Tag Archives: genetics

The Human Genome: Yours for $48,000

The cost of a personal genome has dropped from about the price of a luxury sedan to, well, the price of a slightly less luxurious nice car. Illumina, a genomics technology company headquartered in San Diego, announced the launch of a $48,000 genome-sequencing service at the Consumer Genetics Conference in Boston on Wednesday.

It won’t be the first consumer genome service–Knome, a startup in Cambridge, MA, already offers genome sequencing for just under $100,000–but Illumina is the first company preparing to offer high-volume personal-genome sequencing. Knome, which uses Illumina technology to perform its sequencing, is a boutique service that offers both genome analysis and interpretation.

Many within the genomics industry believe that, as soon as the price is right, an individual’s genome will be sequenced routinely and become part of her medical record. Within the genome lie clues to each person’s risk for disease, his or her reaction to different medications, and other medically useful information.

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On the Quest for Synthetic Life, Scientists Build Their Own Cellular Protein Factory

In an important step towards creating synthetic life forms, genetics pioneer George Church has produced a man-made version of the part of the cell that turns out proteins, which carry out the business of life. “If you going to make synthetic life that is anything like current life … you have got to have this … biological machine,” Church told reporters in a telephone briefing. And it can have important industrial uses, especially for manufacturing drugs and proteins not found in nature [Reuters].

Church’s team built a functional ribosome from scratch, molecule by molecule. Ribosomes are molecular machines that read strands of RNA and translate the genetic code into proteins. They are exquisitely complex, and previous attempts to reconstitute a ribosome from its constituent parts – dozens of proteins along with several molecules of RNA – yielded poorly functional ribosomes, and even then succeeded only when researchers resorted to “strange conditions” that did not recapitulate the environment of a living cell, Church said [Nature blog]. Next, the researchers want to produce man-made ribosomes that can replicate themselves.

Church’s work hasn’t yet been published in a peer-reviewed journal; instead he presented his preliminary results at a seminar of Harvard alumni over the weekend. He described how his research team first disassembled ribosomes from E. coli, a common lab bacterium, into its component molecules. They then used enzymes to put the various RNA and protein components back together. When put together in a test tube, these components spontaneously formed into functional ribosomes…. The researchers used the artificial ribosome to successfully produce the luciferase enzyme, a firefly protein that generates the bug’s glow [Technology Review].

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Study finds value in ‘junk’ DNA

For about 15 years, scientists have known that certain “junk” DNA — repetitive DNA segments previously thought to have no function — could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.

The findings, which increase understanding of how humans differ from other animals, including non-human primates, appear Oct. 17 in the open-access journal PLoS Genetics.

Nearly half of human DNA consists of repetitive DNA, including transposons, which can “transpose” or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common form of retrotransposons in the human genome are Alu elements, which have more than one million copies and occupy approximately 10 percent of the human genome.

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Understanding Apoptosis In Cells May Lead To A Cancer Breakthrough

When a cell’s chromosomes lose their ends, the cell usually kills itself to stem the genetic damage – University of Utah biologists say their discovery about how those cells evade suicide and start down the path to cancer may lead to new treatments.

A new study of fruit flies is the first to show in animals that losing just one telomere, the end of a chromosome, can lead to many abnormalities in a cell’s chromosomes, which are strands of DNA that carry genes.

“The essential point is that loss of a single telomere may be a primary event that puts a cell on the road to cancer,” says Kent Golic, a professor of biology at the University of Utah and senior author of the study, published in the journal Genetics.

Fruit flies have four pairs of chromosomes. Humans have 23 pairs. Each chromosome has two ends, called telomeres, which often are compared with the plastic tips of shoe laces. When those tips are lost or break, the shoelace frays. Previous research has shown that aging and cancer often are associated with loss or shortening of telomeres.

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Human Genetics is Now a Viable Hobby — 23andMe Cuts its Price to $399

Personalized genomics just got a lot more accessible. Until tonight, the cheapest genome scan was available for just under a thousand dollars. Thanks to improvements in microarray technology, 23andMe has been able to cut that cost by more than half — to $399 — well within the reach of cash-strapped grad students, frugal genealogy buffs and other not-so-early adopters.

“By taking advantage of continuing innovation we are able to introduce a new chip that will give people more relevant data at a lower price,” said Anne Wojcicki, co-founder of 23andMe. ”We are excited that we are opening doors for more people to learn about their health and ancestry and for more people to be able to participate in advancing research. It is important to democratize personal genetics and make it more accessible.”

On The Spittoon blog, Wojcicki mentioned that her company has also implemented a major technology upgrade. Among other things, their new chip can check people for a condition that makes taking some drugs extremely dangerous. If you are G6PD deficient, and unwittingly take the malaria drug primaquine, you’ll have a horrible reaction that may include hemolytic anemia and death.

By checking your genetic makeup before taking a new medication, you might be able to avoid that sort of nasty situation. In other words, the new test could give you a lifesaving warning.

Predicting how someone will respond to a drug before they ever take it, just by looking at their genes, is called pharmacogenetics. It is a rather new field, and not ready for prime-time yet, but I have a feeling that services like the one offered by 23andMe will greatly accelerate its development.

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Prevailing Theory of Aging Challenged in Stanford Worm Study

Age may not be rust after all. Specific genetic instructions drive aging in worms, report researchers at the Stanford University School of Medicine. Their discovery contradicts the prevailing theory that aging is a buildup of tissue damage akin to rust, and implies science might eventually halt or even reverse the ravages of age.

“We were really surprised,” said Stuart Kim, PhD, professor of developmental biology and of genetics, who is the senior author of the research.

Kim’s lab examined the regulation of aging in C. elegans, a millimeter-long nematode worm whose simple body and small number of genes make it a useful tool for biologists. The worms age rapidly: their maximum life span is about two weeks.

Comparing young worms to old worms, Kim’s team discovered age-related shifts in levels of three transcription factors, the molecular switches that turn genes on and off. These shifts trigger genetic pathways that transform young worms into geezers. The findings will appear in the July 24 issue of the journal Cell.

The question of what causes aging has spawned competing schools of thought. One side says inborn genetic programs make organisms grow old. This theory has had trouble gaining traction because it implies that aging evolved, that natural selection pushed older organisms down a path of deterioration. However, natural selection works by favoring genes that help organisms produce lots of offspring. After reproduction ends, genes are beyond natural selection’s reach, so scientists argued that aging couldn’t be genetically programmed.

The alternate theory holds that aging is an inevitable consequence of accumulated wear and tear: Toxins, free-radical molecules, DNA-damaging radiation, disease and stress ravage the body to the point it can’t rebound. So far, this theory has dominated aging research.

But the Stanford team’s findings told a different story. “Our data just didn’t fit the current model of damage accumulation, and so we had to consider the alternative model of developmental drift,” Kim said.

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Craig Venter On The World’s Energy Future

Independent geneticist J. Craig Venter raced an international consortium of scientists to map the human genome in the 1990s. Now he’s putting the same cutting-edge science to work on today’s energy crisis, engineering a whole new generation of biofuels. In a rare in-depth interview, we talked to Venter recently about his latest project to save the world, as well as historical flubs, today’s presidential candidates and the future of genetics. —Chris Ladd

So how did you get from mapping the human genome to creating biofuels?
We considered the biggest issues facing society that we thought we could impact. What’s happening to the environment and getting weaned off oil and coal are the biggest issues out there.

Is it similar to the genome project? More daunting?
Nobody thought that such a massive project as sequencing the human genome could be undertaken by a single team, like we did. But that challenge is minor compared to trying to replace the 30 billion barrels of oil that we use globally each year, and the 3 billion tons of coal. The scale of that is beyond my imagination.

I think the real challenge won’t necessarily come from biology, because biology is infinitely scalable, but from engineering. [If we can overcome that,] we have the potential to stop using oil and coal hopefully within the next 10 to 20 years, and even start reducing the CO2 concentrations in the atmosphere.

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Craig Venter is a talented guy. I expect to hear more about him in the future.

How the Personal Genome Project Could Unlock the Mysteries of Life

George Church: sequencing 100,000 genomes

George Church is dyslexic, narcoleptic, and a vegan. He is married with one daughter, weighs about 210 pounds, and has worn a pioneer-style bushy beard for decades. He has elevated levels of creatine kinase in his blood, the consequence of a heart attack. He enjoys waterskiing, photography, rock climbing, and singing in his church choir. His mother’s maiden name is Strong. He was born on August 28, 1954.

If this all seems like too much information, well, blame Church himself. As the director of the Lipper Center for Computational Genetics at Harvard Medical School, he has a thing about openness, and this information (and plenty more, down to his signature) is posted online at arep.med.harvard.edu/gmc/pers.html. By putting it out there for everyone to see, Church isn’t just baiting identity thieves. He’s hoping to demonstrate that all this personal information — even though we consider it private and somehow sacred — is actually fairly meaningless, little more than trivia. “The average person shouldn’t be interested in this stuff,” he says. “It’s a philosophical exercise in what identity is and why we should care about that.”

As Church sees it, the only real utility to his personal information is as data that reflects his phenotype — his physical traits and characteristics. If your genome is the blueprint of your genetic potential written across 6 billion base pairs of DNA, your phenome is the resulting edifice, how you actually turn out after the environment has had its say, influencing which genes get expressed and which traits repressed. Imagine that we could collect complete sets of data — genotype and phenotype — for a whole population. You would very quickly begin to see meaningful and powerful correlations between particular genetic sequences and particular physical characteristics, from height and hair color to disease risk and personality.

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Scientists dig deeper into the genetics of schizophrenia

Researchers at Columbia University Medical Center have illuminated a window into how abnormalities in microRNAs, a family of molecules that regulate expression of numerous genes, may contribute to the behavioral and neuronal deficits associated with schizophrenia and possibly other brain disorders.

In the May 11 issue of Nature Genetics, Maria Karayiorgou, M.D., professor of psychiatry, and Joseph A. Gogos, M.D., Ph.D., associate professor of physiology and neuroscience at Columbia University Medical Center explain how they uncovered a previously unknown alteration in the production of microRNAs of a mouse modeled to have the same chromosome 22q11.2 deletions previously identified in humans with schizophrenia.

“We’ve known for some time that individuals with 22q11.2 microdeletions are at high risk of developing schizophrenia,” said Karayiorgou, who was instrumental in identifying deletions of 22q11.2 as a primary risk factor for schizophrenia in humans several years earlier. “By digging further into this chromosome, we have been able to see at the gene expression level that abnormalities in microRNAs can be linked to the behavioral and cognitive deficits associated with the disease.”

The investigators modeled mice to have the same genetic deletion as the one observed in some individuals with schizophrenia and examined what happens in the expression of over 30,000 genes in specific areas of the brain. When they discovered that the gene family of microRNAs was affected, they suspected that the Dgcr8 gene was responsible. The Dgcr8 gene is one of the 27 included in the 22q11.2 microdeletion and has a critical role in microRNA production, so this was a logical hypothesis. Indeed, when they produced a mouse deficient for the Dgcr8 gene, and tested it on a variety of cognitive, behavioral and neuroanatomical tests, they observed the same deficits often observed in people with schizophrenia.

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Gene glitches may hold secret of a long life

Gene glitches may hold secret of a long life

A series of rare genetic mutations that boost human lifespan have been discovered by a team of scientists studying centenarians and their elderly children.

The genetic glitches are thought to interfere with the normal growth of cells, halting the ageing process.

The discovery mirrors similar findings from studies on animals, which have shown that certain variations of genes linked to an insulin-like growth hormone can extend animals’ lives dramatically.

Dr Nir Barzilai, director of the Institute for Ageing Research at Albert Einstein College of Medicine in New York, found a series of mutations exclusively among centenarians which affect sensitivity to “insulin growth factor 1”, or IGF-1. This hormone influences the development of almost every cell in the body. It is crucial for children’s growth and continues contributing to tissue generation throughout adulthood.

Barzilai’s team discovered the genetic markers after scanning the genetic codes of 384 participants whose ages ranged from 95 to 110, with an average age of 100. They were compared with 312 controls, who came from families with a typical life span, none of whom had lived to 95.