Category Archives: Genome

Sometime very soon the first humans to be genetically edited will be born, and the United States just paved the way.

In December 2015, scientists and ethicists at an international meeting held at the NAS in Washington said it would be irresponsible to use gene editing technology in human embryos for therapeutic purposes, such as to correct genetic diseases, until safety and efficacy issues are resolved.

On February 14th, 2017; the National Academy of Sciences and the National Academy of Medicine issued a report outlining the permissible circumstances upon which the research into editing human embryos could be conducted.

Their latest statement signals that the NASis softening its approach, to the use of gene-editing technology such as CRISPR-CAS9.

Previously genome editing was already being planned for use in clinical trials on people to correct diseases. However, the primary concern is over the utilization of the technology in human reproductive cells or early embryos because the changes would be passed along to offspring.

Although gene editing of human reproductive cells to correct inherited diseases must be approached with caution, caution does not mean prohibition, the committee said in a statement.

The rise in genome editing signals the real end of the human being. Simply put, directly after the first genome alteration and birth, the natural genome would be something entirely man-made.

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The USA Just Approved HUMAN Embryo Genome Modification Research Paving the Way For Designer Babies - The Christian Truther

CRISPR-Cas9 is a precise method of gene editing. It can snip a gene out of the DNA sequence say, a harmful mutation then add a healthy gene to replace it. This new but exciting technique is being used in clinical trials to treat things like hereditary cancer. It could also be a godsend for certain genetic diseases, such as Huntingtons or Tay-Sachs disease, among others. Experimental studies with cancer and blindness are slated to reap benefits this year.

Despite the great promise this new technique affords, there is controversy surrounding applying it to human embryos. One such concern is creating designer babies. Another is accidentally creating a hereditary disease and allowing it to enter the human genome. This could be passed down from parent to child, dooming future generations. But some fear that stifling regulation suppresses innovation and the march of progress. So, of course, there needs to be balance between regulation and freedom of exploration.

The National Academy of Sciences (NAS), aware of the growing debate, put together a committee of experts last year to consider the ethical quandaries the technique presents when applied to human embryos. It's just recently released its report, a full 261 pages, which suggests allowing CRISPR to be performed on embryos in certain instances, and barring others. The committee concluded that cures for serious diseases and disabilities should be allowed, especially when conventional medicine offers no reasonable alternative. But the advisory panel wont abide designer babies or the creation of super soldiers.

The committee suggests opening the door a crack, and allowing gene editing on embryos for research on certain diseases.

Richard Hynes co-chaired the committee. He wrote that since the science is flying by at an outrageous clip, we should keep a tight grasp on it for now. You want to have a good control of what is being done, he wrote. Chinese scientists have already modified the DNA of five embryos as of 2015, using this technique. Sweden is also conducting advanced experiments, fueling the fear that the US could fall behind.

Many hailed the NAS committees move. This framework should allow for more cancer studies and those on genetic diseases, like retinal degeneration, which can lead to blindness. But some say, the guidelines are still too stringent. There are a lot of genetic diseases such as muscular dystrophy, sickle cell anemia, or even Parkinsons, which may benefit from CRISPR experiments. But the panel fears allowing a technique whose outcome isnt entirely known.

University of Wisconsin ethicist Alta Charo was a co-chair of the advisory group. She said that although off-label uses, or those which a drug wasnt intended for, are tolerated with pharmaceuticals commonly, gene editing of embryos would not allow such a practice. Whats more, a social consensus is needed before the gene editing of embryos becomes common practice. It is essential for public discussions to precede any decisions about whether or how to pursue clinical trials of such applications, said Charo. And we need to have them now.

Some fear that this technique could someday be used to add muscle tissue to a persons body to make them stronger or faster, or neural manipulation will be performed to reap greater intelligence. Gene editing may even allow for certain anti-aging features to become available. This last one might be allowed as a sort of preventative medicine.

With these guidelines, Charo and colleagues were clear: you can use gene editing to undo illness but not enhance the human body. Some geneticists find the prospect of genetic enhancement ethically inviolable. Even so, the technique is not able to perform such feats, yet. Genome editing to enhance traits or abilities beyond ordinary health raises concerns about whether the benefits can outweigh the risks, and about fairness if available only to some people," Charo said.

This research could create a backlash. Committee members point out the need for a societal consensus on the gene editing of embryos, before it becomes commonplace.

Should we continue to embrace individuality, or are we destined to edit out everything that makes us unique, creating a race of beautiful, bland, healthy geniuses, and in the end, losing heterogeneity? With it could go innovation, novelty, uniqueness, disruption, and creativity. After all, it is usually the mavericks, the marginalized, and the outliers that revolutionize society. Or would a startling divide be born, between those who could afford gene editing and those who couldnt?

The philosopher Alan Watts once said that if we reached the point where we could design people, we should make as diverse a group of possible, so to have enormous flexibility. For who knows what kinds of people will best populate the late 21st century and beyond.

These guidelines posit a tight way of allowing the exploration of CRISPR for use in the human genome. Currently, the FDA bars the germline engineering, or gene editing, of human offspring. But the guidelines are meant as a crack of light, showing the way, but also a way of beginning the conversation of how we should proceed.

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Genome Editing Has Begun How Will It Be Controlled? | Big Think - Big Think

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In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA. The term was coined in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany, as a portmanteau of the words gene and chromosome.

More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. The term genome can be applied specifically to mean the complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. When people say that the genome of a sexually reproducing species has been "sequenced," typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Most biological entities more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include this auxiliary material, which is carried in plasmids. In such circumstances then, "genomeey" describes all of the genes and non-coding DNA that have the potential to be present.

In vertebrates such as sheep and other various animals however, "genome" carries the typical connotation of only chromosomal DNA. So although human mitochondria contain genes, these genes are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome".

Note that a genome does not capture the genetic diversity or the genetic polymorphism of a species. For example, the human genome sequence in principle could be determined from just half the DNA of one cell from one individual. To learn what variations in DNA underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to any particular DNA sequence, but to a whole family of sequences that share a biological context.

Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either.

The Human Genome Project was organized to map and to sequence the human genome. Other genome projects include mouse, rice, the plant Arabidopsis thaliana, the puffer fish, bacteria like E. coli, etc. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (bacteriophage MS2). The first DNA-genome project to be completed was the Phage -X174, with only 5368 base pairs, which was sequenced by Fred Sanger in 1977. The first bacterial genome to be completed was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. Many genomes have been sequenced by various genome projects. The cost of sequencing continues to drop, and it is possible that eventually an individual human genome could be sequenced for around several thousand dollars (US).

Note: The DNA from a single human cell has a length of ~1.8m.

Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multicellular organisms (see Developmental biology). The work is both in vivo and in silico.

Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number (karyotype), genome size, gene order, codon usage bias, and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005).

Duplications play a major role in shaping the genome. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.

Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.

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Genome | Psychology Wiki | Fandom powered by Wikia

February 16, 2017 by Bill Hathaway Credit: Yale University

An analysis of a patient's deadly brain tumor helped doctors at Smilow Cancer Hospital identify new emerging mutations and keep a 55-year old woman alive for more than five years, researchers report in the journal Genome Medicine.

The median survival rate for patients with glioblastoma multiform (GBM) is only 15 months, but three separate genomic analyses of the tumor identified new mutations that allowed doctors to adjust treatment and keep the patient alive for over five years, through two recurrences of the cancer.

"We were able to identify the molecular profile at each recurrence," said Dr. Murat Gnel, chair and the Nixdorff-German Professor in the Department of Neurosurgery, researcher with Yale Cancer Center, and senior author of the paper. "The molecular make-up of the cancer changed after each treatment and with time, but we were able to adjust treatments based on those profiles."

For instance, the last genomic analysis revealed mutations of the cancerunder selective pressure from targeted therapieshad increased 30-fold, making the patient a good candidate for immunotherapy. Although there was an initial response, the cancer ultimately progressed.

The researchers were able to extend the findings on this case to more than 100 other GBM cases, leading to the observation that most GBMs change their genomic profile during therapy. "These findings have significant implications for precision treatment of these tumors" said Dr. Zeynep Erson Omay, the first author of the study and a research scientist in neurosurgery. "We now do a genetic analysis on every glioma surgically removed at Smilow Cancer Hospital during each recurrence or progression, comparing the molecular genomic profile to the original cancer to make treatment decisions."

With new drugs available, there is hope that "we will soon start to see real changes in patient outcomes," Gunel said.

Explore further: Research team tracks twists and turns on the road to malignancy

More information: E. Zeynep Erson-Omay et al. Longitudinal analysis of treatment-induced genomic alterations in gliomas, Genome Medicine (2017). DOI: 10.1186/s13073-017-0401-9

Journal reference: Genome Medicine

Provided by: Yale University

Gliomas can begin as benign growth in brain tissue but almost all eventually morph into malignant cancers called GBMs. Despite medical and surgical advances, GBMs remain one of the most deadly cancers in humans.

Survival for patients with glioblastoma, an aggressive and deadly brain cancer, could be determined by the complexity of their tumor, according to researchers at the Translational Genomics Research Institute (TGen).

Researchers leading the largest genomic tumor profiling effort of its kind say such studies are technically feasible in a broad population of adult and pediatric patients with many different types of cancer, and that some ...

Nearly the entire genetic landscape of the most common form of brain tumor can be explained by abnormalities in just five genes, an international team of researchers led by Yale School of Medicine scientists report online ...

Blood samples can be just as effective as invasive tissue biopsies in monitoring cancer and can help doctors better prescribe treatment, a study revealed Saturday.

Next-generation sequencing for patients at UCSF Medical Center is prompting changes in brain tumor diagnoses for some children and a retooling of treatment plans in many cases. Sequencing is also providing valuable insights ...

A new study that confirms the role of a protein called PAK4 in the movement and growth of pancreatic cancer cells could help researchers find new ways to tackle the disease.

Researchers in Germany have discovered that a tumor suppressor protein thought to prevent acute myeloid leukemia (AML) can actually promote a particularly deadly form of the disease. The study, "RUNX1 cooperates with FLT3-ITD ...

Less aggressive cancers are known to have an intact genomethe complete set of genes in a cellwhile the genome of more aggressive cancers tends to have a great deal of abnormalities. Now, a new multi-year study of DNA ...

An Australian-led international research effort has revealed that genetic changes normally linked to breast, colon and ovarian cancers could also drive a rare form of pancreatic cancer.

Scientists at Winship Cancer Institute of Emory University have mapped a vast spider web of interactions between proteins in lung cancer cells, as part of an effort to reach what was considered "undruggable."

To understand what makes breast cancer spread, researchers are looking at where it lives - not just its original home in the breast but its new home where it settles in other organs. What's happening in that metastatic niche ...

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Genome analysis helps keep deadly brain cancer at bay for five years - Medical Xpress

Genome analysis helps keep deadly brain cancer at bay for five ... Science Daily An analysis of a patient's deadly brain tumor helped doctors identify new emerging mutations and keep a 55-year old woman alive for more than five years, ... and more »

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Genome analysis helps keep deadly brain cancer at bay for five ... - Science Daily

Science Daily

Genome surgery with CRISPR-Cas9 to prevent blindness Science Daily Scientists at the Center for Genome Engineering, within the Institute for Basic Science (IBS) report the use of CRISPR-Cas9 in performing "gene surgery" in the layer of tissue that supports the retina of living mice. Published in Genome Research, this ... Human genome editing report strikes the right balance between risks and benefitsMedical Xpress The end of inherited diseases moves a step closerFinancial Times Could gene editing help avoid disease? MaybeThe Sentinel Scientific American (blog) -Science Recorder all 37 news articles »

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Genome surgery with CRISPR-Cas9 to prevent blindness - Science Daily

Human genome editing, like self-driving cars or drone delivery, isbecoming apart of our everyday reality faster than we realize it.

Apanel discussion held at The Rockefeller University entitled "The Future of Gene Editing: A multi-disciplinary panel discussion" broughttogether four expertswho tackle the challenges of human gene-editing from different approaches and perspectives, based on their individual focuses and specialties. Why does this particular area of science need so much conversation?

There are significant concerns, to be sure, especially about unintended consequences. People are particularly nervous about gene drive technology and the release of altered species into the environment. Fears include these altered species entering the food chain, causing the extinction of their or another species and the creating of organisms that we never thought possible, if mutations were to occur, such as super bugs.

Somewhere in the middle of these extremes liesan incredibly difficult, emotional, human conversation that needs to draw lines in new territory where we are not comfortable and have had no practice finding boundaries.

Jamie Metzl(Senior Fellow, Atlantic Council) introduced the subject with the perspective thatgene editing is the single most important topic that should be discussed at this moment in time. Why? Because, as Metzl said, "this is the time when our species took control of our evolutionary process." Moreover, there is no clear answer as to where lines should be drawn between scientific progress and going too far.

One option would be to throw up our hands and let people do what they want - why restrict science? But, the technology behind CRISPR can be done by almost anyone with a pipette, so, wemustdefine therules of engagement. But, stifling all progress because we are scared of the unknown is also not the best answer.

Metzlstarted with a comparison between two people who talked abouttraveling to the Moon - Jules Verne, who wrote: "From the Earth to the Moon" in 1865 and JFK whospoke about goingto the moon just seven years before Apollo 11.Metzl's point is that, when it comes to human gene-editing,we are in 1962, not 1865,and we need to think about itin the present, not as a hypothetical that may happen at some point in the future. As Metzlsays, this is not a discussionabout science, but, a"science-based conversation about the future of our species."

The other panel participants wereRoberto Barbero (the Assistant Director of Biological Innovation, White House Office OfScienceAnd TechnologyPolicy), S. Matthew Liao(Director, Center for BioethicsNYU) and Marnie Gelbart (Director of Programs, Personal Genetics Education Project, Harvard University.)

An ongoing challenge in science communication is in engaginga public that neither truly understands nortrustsscience. Marnie Gelbartraised the issue ofhow can we get everyone to the table forthis conversation? People have concerns that theirgenetic informationmaybe used against them. Also, like most health care advances, access is a concern; gene editing will probably be available to the people who can pay for it - where does that leave everyone else?

For comparison, we can look at the issue of genetically modified organisms (GMOs) - a far less complicated and emotionalissue than human gene-editing. GMOsare the scientific issue with the widest gap in understanding between scientists and the public, with 88% of scientists reporting that GMOsare safe to eat, as compared to just 37% of the public. Scientists understand the biology behind the creation of GMOs, but, have had a difficult time explaining it to the public. Lacking that understanding leaves a lot of spacefor fear and uncertainty.

If we cannot successfully communicate aboutGMOs, it seems unlikely that gene editing is going to be conveyed correctly. As science communicators, we certainly have our work cut out for us.

MatthewLiao took a more philosphicaltack- how willwe decide which traits to alter? He presented fascinating approachesthat can be used in such decision making that will certainly be the topic of futurearticles. In short, he tackles this question from a perspective of human rights - and works on the assumption that every person has equal moral status, regardless of our differences. Further, he focuses on distilling down the minimum framework of what makes a human capable of pursuing a good life. And, this is where his work can gettricky because two people can easily disagree on what those traits are creating A LOT of gray area in the middle. But, at some point, we are going to have to decide on what type of human we are comfortable creating while realizing that diversity is the greatest strength of any species.And, as most of us are probablynot comfortable making those decisions, it is the work of people like Matthew that will come to the forefront.

Overall, the panel discussion and, in particular, the audience's participation,raised many good questions that need to be asked and addressed.The last words of JFK's speech in 1962are as applicable to gene editing as they were at that time to space travel.

"Well, space is there, and we're going to climb it, and the moon and the planets are there, and new hopes for knowledge and peace are there. And, therefore, as we set sail we ask God's blessing on the most hazardous and dangerous and greatest adventure on which man has ever embarked."

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The Rockefeller University Hosts Panel on Human Genome Editing - American Council on Science and Health

UNIVERSITY PARK, Pa. A $6.1 million, five-year grant from the National Institute of Diabetes, Digestive and Kidney Diseases at the National Institutes of Health may help researchers leverage massive amounts of genomic data to develop medical treatments and pharmaceuticals, according to an international team of researchers.

The project called VISION or Validated Systematic Integration of Hematopoietic Epigenomes -- will integrate and functionally validate large amounts of emerging genomic and epigenetic data, according to Ross Hardison, T. Ming Chu Professor of Biochemistry and Molecular Biology, Penn State and a member of the Genome Sciences Institute of the Huck Institutes of the Life Sciences.

Hardison, who will lead the international multidisciplinary team, added that the group will try to develop new tools for using data to facilitate advances both in basic research as well as medical applications, such as precision medicine.

The project will focus on blood cell development as a model system for gene regulation in mammals. Blood cell development is vitally important to health because humans must continually replace old and damagedcells, and because many diseases, like leukemias and anemias, result from mis-regulation of gene expression during blood formation.

"We are excited about this project because the methods we are developing can be applied not only to diseases that affect blood, but others as well," Hardison said. "A person's genetic profile can have a significant impact on disease susceptibility and response to specific treatments. However, the critical genetic variants that make up that genetic profile most often do not code for protein, but rather they are located in the much larger noncoding genome. We are studying these noncoding regions and finding new ways to extract valuable information about functional elements within them, which in turn informs us about how genetic variants play a role in disease."

The results of the VISION project are being provided to the research community in readily accessible, web-based platforms and online tools that will allow researchers to extract meaningful, experimentally validated interpretations from the data andproduce a guide for investigators to translate insights from mouse models to human clinical studies.

Hardison is working with Cheryl Keller, project manager, Yu Zhang, associate professor of statistics, andFeng Yue, assistant professor of biochemistry and molecular biology, College of Medicine, all at Penn State; Mitchell Weiss, chair of the department of hematology, St. Jude Children's Research Hospital; Gerd Blobel, Professor of Pediactrics, University of Pennsylvania abd Children's Hospital of Philadelphia; James Taylor, associate professor of biology and associate professor of computer science, Johns Hopkins University; David Bodine, chief and senior investigator, National Human Genome Research Institute, NIH; Berthold Gttgens, principal investigator and professor of haematology, Cambridge Stem Cell Institute, University of Cambridge; Douglas Higgs, group head and principal investigator, and Jim Hughes, associate professor of genome biology, both of the Weatherall Institute of Molecular Medicine, Oxford University.

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Grant to help pave a big data highway to explore genome, enhance health - Penn State News

Editing the genomes of human embryos should be allowable to treat or prevent serious diseases and disabilitiesbut only amid stringent oversight and safety protocols and only if no reasonable alternatives existaccording to a reportreleased Tuesday by the National Academy of Sciences and the National Academy of Medicine.

The expert panel22 of the worlds leading experts on genetics, bioethics, medicine, and lawis still completely opposed to such efforts. But amid new, powerful genome-editing tools, such as CRISPR/Cas9, the experts were forced to reconsider genome editings potential for good.

Human genome editing holds tremendous promise for understanding, treating, or preventing many devastating genetic diseases, and for improving treatment of many other illnesses, Alta Charo, co-chair of the panel and a professor of law and bioethics at the University of Wisconsin-Madison, said in a statement.

But critics say this endorsement may help legitimize irresponsible applications. This opens the door to advertisements from fertility clinics of giving your child the best start in life with a gene-editing packet, Marcy Darnovsky, executive director of the Center for Genetics and Society, a public interest group based in California, told The New York Times.

For now, the discussion is all theoretical. Though technology is advancing swiftly, real human applications and clinical trials are still years away. In the meantime, the panel recommends that policy makers foster public discussion and engagement on the issues to make sure that any new rules account for social, ethical, and legal considerations.

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Genome-edited humans get green light from expert panel - Ars Technica

Gene variant identified for Kawasaki disease susceptibility Science Daily "This is the first successful analysis of whole genome sequence from a family that revealed a new gene implicated in KD susceptibility," said senior author Jane C. Burns, MD, professor and director of the Kawasaki Disease Research Center at UC San ...

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Gene variant identified for Kawasaki disease susceptibility - Science Daily