Category Archives: Genome

Breaking the Human Genome Code - Opening Pandora #39;s Box
Recent technology advances have resulted in the ability to sequence anyone #39;s genome cheaply and quickly, but we are only just beginning the journey to discover the true meaning of our individual...

By: The University of Sheffield

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Breaking the Human Genome Code - Opening Pandora's Box - Video

Citing the need to keep up with a rapidly changing field of science, Canadas principal entity for supporting research in genomics is changing its approach.

On Tuesday, Genome Canada is expected to announce it will spend $15.5-million over the next two years to jump-start the creation of what it calls an innovation network by doling out funds to 10 research centres across the country. Matching funds from other public and private sources will bring the initial investment in the network to $31-million. In addition, the centres will compete with one another to divide a $15-million pot earmarked for technology development.

The funding replaces an earlier five-centre model and puts more emphasis on collaboration between centres to avoid building up silos that cannot talk to each other, said Genome Canada president Pierre Meulien.

The expanded network represents a pivot for the non-profit organization, which channels federal money toward the branch of science that deals with the decoding and analysis of DNA sequences.

When Genome Canada was established in February, 2000, the price tag for sequencing a single human genome was about $100-million. Since then, a revolution in sequencing technology has pushed the price down to just more than $1,000 per genome and the field is increasingly concerned with comparing genetic differences among populations (of humans and many other organisms).

To reflect the change, Dr. Meulien said that the new network will include substantial investments in Canadas capacity to do bioinformatics, which marries computing power with the reams of data now available as genetic sequences accumulate. Analysis of such data has already yielded important breakthroughs in identifying the causes of genetically inherited diseases and in spotting genetically based susceptibilities to more complex maladies such as cancer and diabetes.

Data generation is getting easier, but in the end you have to interpret and analyze all of that data, said Guillaume Borque, co-director of the Canadian Centre for Computational Genomics, a collaboration between McGill Univeristy and the University of Toronto and one of the new centres in the expanded network.

Other new centres that will be included for the first time under the Genome Canada funding umbrella demonstrate a broader trend in the field to link genes identified through sequencing to their biological functions and health implications. For example, the Toronto Centre of Phenogenomics, another of the nodes, specializes in creating strains of mice with specific genetic mutations. that can be used in the development of new approaches for disease.

Its the whole picture thats going to give rise to new treatments and diagnostics, said Dr. Meulien.

The new network amounts to a retooling of the countrys genomics infrastructure, he added, marking a shift from the era when Genome Canada was needed to ensure that Canadian scientists had access to an expensive but crucially important new technology for biomedical research. Now, the research that the organization funds has expanded beyond health, with applications in agriculture and environmental science, among other areas.

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Genome Canada to create innovation network of 10 research centres

14 hours ago by Anthony Wrigley And Ainsley Newson, The Conversation In the future, our DNA could be different by design. Credit: http://www.shutterstock.com

The ability to precisely and accurately change almost any part of any genome, even in complex species such as humans, may soon become a reality through genome editing. But with great power comes great responsibility and few subjects elicit such heated debates about moral rights and wrongs.

Although genetic engineering techniques have been around for some time, genome editing can achieve this with lower error rates, more simply and cheaply than ever although the technology is certainly not yet perfect.

Genome editing offers a greater degree of control and precision in how specific DNA sequences are changed. It could be used in basic science, for human health, or improvements to crops. There are a variety of techniques but clustered regularly inter-spaced short palindromic repeats, or CRISPR, is perhaps the foremost.

CRISPR has prompted recent calls for a genome editing moratorium from a group of concerned US academics. Because it is the easiest technique to set up and so could be quickly and widely adopted, the fear is that it may be put into use far too soon outstripping our understanding of its safety implications and preventing any opportunity to think about how such powerful tools should be controlled.

The ethics of genetics, revisited

Ethical concerns over genetic modification are not new, particularly when it comes to humans. While we don't think genome editing gives rise to any completely new ethical concerns, there is more to gene editing than just genetic modification.

First, there is no clear consensus as to whether genome editing is just an incremental step forward, or whether it represents a disruptive technology capable of overthrowing the current orthodoxy. If this is the case and it's a very real prospect then we will need to carefully consider genome editing's ethical implications, including whether current regulation is adequate.

Second, there are significant ethical concerns over the potential scope and scale of genome editing modifications. As more researchers use CRISPR to achieve more genome changes, the implications shift. Our consideration of a technology that is rarely used and then only in specific cases will differ from one that is widely used and put to all sorts of uses.

Should we reach this tipping point, we will have to revisit the conclusions of the first few decades of the genetic modification debate. Currently modifying plants, some animals, and non-inheritable cells in humans is allowed under strict controls. But modifications that alter the human germ-line are not allowed, with the exception of the recent decision in the UK to allow mitochondrial replacement.

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Genome editing poses ethical problems that we cannot ignore

What does genome mean?
What does genome mean? A spoken definition of genome. Intro Sound: Typewriter - Tamskp Licensed under CC:BA 3.0 Outro Music: Groove Groove - Kevin MacLeod (incompetech.com) Licensed...

By: What Does That Mean?

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What does genome mean? - Video

IMMEDIATE "BAN EDITING the HUMAN GENOME" Scientists #39; warning.
DNA Editing, splicing, cutting...new method of recombinant DNA editing is known by the acronym "Crispr-Cas9." The new technology of Biotech is what these scientists consider "Dangerous new...

By: MLordandGod

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IMMEDIATE "BAN EDITING the HUMAN GENOME" Scientists' warning. - Video

Jennifer Doudna (UC Berkeley / HHMI): Genome Engineering with CRISPR-Cas9
http://www.ibiology.org/ibiomagazine/jennifer-doudna-genome-engineering-with-crispr-cas9-birth-of-a-breakthrough-technology.html Talk Overview: Jennifer Doudna tells the story of how studying...

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Jennifer Doudna (UC Berkeley / HHMI): Genome Engineering with CRISPR-Cas9 - Video

Raleigh, NC (PRWEB) March 28, 2015

Genomic medicine experts have sequenced the genomes of two people with peritoneal mesothelioma, revealing, for the first time, key information for understanding and treating this intractable cancer. Click here to read the newly posted story on the Surviving Mesothelioma website.

Research scientists at the University of British Columbia, the British Columbia Cancer Agency, and PhenoPath lab in Seattle, Washington used genome mapping to reveal underlying molecular alterations and mutations that can lead to peritoneal mesothelioma.

The Personalized OncoGenomics initiative at the British Columbia Cancer Agency provides a unique opportunity to learn how to best analyze, interpret and apply rapidly emerging molecular information in the clinic, writes lead investigator Brandon Sheffield of the University of British Columbia.

News of the mesothelioma genome sequencing, published in the online open access medical journal PLoS One, may eventually help clinicians treat the disease more effectively.

Understanding the genetic anomalies and mutations that underlie a rare cancer like peritoneal mesothelioma is vital to treating it effectively and even to eventually finding a cure, says Surviving Mesotheliomas Managing Editor, Alex Strauss.

To read the full article on the genome sequencing of peritoneal mesothelioma and what it may mean for future treatments, see Peritoneal Mesothelioma: Genome Sequencing Paves the Way for Personalized Treatments now available on the Surviving Mesothelioma website.

Sheffield, BS, Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing, March 23, 2015, PLoS One, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119689

For nearly ten years, Surviving Mesothelioma has brought readers the most important and ground-breaking news on the causes, diagnosis and treatment of mesothelioma. All Surviving Mesothelioma news is gathered and reported directly from the peer-reviewed medical literature. Written for patients and their loved ones, Surviving Mesothelioma news helps families make more informed decisions.

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New Genomics Research May Help Doctors Tailor Mesothelioma Treatment, According to Surviving Mesothelioma

SciCafe: Mapping the Urban Microbiome, Genome, and Metagenome
Every year, scientists are learning more and more about the human microbiome, or the collection of microorganisms and bacteria that live in and on our bodies. But what about our macrobiomes...

By: American Museum of Natural History

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SciCafe: Mapping the Urban Microbiome, Genome, and Metagenome - Video

Eric Contra Schoffstall Hacking the Human Genome | .concat() 2015
Genetics: the final frontier. What is the link between the human genome and JavaScript? Do you want to find out why your body does that weird thing? In this talk we will unravel the mystery...

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Eric Contra Schoffstall Hacking the Human Genome | .concat() 2015 - Video

CELLOU BINANI/AFP/Getty

A woman gets vaccinated on 10 March 2015 at a health centre in Conakry, Guinea, during the first clinical trials of the VSV-EBOV vaccine against the Ebola virus.

The Ebola virus is evolving more slowly than previously thought, contends a controversial study of viral genomes from the current West African epidemic. The findings, published in Science on 26 March1, allay concerns that the pathogen could become more difficult to control and thwart therapies and vaccines in development.

But other experts say that the papers focus on the pace at which Ebola virus is changing is misplaced; the more important issue is whether the virus has gained mutations that make it more transmissible or dangerous to humans.

The ongoing epidemic, which has killed more than 10,000 people, mostly in Liberia, Sierra Leone and Guinea, is now waning. But researchers say that it is important to chart the evolution of the virus so that they can track its spread more accurately and watch for strains that are acquiring worrisome mutations.

Researchers first described viral genome sequences from the current epidemic in April 2014, from patients in Guinea2. Then in late August, Pardis Sabeti, a computational geneticist at the Broad Institute in Cambridge, Massachusetts, and her collaborators reported 99 Ebola genome sequences from 78 patients in Sierra Leone3.

The paper identified the chain of transmissions that had exported the virus from Guinea to Sierra Leone. It also noted that the Ebola viruses from West Africa contained hundreds of mutations not seen in previous outbreaks all of which occurred farther east including many that had altered the virus's proteins. The team estimated that the viruses were evolving at twice the rate during the outbreak, compared to Ebolas long-term rate of change in its animal host. They speculated that mutations hindering the virus had yet to be purged from its genome through natural selection, leading to a faster rate of evolution, at least in the short term. The team cautioned that the virus could develop mutations that would make it more harmful as the epidemic wears on but found no evidence that this had occurred.

We have always been clear that our study only provided data for what everyone already knows that viruses mutate, says Sabeti. Anthony Fauci, director of the US National Institute of Allergy and Infectious Diseases (NIAID) in Bethesda, Maryland, says that many people misconstrued this observation as meaning that the virus was gaining new properties and potentially even the ability to spread through the air, like the common cold, rather than just through direct contact with bodily fluids. The data never said that, but it was the way people interpreted the data, he says. People were getting concerned.

A paper posted to the bioRxiv.org preprint site in November, meanwhile, questioned the significance of the doubled rate of evolution4. The conclusions ultimately left readers, and indeed the scientific community at large, with the impression that Ebola virus is fast-evolving and possibly adapting to humans, the authors wrote, adding that more sequence data were needed to determine how Ebola was changing.

In the new Science paper, Heinz Feldmann, head of the NIAID's Laboratory of Virology in Hamilton, Montana, and his collaborators report genome sequences from two small clusters of cases, after the virus spread to Mali last October and again in November. The team used the data to recalculate Ebolas rate of evolution. The result is a figure about half that of Sabetis team's, and more in line with the virus's long-term rate of evolution.

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Ebolas fast evolution questioned