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A storage robot deposits samples in the world’s largest blood and urine freezer at Biobank in Manchester, England.

 

 

A global coalition of health experts, including Dr. Francis Collins of the NIH, plan for a genetic future, with the help of robots

 

The New York Times, June 5, 2013, by Gina Kolata  —  More than 70 medical, research and advocacy organizations active in 41 countries and including the National Institutes of Health announced Wednesday that they have agreed to create an organized way to share genetic and clinical information. Their aim is to put the vast and growing trove of data on genetic variations and health into databases — with the consent of the study subjects — that would be open to researchers and doctors all over the world, not just to those who created them.

Millions more people are expected to get their genes decoded in coming years, and the fear is that this avalanche of genetic and clinical data about people and how they respond to treatments will be hopelessly fragmented and impede the advance of medical science. This ambitious effort hopes to standardize the data and make them widely available.

“We are strong supporters of this global alliance,” said Dr. Francis Collins, director of the National Institutes of Health. “There is lots of momentum now, and we really do want to move quickly.”

In just the past few years, the price of determining the sequence of genetic letters that make up human DNA has dropped a million fold, Dr. David Altshuler, deputy director and chief academic officer at the Broad Institute of Harvard and M.I.T., explained. As a result, instead of having access to just a few human genomes — the complete genetic material of a person, including genes and regions that control genes — researchers can now study tens of thousands of them, along with clinical data on peoples’ health and how they fared on various treatments. In the next few years, Dr. Altshuler said, researchers expect that millions of people will have their genomes sequenced.

“The question is whether and how we make it possible to learn from these data as they grow, in a manner that respects the autonomy and privacy choices of each participant,” Dr. Altshuler said. No one wants to put DNA sequences and clinical data on the Internet without the permission of patients, he said, so it also is important to allow people to decide if they want their data — with no names or obvious identifiers attached — to be available to researchers.

But there are no agreed-upon standards for representing genetic data or sharing them, experts say. And there are no common procedures for assuring that patients consent to sharing their information.

“Each institution has its own approach,” Dr. Altshuler said.

In cancer research, for example, medical centers test cancer cells to find gene mutations. The goal of these research tests is to help diagnose and identify treatments that might help individual patients. But there are no common methods for doing these tests or analyzing the data and each research group keeps its data to itself, said Dr. Charles L. Sawyers, chairman of the human oncology and pathogenesis program at Memorial Sloan-Kettering Cancer Center. As a result, the centers often have too little experience with a particular mutation to know what it really means. A person might be told at one cancer center that a new treatment would help and at another that it would not.

“That’s scary,” said Dr. Sawyers, who is also president of the American Association for Cancer Research, a nonprofit scientific organization.

Medical researchers say the best way forward is to have shared databases. Do patients with a particular genetic aberration tend to do well with a particular therapy? Do patients with another mutation have greater odds of developing cancer?

Dr. Collins noted that cancers are so genetically complex that, most of the time, a mutation seen in a cancer patient will be uncommon. To figure out its significance, data from hundreds of thousands of patients — the world’s collected data — on that mutation are needed.

“You need large data sets,” Dr. Collins said. “You need very large numbers of patients.”

Pooled data are also needed to understand gene mutations that lead to rare diseases in children, Dr. Altshuler said. A disease might occur in one in 1,000 or one in 10,000 or one in 100,000 babies, he said. A medical center might never see a child with that disease, or might see just one.

“Since everyone sees zero or one, no one ever learns,” Dr. Altshuler said.

Brad Margus, an advocate for children with rare diseases, enthusiastically supports the idea of data sharing. As the father of two sons with a rare disease, ataxia telangiectasia, or A-T, and founder and volunteer president of the A-T Children’s Project, he says he learned how progress is made.

“There is this perception that the key to the next breakthrough is from someone finding a gene that is sitting somewhere and someone having a eureka moment,” Mr. Margus said. “What I learned is that it does not usually happen that way.” Often what is needed are huge genetic data sets, he added, “so people can be proactive when they have an idea.”

Pooled data are also needed to understand the genesis of big killers like heart disease, researchers said.

Recently, for example, Dr. Sekar Kathiresan, director of preventive cardiology at Massachusetts General Hospital and a geneticist at the Broad Institute, sought to find out whether high density lipoprotein, or H.D.L., the so-called good cholesterol, actually protected people against heart disease. Did people who happened to have genetic changes that resulted in lifelong high levels of HDL have a lower risk, he asked?

They did not, he concluded, but his study required genetic data from more than 100,000 people collected in 20 studies by researchers from around the world. It took three years to gather the data, put them in a form that allowed investigators to analyze them, and to do the analysis.

“We need standard formats so we don’t have to spend two years figuring out how to merge data together,” Dr. Collins said.

Over the past couple of years, genetics researchers puzzled over the data-sharing problem, seeing it as a key to making progress. On Jan. 28, 50 leading researchers from eight countries met and agreed on the need for a global alliance. The group, which included ethicists and disease advocates, stressed that because individual study subjects had to be able to decide whether to share their genetic and clinical information, the system for data sharing had to include ways to track and manage these permissions.

The group wrote a white paper and a letter of intent that has now been endorsed by an ever-growing international group.

“For us, this is a gratifying development,” Dr. Collins said.

 

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Source: University of Buffalo

 

 

SingularityHub.com, June 5, 2013, by Peter Murray  —  Only about two percent of the human genome contains genes. The other 98 percent has been likened to cosmology’s dark matter that fills the space between stars – there’s a lot of it, but nobody really knows what it does. Over the years scientists have put faith into the logic of evolution: if it’s there, it must serve a purpose. But a recent study shows that not all genomes are created equally. Unlike human genomes, the carnivorous bladderwort’s genome makes the most of its allotted bases having only an estimated 2 percent of non-coding DNA, or so-called “junk” DNA.

 

The genome of the carnivorous bladderwort plant (Utricularia gibba) is minuscule compared to the human genome – 82,000 bases versus our near 3 billion. But while it’s small, the genome is extremely efficient. About 97 percent of its genome codes for an estimated 28,500 genes and the short sequences that control those genes. The authors of a study mapping the bladderwort genome surmise that, through many generations, the non-coding portion of the carnivorous bladderwort’s genome has been systematically removed, resulting in just 3 percent of non-coding DNA.

Non-coding DNA is DNA that does not code for proteins, the structural building blocks of the body. Their stretches of non-protein coding DNA contains the all important regulatory sequences that control when and where genes are turned on and off, areas that produce non-coding RNA, the function of which largely remains a mystery, and introns, those good-for-nothing wastes of space. But while it’s not clear what purpose the non-protein coding regions of the genome serve, they’ve generally been assumed to have some useful function – evolution is driven by the selection for survival, how could it make junk?

The current study, conducted by the Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) in Mexico and the University of Buffalo, however, reaches a different conclusion.

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The bladderwort’s near absence of non-coding DNA doesn’t necessarily make our non-coding DNA junk. The two species may have evolved different genomic strategies. [Source: Wikipedia]

“The big story is that only 3 percent of the bladderwort’s genetic material is so-called ‘junk’ DNA,” Victor Albert, professor of biological sciences at the University of Buffalo, said in a press release. “Somehow, this plant has purged most of what makes up plant genomes. What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed.”
The human genome also went through a phase of simplification – in 2004 when it was shown to have about 20,000 to 25,000 fewer genes than scientists originally thought it should have. Still, at about 40,000 times the size of the bladderwort genome, it’s vastly more complex.

Which is why we shouldn’t automatically assume our genome works the same way.

Human physiology is much more intricate than that of the bladderwort. With all its different organs and cell types and the unique functions they serve, it would be shortsighted to conclude that the trimming which resulted in the bladderwort’s genome is a general evolutionary rule. That is, if the human genome were to trip the non-coding fat, it would still give us the diverse physiology our bodies require.

Counter to this idea are recent studies put forth by the ENCODE, a National Human Genome Research Institute project that seeks to identify all the functional elements of the human genome recently published a series of studies that send a clear message: it ain’t junk. The studies reach the collective conclusion that 80 percent of the genome actually does have important function – they don’t code for genes, but rather, affect the different biochemical processes that occur in cells.

 

The bladderwort is interesting, not only for its highly efficient genome, but all carnivorous plants are, by definition, awesome. The aquatic plant is found on all continents except Antarctica. Its water-filled bladders act as traps, sucking in small insects unlucky enough to contact the bladder and trigger it. And while the meat-eating green has done away with its non-coding DNA, one species’ junk could be another’s treasure. Projects like ENCODE that explore the genomes’ dark matter will bring its function – or lack thereof – to light. Genomic divergence of the two species could be a true mark of different evolutionary paths such that an almost entirely coding genome might reveal something about, not only our very non-coding genome, but the fundamentals that underly the evolution of all life.