Category Archives: Genome

The genome is the entire set of genetic instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes, found in the nucleus, as well as a small chromosome found in the cells' mitochondria. Each set of 23 chromosomes contains approximately 3.1 billion bases of DNA sequence.

"Genome" is a funny word. Nobody can figure out how to pronounce it. Is it "jeh-NOHM" or "JEE-nohm"? I've heard various opportunities for mispronunciations, some of which are pretty funny. But basically, it is the entire instruction set of an organism; all of the DNA. For humans, that amounts to about 3.1 billion letters of the code--As, Cs, Gs, and Ts--all in the right order, spread across all of those chromosomes.

Francis S. Collins, M.D., Ph.D.

Occupation Director, National Institutes of Health; Former Director, National Human Genome Research Institute

Biography Dr. Francis S. Collins, director of the National Institutes of Health, is noted for his landmark discoveries of disease genes and his visionary leadership of the Human Genome Project, a complex multidisciplinary scientific enterprise directed at mapping and sequencing human DNA. Dr. Collins was the director of the National Human Genome Research Institute from 1993 to 2008. His research has led to the identification of genetic variants associated with type 2 diabetes and the genes responsible for cystic fibrosis, neurofibromatosis, Huntington's disease and Hutchinson-Gilford progeria syndrome. In 2007, Dr. Collins received the Presidential Medal of Freedom, the nation's highest civil award, for his revolutionary contributions to genetic research.

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Talking Glossary of Genetic Terms - Genome.gov

Genome Day 2017 rated a big thumbs up from the nearly 400 eighth-graders, teachers, and civic and business leaders who gathered last Thursday on the Buffalo Niagara Medical Campus (BNMC) to extract DNA from cells in their cheeks.

The experiment started by spitting into a cup, which was great, according to Tamara from PFC William J. Grabiarz School of Excellence School 79. Its cool to see my own spit in the tube.

In addition to the DNA extraction, students tried to complete a karyotype to identify chromosomal differences, build an origami DNA model and identify genetic mutations by interpreting sequences from healthy cells and tumor cells.

Brian from Waterfront Elementary School School 95 said the experience was interesting. I want to study chemistry or biology or even something like environmental stuff, he said.

Organizers were delighted to hear these comments at the third annual Genome Day, part of a private/public partnership designed to intrigue students about STEM fields and encourage them to consider careers in science, technology, engineering and math.

It was equally delightful for volunteer leaders like Aziz Shittu, a UB pre-med undergraduate. I love teaching kids who are interested in science or technology or possibly considering the medical field, Shittu said.

A first timer this year, Shittu joined more than 50 other graduate students, postdocs, researchers and faculty members from UB, UBs New York State Center of Excellence in Bioinformatics and Life Sciences (CBLS) and Roswell Park Cancer Institute who consider Genome Day a compelling opportunity for getting out of the lab to mingle with younger students.

This event offers students another opportunity for us to plant the seed of possible STEM careers and college, said David Mauricio, chief of strategic alignment and innovation for the Buffalo Public Schools and an original BPS STEM Experience planning member. It can help set them on the path for future success.

The small-group workshops followed brief remarks by Buffalo Mayor Byron Brown, who encouraged students to take advantage of what the schools have to offer, including events like Genome Day.

CBLS Executive Director Norma Nowak told the students she was a product of the Buffalo Public Schools and had used that education to start her biomedical technology business, Empire Genomics; become a faculty member in the Jacobs School of Medicine and Biomedical Sciences, and continue to pursue her research passion as a genomics pioneer and director of the CBLS.

Buffalo Public Schools Superintendent Kriner Cash suggested the students embrace their passions and their talents. Cash also congratulated Buffalo Academy of Visual and Performing Arts 10th-grader Desanay Nalls, who was the winning student designer for bus-shelter posters.

Desanay referenced the movie Hidden Figures, based on the true story of African-American women mathematicians who served a vital role in NASA during the early years of the U.S. space program, in challenging her peers. I am no longer, you are no longer, we are no longer hidden in plain sight, she said, noting that the students, like the women in the story, can persevere to a future that is shaped by science, created by technology, taught by engineering and defined by math.

Poster competition sponsors Niagara Frontier Transportation Authority and Lamar Transit were among numerous Genome Day sponsors, including UB; CBLS; UBs Genome, the Environment and the Microbiome (GEM) Community of Excellence; Roswell; the city of Buffalo; BNMC; Buffalo and Erie County Public Library; Buffalo Museum of Science; and the Buffalo Public Schools.

SUNY Trustee Eunice Lewin inspired the public/private partnership, facilitated through UBs Office of the Vice President for Research and Economic Development.

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BPS students learn more about their bodies at third annual Genome Day - University at Buffalo Reporter

Longtime University of Oregon donors Sharon and Lloyd Powell a 1955 UO graduate have made a significant gift to the Center for Genome Function, a UO initiative led by an emerging team of UO biologists.

All of us in the labs are so grateful to Sharon and Lloyd for their investment in genome science at the UO, said lead researcher Eric Selker. Their gift will help us continue to claim a leadership position at the forefront of genetic research.

The centers innovative research seeks to understand the underlying processes of human genetics. Team members are helping fuel discoveries in the areas of cancer, neurological disorders, aging, infertility, birth defects, the side effects of drugs and environmental factors, and others.

The Powells gift provides essential support for the center, according to Selker, and is available for such expenses as lab startup costs, instrumentation and graduate student support.

The Powells have given extensively to the business school and intercollegiate athletics Powell Plaza outside Hayward Field is named for the family and Lloyd Powell has received the UOs Pioneer Award and Presidential Medal. He also served the UO Foundation as a trustee.

But it was the Powells 50-year relationship with UO fundraiser Herb Yamanaka, combined with Sharon Powells interest in science, which led to the gift.

Sharon wrote to me out of the blue, Yamanaka recalled. She said, Wed love to help you with any research you are doing around the human genome. It was a nice surprise. What a wonderful email to receive from two most generous Ducks.

Yamanaka has known Lloyd Powell dating back to Powells college days as a football player under UO coach Len Casanova. And theyve maintained that friendship as three generations of Powells attended the UO. Sons Peter and Tom, daughter-in-law Maryanne (Molly), and grandsons Brendan, Lane and Tate have grown into an extended family of Powell Ducks.

The Center for Genome Function is one focus of the UOs Clusters of Excellence hiring initiative. The clusters support UO President Michael Schills goal to hire an additional 80 to 100 tenure-track faculty members over the next five years to boost UO academics and research.

The Center for Genome Function added one new tenure-track faculty member in the past year, with plans to add two more. Jeffrey McKnight, formerly a Leukemia and Lymphoma Society fellow at the Fred Hutchinson Cancer Research Center in Seattle, joined current faculty members Selker and Diana Libuda.

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Powell gift supports fledgling UO Center for Genome Function ... - AroundtheO

I was in high school when the human genome made it to front pages of newspapers around the world. Unlocking our genetic code had taken $2.7 billion and close to 15 years to finish. That was 2001.

Today, it costs only about $1,000 to sequence a whole genome a dollar figure low enough for personal genome sequencing to make sense. But what might it mean to get your own genome sequenced?

That was the question Carl Zimmer, bestselling author and science columnist for the New York Timesand other publications, explored at a symposium organized by the Stanford Center for Computational, Evolutionary Human Genomics this week.

Zimmers investigation into his genome began when a geneticist asked him if hed like his genome sequenced. I was stunned that the question could be asked, Zimmer said. It was like saying Would you like to go to Jupiter?

First, Zimmer said he signed up with the company Illumina to have his genome read. Days later, his clinical report came in with nothing to say about the more than 1,500 genes they had examined. The most detailed response was: Your muscle fibers are built for power, Zimmer said.

A boring genome is a good genome, Zimmer said. If theyd said, youve got Huntingtons, it wouldve been bad for me, but a great story.

Illuminas analysis reflected a tiny sampling of the information the genome contained, Zimmer said. Knowing that wasnt how scientists study genomes, Zimmer got his hands on the raw data the full 60 gigabytes of his blueprint DNA.

He said he found more than 20 scientists who volunteered to peer into what he calls the Zimmerome. Among the many things Zimmer discovered was that he has a mutation that puts him at risk for high cholesterol and another that makes it difficult to break down drugs. Zimmer said he learned he shares 1.4 million DNA variations with two random individuals from China and Nigeria. In addition, he found out that 2 percent of his genes are from Neanderthals and he has a surprising Italian ancestry hes still trying to trace all of which he chronicled in a series that appeared on STATcalled the Game of Genomes.

Zimmer said the experience taught him that although genome sequencing is now easy to access, its still quite difficult to extract meaningful information from our genes. The scientific community is still very far from being able to decipher the function of every single element in our genome, he said.

He found that currently, genome sequencing can help identify a variety of genetic disorders. But it is less clear what a healthy individual might gain from having his or her genome read.

Theres a disconnect between the morning-in-the-forest kind of hoopla about what you can find about your genome and what [scientists] can actually deliver to people who are healthy, Zimmer said. Its a fundamentally hard problem.

As Zimmer wrote in the Game of Genomes, This genomic noodling is great fun, although it may not mean that much to my own existence. Yet.

Previously:Here be dragons: Hard-to-sequence sections of genome remainandA leader in the Human Genome Project shares tale of personalized medicine, from 1980 until today Photo by Saul Bromberger and Sandra Hoover Photography

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What Can You Learn From Your Own Genome? Science Writer Carl ... - Scope (blog)

Colored scanning electron micrograph of baker's yeast, conventionally grown in the lab. So far, researchers have been able to synthesize six of the yeast's 16 chromosomes from scratch, and think they may be able to complete all 16 by 2018.

Scientists have taken another important step toward creating different types of synthetic life in the laboratory.

An international research consortium reports Thursday that it has figured out an efficient method for synthesizing a substantial part of the genetic code of yeast.

"We are absolutely thrilled," says Jef Boeke, a geneticist at New York University School of Medicine, who is leading the project. "This is a significant step toward our goal."

The milestone is the latest development in the intensifying quest to create living, complex organisms from scratch in the lab. This group previously reported it had completely synthesized one of yeast's 16 chromosomes, which are the molecular structures that carry all of an organism's genes.

Now, in a series of seven papers published in the journal Science, the group reports it has completed five more, and is on track to having a fully synthetic yeast genome finished by the end of the year.

"We're chugging along toward that goal," Boeke says.

The advance is being praised by many biologists, geneticists and others as an important advance. And even bioethicists and environmentalists who are worried about possible ethical and environmental implications praised the project for its careful approach.

But the increasing ability to manipulate the basic building blocks of life is stirring concerns about someday using this technology to create synthetic genomes of other organisms, especially humans.

The yeast project is significant because it provides insights into how human cells work, Boeke says.

Geneticist Jef Boeke of New York University studies DNA sequences from baker's yeast. NYU Langone Medical Center/Screenshot by NPR hide caption

Geneticist Jef Boeke of New York University studies DNA sequences from baker's yeast.

Though single-celled, yeast are among the complicated group of organisms called eukaryotes. That means, like humans, yeast contain organelles, and package their DNA inside a nucleus.

"They are a great model for understanding the basic wiring of higher cells," Boeke says.

The project enlisted labs around the world to painstakingly assemble yeast chromosomes from the four basic chemical building blocks of DNA adenine, cytosine, guanine and thymine.

"We're essentially swapping out the code, if you will, in a living yeast cell with sort of a 21st Century version of the operating system," he says.

The team has shown that all six of the chromosomes assembled so far function inside yeast cells, even when several are simultaneously inserted into the same cell. That's true even when significant portions of individual chromosomes have been rewritten.

"We can kind of torture the genome of the yeast in some pretty extreme ways and the yeast sort of shrugs its shoulders and doesn't seem to care that much about it," Boeke says.

That bodes well for one of the goals of the project: creating synthetic yeast that could be used like tiny factories to produce more than bread, beer and wine. The scientists hope to use yeast to produce new drugs to treat diseases as well as for other purposes, possibly including manufacturing new forms of fuel.

"We're also developing some really practical tools for improving the yeast so that it can do a much better job at making useful products for us," Boeke says.

Others experts agree.

"This is really going to allow us to understand how to design cells from the bottom up that can be reprogrammed for many applications," says Daniel Gibson, vice president of DNA technologies at Synthetic Genomics, of La Jolla, Calif., who wrote an article accompanying the new research

Another goal is to learn new things about basic biology, Boeke says.

"A great quote from Richard Feynman of the Feynman lectures on physics is: 'What I cannot create, I cannot understand,' " says Boeke. "And that's kind of a motto for our field, I guess you would say."

The techniques the scientists are developing could also be used to synthesize from scratch the genomes of other much more complex organisms, Boeke says. For example, the group has developed an efficient way to identify and fix errors in the genomes they're working on, similar to the way computer programmers debug computer programs.

"This is absolutely setting the stage for being able to do these kinds of manipulations on a much larger scale in much larger genomes, such as those of plants and animals and even of the human genome," Boeke says.

That includes synthesizing the whole human genome. Boeke is already working on that with George Church, a prominent Harvard University geneticist.

"This is a whole new era where we're moving beyond little edits on single genes to being able to write whatever we want throughout the genome," Church says. "The goal is to be able to change it as radically as our understanding permits."

That prospect worries some biologists, environmentalists, bioethicists and others. The concern is that synthetic microbes, plants or animals might damage the environment in unpredictable ways if they're released either accidentally or on purpose.

"You can think of it of like introducing an invasive species into a different environment," says Todd Kuiken, a senior research scholar at North Carolina State University's Genetic Engineering and Society Center. "It will have some type of impact to the system."

Others fear terrorists could use this technology to brew new biological weapons.

Boeke says the yeast project is being done with careful safeguards and tight ethical scrutiny. But he acknowledges that the possibility of creating a synthetic human genome stirs alarm.

"The biggest concern, of course, is people are worried that our goal is to make a synthetic human a human powered by a synthetic genome," he says. "And this is why we are very adamant that our applications are in engineering of cells that could be used as therapies for humans. Don't make an organism from it."

But others think society is nowhere near ready for the manufacturing of a synthetic human genome.

"Having that kind of knowledge and that kind of power over the human genome in a world as riven by injustice as the world in which we currently live would not be a good way to go would not be a justifiable direction," says Laurie Zoloth, a bioethicist at Northwestern University. But she praises the yeast project.

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Scientists Closer To Creating A Fully Synthetic Yeast Genome - NPR

Science Daily

A three-dimensional map of the genome: Gene mapping technique ... Science Daily Cells face a daunting task. They have to neatly pack a several meter-long thread of genetic material into a nucleus that measures only five micrometers across. and more »

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A three-dimensional map of the genome: Gene mapping technique ... - Science Daily

The proteins that domesticated our genomes Science Daily EPFL scientists have carried out a genomic and evolutionary study of a large and enigmatic family of human proteins, to demonstrate that it is responsible for harnessing the millions of transposable elements in the human genome. The work reveals the ... and more »

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The proteins that domesticated our genomes - Science Daily

Researchers have identified 18 additional gene variations that appear to increase the risk of autism, according to the latest study from the Autism Speaks MSSNG project, the worlds largest autism genome sequencing program.

The research, published in the journal Nature Neuroscience, involved the analysis of 5,205 whole genomes from families affected by autism. The omitted letters in MSSNG (pronounced missing) represent the missing information about autism that the research program seeks to deliver.

Its noteworthy that were still finding new autism genes, let alone 18 of them, after a decade of intense focus, said study co-author Mathew Pletcher, Ph.D., Autism Speaks vice president for genomic discovery. With each new gene discovery, were able to explain more cases of autism, each with its own set of behavioral effects and many with associated medical concerns.

So far, research using the MSSNG genomic database has identified 61 genetic variations that affect autism risk. The researchers have linked several of these variations with additional medical conditions that often accompany autism. The goal, Pletcher said, is to advance personalized treatments for autism by deepening our understanding of the conditions many subtypes.

The researchers found that many of the 18 newly identified autism genes impact the operation of a small subset of biological pathways in the brain. All of these pathways affect how brain cells develop and communicate with each other.

In all, 80 percent of the 61 gene variations discovered through MSSNG affect biochemical pathways that have clear potential as targets for future medicines, Pletcher said.

Increasingly, autism researchers are predicting that personalized, more effective treatments will be developed from understanding these common brain pathways and how different gene variations alter them.

The unprecedented MSSNG database is enabling research into the many autisms that make up the autism spectrum, said the studys senior investigator, Stephen Scherer, Ph.D.

For example, some of the genetic alterations found in the study occurred in families with one person severely affected by autism and others on the milder end of the spectrum, Scherer said.

This reinforces the significant neurodiversity involved in this complex condition, he said. In addition, the depth of the MSSNG database allowed us to identify resilient individuals who carry autism-associated gene variations without developing autism. We believe that this, too, is an important part of the neurodiversity story.

The findings reveal how whole genome sequencing can guide medical care today. For example, at least two of the autism-associated gene changes described in the paper were linked to an increased risk for seizures. Another was tied to an increased risk for cardiac defects, and yet another with adult diabetes.

The results show how whole genome sequencing for autism can provide additional medical guidance to individuals, families and their physicians, say the researchers.

Source: Autism Speaks

APA Reference Pedersen, T. (2017). Genome Database IDs 18 More Autism Genes. Psych Central. Retrieved on March 8, 2017, from https://psychcentral.com/news/2017/03/08/genome-database-ids-18-more-autism-genes/117319.html

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Genome Database IDs 18 More Autism Genes - PsychCentral.com

Spectrum

World's largest autism genome database shines new light on many 'autisms' Science Daily It involved the analysis of 5,205 whole genomes from families affected by autism -- making it the largest whole genome study of autism to date. The omitted letters in MSSNG (pronounced 'missing') represent the missing information about autism that the ... Sequencing thousands of whole genomes yields new autism genesSpectrum 18 new genes have been linked to autism spectrum disorderWired.co.uk DNA Scan Uncovers 18 Genes Newly Associated With AutismNBCNews.com all 13 news articles »

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World's largest autism genome database shines new light on many 'autisms' - Science Daily

March 08, 2017 07:30 ET | Source: Intellia Therapeutics, Inc.

CAMBRIDGE, Mass., March 08, 2017 (GLOBE NEWSWIRE) -- Intellia Therapeutics, Inc. (NASDAQ:NTLA), a leading genome editing company focused on the development of potentially curative therapies, today reported updated data showing increased levels of genome editing efficiency in vivo and durability results with its CRISPR/Cas9 technology, following a single administration. Using its lipid nanoparticle (LNP) technology, Intellia achieved approximately a 97 percent reduction in serum transthyretin (TTR) protein driven by 70 percent gene editing efficiency in the mouse liver. These results are extremely promising, as they demonstrate compelling activity with lipid nanoparticles observed in the liver following a single dose, said Executive Vice President, R&D John Leonard, M.D. We are excited by the extent of the effect, which confirms the power of CRISPR/Cas9 for potential therapeutic uses. These high levels of gene editing are the result of Intellias effort to identify highly efficient delivery of CRISPR/Cas9 using lipid nanoparticles. The data advance our efforts as we look to transform the way we treat disease. The data are being presented for the first time at the Cowen and Company 37th Annual Health Care Conference in Boston on Wednesday, March 8, 2017 at 8:40 am ET. Complete data are being presented on March 22, 2017 at the Le Stadium Conference on Messenger RNA Therapeutics in Orleans, France. Data showed robust editing and sustained results including:

Study Background

The ongoing, preclinical editing studies were designed to explore the use of lipid nanoparticles for delivery of CRISPR/Cas9 components to the liver in mice and to mediate editing of target DNA within hepatocytes. For the LNPs in the studies, Cas9 mRNA was co-formulated with chemically synthesized gRNAs targeting the mouse TTR gene, and administered via one intravenous tail vein injection. Additional studies were performed to evaluate the impact of editing of variables in guide format, degree of guide chemical modification, and dose response on editing efficiency. The durability of the liver editing was evaluated through a four-month time period, and pharmacokinetic (PK) parameters for Cas9 mRNA and sgRNA were measured.

About Intellia Therapeutics

Intellia Therapeutics is a leading genome editing company, focused on the development of proprietary, potentially curative therapeutics using the CRISPR/Cas9 system. Intellia believes the CRISPR/Cas9 technology has the potential to transform medicine by permanently editing disease-associated genes in the human body with a single treatment course. Our combination of deep scientific, technical and clinical development experience, along with our leading intellectual property portfolio, puts us in a unique position to unlock broad therapeutic applications of the CRISPR/Cas9 technology and create a new class of therapeutic products. Learn more about Intellia Therapeutics and CRISPR/Cas9 at intelliatx.com; Follow us on Twitter @intelliatweets.

Forward-Looking Statements

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. These forward looking statements include, but are not limited to, express or implied statements regarding our ability to advance CRISPR/Cas9 into therapeutic products for severe and life-threatening diseases; the potential timing and advancement of our clinical trials; the potential targets or indications we may pursue; and potential commercialization opportunities for product candidates. Any forward-looking statements in this press release are based on management's current expectations of future events and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those set forth in or implied by such forward-looking statements.These risks and uncertainties include, but are not limited to, the risk that any one or more of our product candidates will not be successfully developed and commercialized, the risk that positive results from a preclinical or clinical study may not necessarily be predictive of the results of future preclinical or clinical studies, risks related to our ability to protect and maintain our intellectual property position, the risk of cessation or delay of any of the ongoing or planned clinical trials and/or our development of our product candidates, the risk that the results of previously conducted studies involving similar product candidates will not be repeated or observed in ongoing or future studies involving current product candidates, and the risk that our collaboration withNovartis or Regeneronwill not continue or will not be successful. For a discussion of other risks and uncertainties, and other important factors, any of which could cause our actual results to differ from those contained in the forward-looking statements, see the section entitled "Risk Factors" in our most recent quarterly report on Form 10-Q filed with the Securities and Exchange Commission, as well as discussions of potential risks, uncertainties, and other important factors in our subsequent filings with theSecurities and Exchange Commission.All information in this press release is as of the date of the release, and Intellia Therapeutics undertakes no duty to update this information unless required by law.

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Intellia Therapeutics Demonstrates Pioneering CRISPR/Cas9 Genome Editing Efficiency Data Using Lipid ... - GlobeNewswire (press release)