Category Archives: Genome

Discussing "decoding the hookworm genome" with Dr. Makedonka Mitreva
Makedonka Mitreva, PhD, Assistant professor of medicine and genetics and a member of The Genome Institute at the Washington University School of Medicine dis...

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Discussing "decoding the hookworm genome" with Dr. Makedonka Mitreva - Video

HUMAN GENOME PROJECT 2011
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HUMAN GENOME PROJECT 2011 - Video

The Human Genome Project, 3D Animation (1)
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We got the human genome a decade ago. Where are the drugs?

My grandfather was found wandering shoeless in the town where he was born, 50 miles from home. That was the first day we knew. Or, it was the last day we could pretend. A stranger placed a call to my father at his apartment in Evanston, Illinois, after finding my grandfather on those wintery streets, untucked and empty-eyed.

On a regular day, hed take the L from Evanston into Chicago and place some bets at the track. He liked to play the ponies, and he whittled down his paychecks at the bar. My grandfather kicked alcoholism at age 65. He didnt touch a drop for 16 years until his death, something he was proud of; but in the last decade, he was vanishing. On this day, alcohol couldnt explain his disappearance. By the afternoon, something was amiss. Hours later, into the night, the telephone rang. Did we know an Anthony Kozubek?

He was a child raised in the depth of the Great Depression. He could fix anything. Repair your front steps. Fix your plumbing. Install new gutters. One time he visited our house, and within an hour was upon our roof. We didnt have a ladder so he built us one. A few hours later, he built us a back staircase. He told us, maybe to build the lore of his hardscrabble life, that as a child he recycled his sisters shoes for his by cutting off the heels.

The son of Polish immigrants, my grandfather grew up on a polyglot street, and he began drinking with purpose in his teens. My grandmother stowed money in cans so that he wouldnt spend it. He was a boxer. Tall and lithe, he fought amateur Golden Gloves bouts in his Chicagoan youth in the 1930s. (His brother Joe traveled to New York and sparred with heavyweight champ Jack Sharkey). He fought and he drank, inside the ring and outside, and it continued while he served the U.S. Armys Engineer Corp.

He didnt talk about WWII, but years later we learned of his station transfers through the jackbooted continent based on records of his stints in the brig. The poor arent born into this world; they come crashing into it. When he learned he was having a son, my grandfather and his brother-in-law celebrated with drinking, stumbling and shattering a store-front display window, landing in a heap of plate glass.

He would later suffer from late-onset Alzheimer's disease. (Jim Kozubek)

Years later, my father would scribble down notes in journals, detailing those past events, documenting hard lives that built the foundation for us. We had recovered my grandfather from those slippery streets, but his faulty memory couldnt be rescued. In fact, his lack of recognition was jarring. When my father was preparing to remove his clothes from a dresser, he recalls, my grandfather protested, "You can't take those clothes, they belong to my son." Alzheimers "moments" drop like chasms.

And yet, this is not one elegiac story, it is many. Five million people in the United States have Alzheimers disease. This number will double in a decade. If any of us live to be 85, the chances of having the disease or some form of dementia is about one in three. The explanation for why some of us get it and some dont is a largely unsolved genetic riddle. My grandfather eventually died from it. My grandmother is now 96-years-old, writes me cards with lacy cursive, and regularly beats me at Scrabble.

Recently, my father subscribed to a service that allowed us to mail in a cheek swab to learn about our genetic ancestry. I learned that I belonged to Haplogroup Ra type of ethnic branch on our genetic treethat I am German and Polish (which I knew), and by a small fraction Ashkenazi Jewish (which I didnt know), and I received a colorful map of my ancestors probable traipses through Europe. But though it was an option on the test, my father did not want to know about our risk for Alzheimers, it turns out. And for good reasonthere is not a single meaningful drug to treat Alzheimers.

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Why Can't We Prevent Alzheimer's?

Introduction to genome browsers using Ensembl
This video provides a basic introduction to genome browsers, with a focus on data and analysis available in Ensembl. A brief overview of genome sequencing, i...

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Introduction to genome browsers using Ensembl - Video

Macaques in China are the first primates born with genomes engineered by precision gene-targeting methods.

Prime cuts: The faint ladder-rung patterns in an image of a DNA gel show that genome editing successfully modified a gene in two macaque infants (central columns), but not in an untreated animal (right column). The left column shows a size standard.

Researchers at Nanjing Medical University and Yunnan Key Laboratory of Primate Biomedical Research in Kunming, China, have created genetically modified monkeys using a new method of DNA engineering known as Crispr. The infant macaques show that targeted genome editing is feasible in primatesa potential boon for scientists studying complex diseases, including neurological ones, and an advance that suggests that the method could one day work in humans. The work was reported in the journal Cell on Thursday.

Scientists have previously used the new genome-editing technique to delete, insert, and modify DNA in human cells and other animal cells grown in petri dishes. The method has also been used to create gene modifications in whole animals such as mice, rats, and zebrafish. The new study shows for the first time that Crispr can create viable primates with genomes modified at specific targeted genes.

The Chinese researchers injected single-cell macaque embryos with RNAs to guide the genome-editing process. The team modified three genes in the monkeys: one that regulates metabolism, another that regulates immune cell development and a third that regulates stem cells and sex determination, says study coauthor Wezhi Ji, a researcher at the Yunnan Key Laboratory of Primate Biomedical Research. The researchers found that the genome-editing tools created multiple changes in their target genes at different stages of embryonic development. The infant monkeys are too young for the team to yet determine if the genetic changes have an effect on physiology or behavior, says Ji. But, he adds, data from this species should be very useful for curing human disease and improving human health.

Researchers have previously created a handful of transgenic monkeys, such as a rhesus macaque that produces the disease-causing version of theHuntingtons gene. Researchers at Emory University in Atlanta created this avatar of human disease by injecting a virus into macaque eggs. The virus delivered a disease-version of the human Huntingtons gene into a random location in the monkeys genome.

Primate pioneers: Twin infant macaques whose genomes were modified within three different genes.

Crispr, on the other hand, can be used to insert, delete, or rewrite a DNA sequence at a specific location within a genome. Like the random viral insertion used by the Emory team, the Crispr method employed by Ji and colIeagues can create genetically modified animals in a single generation, an important consideration for researchers working with animals that can take three years to reach sexual maturity and are expensive and difficult to rear.

Others say they are anxious to use Crispr to create their own monkeys. Robert Desimone, director of MITs McGovern Brain Institute for Brain Research, says he and colleagues are planning on using genome editing to create modified monkeys. He says its possible the success of the Chinese researchers will encourage other groups to use primates in their work. Although mice are giving us tremendous insight into basic brain biology and the biology of the disease, theres still a big gap in between the mouse brain and the monkey brain, says Desimone.

For example, he says, lots of drugs that work in mice to treat disease dont work in humans. Desimone says hes hoping that some success in monkeys will interest drug companies in neurosciencealluding to a recent trend of large drug companies abandoning research on brain diseases because the work often proved unsuccessful. The hope is that disease and drug research in monkeys will more likely lead to therapies in humans because the primates share complex behaviors and social structures. We are cautiously optimistic, says Desimone.

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Monkeys Modified with Genome Editing

Listen The genome test that may change everything Researcher Andrew Burton/Getty Images Kenneth Beckman: Director of the Biomedical Genomics Center at University of Minnesota Ashlee Vance: Technology writer for Bloomberg Businessweek

Genomics company Illumina unveiled a machine that can sequence a human genome for $1,000. The machine, named HiSeq X, hits a once-elusive benchmark but won't be available to the general population for some time.

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The biotech industry has been trying to reach the $1,000 genome mark for years. It's a figure that should make full genome sequencing much more mainstream. As more people get sequenced, researchers get more data to use in their analysis of how DNA variations manifest themselves in diseases. The high-speed, low-cost sequencing system arrives at a crucial time, with a number of biotech companies, research centers, and hospitals starting to show real clinical breakthroughs. "To figure out cancer, we need to sequence hundreds of thousands of cancer genomes, and this is the way to do it," Flatley said.

About a decade ago it cost much more than $1 billion to sequence a human genome, and the process took months. Illumina's new machine can knock out dozens of genomes in about a day. The HiSeq X systems, which cost $1 million each, should end up at large research centers and will be sold in groups of 10. Illumina has unveiled a smaller, $250,000 system called the NextSeq 500, which can fit on a laboratory counter and handle one genome at a time.

Kenneth Beckman, director of the Biomedical Genomics Centers at the University of Minnesota, calls next-generation sequencing "the killer app of genomics."

He joins The Daily Circuit along with Businessweek's Ashlee Vance to discuss what this new development means for health care and what else we can expect from biotechnology advances.

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New machine can sequence $1,000 human genome

Ch 14 The Human Genome

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Ch 14 The Human Genome - Video

Bravely Default Part 67 [Chapter 5 Genome Abilities]
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Hertz Fellow Erez Lieberman-Aiden
Erez studied in applied mathematics at Harvard and as a student at the Harvard--MIT Division of Health Science and Technology. His work integrates mathematic...

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Hertz Fellow Erez Lieberman-Aiden - Video