Category Archives: Genome

From Genome Function to Biomedical Insights: Defining the Scientific Challenges - Ewan Birney
March 10-11, 2015 - From Genome Function to Biomedical Insight: ENCODE and Beyond More: http://www.genome.gov/27560819.

By: GenomeTV

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From Genome Function to Biomedical Insights: Defining the Scientific Challenges - Ewan Birney - Video

Black Hole High Season 02 Episode 04 17 genome
Black Hole High (also known as Strange Days at Blake Holsey High) is a Canadian science fiction television program which first aired in North America in ...

By: Arthur Briard

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Black Hole High Season 02 Episode 04 17 genome - Video

Introduction to Ensembl Genome Browser/Biomart : answer 2
Practical session of a training on Ensemble Genome Brower/Biomart : Answer to question 2 (Ensembl) (http://ngs.igbmc.fr/~royl/wiki/doku.php?id=training:introduction2ensembl)

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Introduction to Ensembl Genome Browser/Biomart : answer 2 - Video

Abstract Genome Simulation III
Evolving Heterogeneus Inheritance. Introduction: 3 spheres (green, blue and red) are introduced into a process tank. All the factors that determine the composition of each of the spheres are...

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Abstract Genome Simulation III - Video

A new technology called CRISPR could allow scientists to alter the human genetic code for generations. That's causing some leading biologists and bioethicists to sound an alarm. They're calling for a worldwide moratorium on any attempts to alter the code, at least until there's been time for far more research and discussion.

It's not new that scientists can manipulate human DNA genetic engineering, or gene editing, has been around for decades. But it's been hard, slow and very expensive. And only highly skilled geneticists could do it.

Recently that's changed. Scientists have developed new techniques that have sped up the process and, at the same time, made it a lot cheaper to make very precise changes in DNA.

There are a couple of different techniques, but the one most often talked about is CRISPR, which stands for clustered regularly interspaced short palindromic repeats. My colleague Joe Palca described the technique for Shots readers last June.

Why scientists are nervous

On the one hand, scientists are excited about these techniques because they may let them do good things, such as discovering important principles about biology. It might even lead to cures for diseases.

The big worry is that CRISPR and other techniques will be used to perform germline genetic modification.

Basically, that means making genetic changes in a human egg, sperm or embryo.

Those kinds of changes would be passed down for generations. And that's something that's always been considered taboo in science.

One major reason that it's considered off limits, ethically, is that the technology is still so new that scientists really don't know how well it works.

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Scientists Urge Temporary Moratorium On Human Genome Edits

ENCODE 2020: Improving the syntax for understanding functional elements in the genome - Laurie Boyer
March 10-11, 2015 - From Genome Function to Biomedical Insight: ENCODE and Beyond More: http://www.genome.gov/27560819.

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ENCODE 2020: Improving the syntax for understanding functional elements in the genome - Laurie Boyer - Video

Additional suggestions related to genome function - Richard Myers
March 10-11, 2015 - From Genome Function to Biomedical Insight: ENCODE and Beyond More: http://www.genome.gov/27560819.

By: GenomeTV

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Additional suggestions related to genome function - Richard Myers - Video

The International Society for Stem Cell Research has released a statement calling for a moratorium on attempts to apply nuclear genome editing of the human germ line in clinical practice

In a statement released yesterday, the International Society for Stem Cell Research called for a moratorium on attempts at clinical application of nuclear genome editing of the human germ line to enable more extensive scientific analysis of the potential risks of genome editing and broader public discussion of the societal and ethical implications.

Technologies used to introduce changes into the DNA sequence of cells have advanced rapidly, making genome editing increasingly simple. Genome editing is feasible, not just in the somatic cells of an adult organism, but also in early embryos, as well as the gametes (sperm and egg) that carry the inheritable, germline DNA. Research involving germline nuclear genome editing has been performed to date in many organisms, including mice and monkeys, and applications to human embryos are possible.

The ISSCR statement raises significant ethical, societal and safety considerations related to the application of nuclear genome editing to the human germ line in clinical practice. Current genome editing technologies carry risks of unintended genome damage, in addition to unknown consequences. Moreover, consensus is lacking on what, if any, therapeutic applications of germ line genome modification might be permissible.

The statement calls for a moratorium on attempts to apply nuclear genome editing of the human germ line in clinical practice, as scientists currently lack an adequate understanding of the safety and potential long term risks of germline genome modification. Moreover, the ISSCR asserts that a deeper and more rigorous deliberation on the ethical, legal and societal implications of any attempts at modifying the human germ line is essential if its clinical practice is ever to be sanctioned.

In calling for the above moratorium, the ISSCR is not taking a position on the clinical testing of mitochondrial replacement therapy, a form of germline modification that entails replacing the mitochondria (found outside the nucleus) in the eggs of women at risk of transmitting certain devastating diseases to their children.

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A full copy of the ISSCR statement is available at http://www.isscr.org/statement-on-human-germline-genome-modification.

About the International Society for Stem Cell Research:

The International Society for Stem Cell Research is an independent, nonprofit membership organization established to promote and foster the exchange and dissemination of information and ideas relating to stem cells, to encourage the general field of research involving stem cells and to promote professional and public education in all areas of stem cell research and application.

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The ISSCR issues statement on human germline genome modification

Scientists also say that replacing a defective gene with a normal one may seem entirely harmless but perhaps would not be.

"We worry about people making changes without the knowledge of what those changes mean in terms of the overall genome," Dr. Baltimore said. "I personally think we are just not smart enough and won't be for a very long time to feel comfortable about the consequences of changing heredity, even in a single individual."

Many ethicists have accepted the idea of gene therapy, changes that die with the patient, but draw a clear line at altering the germline, since these will extend to future generations. The British Parliament in February approved the transfer of mitochondria, small DNA-containing organelles, to human eggs whose own mitochondria are defective. But that technique is less far-reaching because no genes are edited.

Read MoreFDA approves first DNA-based test for colon cancer

There are two broad schools of thought on modifying the human germline, said R. Alta Charo, a bioethicist at the University of Wisconsin and a member of the Doudna group. One is pragmatic and seeks to balance benefit and risk.

The other "sets up inherent limits on how much humankind should alter nature," she said. Some Christian doctrines oppose the idea of playing God, whereas in Judaism and Islam there is the notion "that humankind is supposed to improve the world." She described herself as more of a pragmatist, saying, "I would try to regulate such things rather than shut a new technology down at its beginning."

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Scientists question editing of DNA

IMAGE:This is a diagram of chromosome shattering. view more

Credit: Mirjam de Pagter

The human genome can be very forgiving. When children inherit chromosomes from their parents, some minor genetic changes frequently occur with few, if any, consequences. One exception, as researchers report in the March 19 issue of the American Journal of Human Genetics, is chromosomal shattering, termed chromothripsis, which the authors found in healthy mothers who had each given birth to a severely affected child. The findings could have important implications for genetic testing and issues related to infertility.

"Our study shows that despite its dramatic effects on chromosomal architecture, chromothripsis--which involves shattering of one or multiple chromosomes followed by random reassembly--does not necessarily lead to disease," says senior author Wigard Kloosterman, PhD, of University Medical Center Utrecht, in The Netherlands. "However, the presence of this phenomenon in healthy individuals impacts reproduction by leading to difficulties getting pregnant, miscarriages, and the birth of children with multiple birth defects, including intellectual disability."

Dr. Kloosterman and his team studied three families whose children suffer from multiple abnormalities due to chromothripsis that they inherited from their mothers. Although the children's mothers were unaffected or only mildly affected, the women's genomes harbored even more genome breakage than their children's. Two of the mothers had experienced prior difficulties with getting pregnant, which was probably associated with their complex genomic rearrangements.

Although these results highlight the amazing ability of the human genome to tolerate gene disruption, they also indicate that chromothripsis can impact female reproduction and should be considered during counseling of couples dealing with infertility.

Dr. Kloosterman noted that it is difficult to estimate the frequency of chromothripsis in the general population, and many of the commonly used analytical techniques lack the resolution to detect it to its full extent. The chromothripsis in the three mothers in this study was balanced, meaning that there were no deletions or duplications (changes in the number of copies of a gene) of any of the genes that were rearranged. Two children inherited only a subset, rather than all, chromothripsis chromosomes from their mother. In the third family, an additional rearrangement occurred during chromosome transfer to the child. In all three children, the alterations resulted in deletions and duplications of chromosomal regions, which most likely explains the children's birth defects.

"If one would solely perform currently widely used array-based diagnostic tests for detecting the number of copies of a gene in these families, one would only detect the genomic defects in the children but fail to detect the changes in the mother," said Dr. Kloosterman. "This would lead to a substantial underestimation of the recurrence risk for future pregnancies." Therefore, it is important to use a combination of genetic screening techniques, preferably whole-genome sequencing, in certain cases, he explained.

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This research was supported by the Child Health priority program from the University Medical Center Utrecht.

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Chromosome shattering may be a hidden cause of birth defects