are good enough for a health insurer. After a stay in a hotel, a piece of hair, some dander, the tiny saliva left on a glass will be enough for getting a good genetic profile. In fact, it is said the US president has a DNA cleanup crew everywhere he goes now; they pick up bedsheets, pillowcases, glasses, everythingWonder what he has to hide 🙂

abraham.samma 2 days ago Putting aside the assertions made by geoffrey and darrend below, I think their overall sentiment can be aptly summarised in one word; distrust. It is a sentiment that resonates with everyone I think. The genome is about as personal as you can get wrt to the patients medical profile. I dare say we need to be more serious about how this kind of information can be abused and research better ways to ensure data integrity and security. Atleast, more serious than how we currently manage other corporate entities like banks.

canoeberry 2 days ago For profit companies and private medical data do not mix unless there are serious standards put in place, and serious repercussions if they are violated. And even then Id be worried with a company like Google, whose business is to sell as much about us as they know to advertisers. However, I have NO DOUBT that putting together a bunch of genomes in a machine learning world could be and will be a revolutionary way to advance medicine. Incredibly hard to do now but every year hardware gets better and we could definitely learn a lot from doing number crunching on large numbers of genomes

RJWilton 2 days ago Dont kid yourselves, people. Theres always a few visionaries out there touting the potential of aggregating your personal information. (Gee. Personalized pop-up advertising. How nice.) But ask yourselves: wheres the big money in this picture? Answer: Marketing. (Dear Google, please send us a list of everybody whose genome says theyre likely to want what were selling.) Health insurance. (What passes as a pre-existing condition is nothing compared to what can be harvested from your genome.) Big pharma. (What do the genomes tell us about the next big drug?) And so on. And, given the frequency with which even the easiest stuff to protect (think credit card numbers) gets hacked into the dark Internet, just how eager are you to post your genome online? Google ought to be paying us, not the other way around. And indemnifying us, too, while theyre at it. And Id still be awfully reluctant

mkogrady 2 days ago @RJWilton If the big picture is marketing, and the results of targeted marketing means (I hope) cheaper medications for that specific target audience, then wheres the harm? If a pharmaceutical company sees the potential to invest a couple million dollars on a treatment that will be needed by 10 million people, and the end cost is cheaper BECAUSE they know beforehand what the potential target market is, then I say thats a good thing.

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Despite personalized medicine potential, distrust lingers over Googles genome play

The Big Data Savings Fallacy
How to use Google Trends and Google Correlate properly:The original unabridged version of the video that went viral (with the cute donkey).By A. Skeptic.2014 Big Data is the business equivalent...

By: Klaus Gottlieb

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The Big Data Savings Fallacy - Video