A team of scientists at the Oregon National Primate Research Center and the Oregon Health & Science University are reporting a remarkable advance in the treatment of inherited genetic disease in the journal Nature.

They show it is possible to repair a tiny part of a human egg cell that, when broken, causes a host of awful inherited genetic diseases.  Those diseases cause disability and the death for many children and adults.  What is equally remarkable is that the treatment they report is illegal in Britain, Germany, Costa Rica, Norway and Sweden and would be illegal to provide using federal dollars in the United States.

What did the Oregon scientists do?  And why is it so ethically controversial?

Mitochondria are the batteries of human cells.  They convert oxygen and nutrients into a chemical that is the source of the energy that allows chromosomes to move and recombine and, once a sperm arrives, a fertilized embryo to grow.  Every cell in your body has mitochondria inherited from your mother’s egg.  When these little cellular engines have a genetic problem,  it can make for terrible diseases in any child that inherits them. 

About 4,000 U.S. children are born each year with mitochondrial diseases.  They may become blind,  paralyzed or suffer severe cognitive impairment.

The Oregon team showed that they could fix the problem of damaged mitochondria in an egg cell by transplanting the DNA in the nucleus of eggs with diseased mitochondria into eggs with healthy mitochondria that had the nucleus removed.  They did this both in monkeys and humans.  A child born as a result of this genetic transplant—referred to as a spindle transfer-- would be the genetic offspring of two mothers.

The child would have healthy mitochondrial DNA from the egg of a donor mom. He or she would also have DNA from the mom with the mitochondria problem. 

This is amazing genetic engineering.  Gene transfer in human eggs has and will provoke a lot of controversy.

When the Oregon team did their studies they proved the transplanted genes would work in a human egg by making them into viable embryos.  Those embryos were studied in various ways to prove they were normal -- and then destroyed.  There is no other way to prove that transplanting genes between eggs could someday cure children of terrible diseases without the kind of experiment the Oregon group did.

While monkeys have been used in the past, this is the first paper reporting success in the genetic engineering of human eggs.

But to go forward, more such experiments will need to be done to ensure the safety of the technique.  Currently there is a ban in the U.S. on doing this kind of research with federal funds. Federal law forbids using federal taxpayer dollars to pay for any research involving the destruction of a human embryo.

This experiment also crosses a bright ethical line. Changing genes in the lungs of people with cystic fibrosis or in the eyes of people with retinitis pigmentosa or macular degeneration may fix the broken body part, but the change is not passed on to future generations.

When you change genes in an egg, even in the mitochondria of an egg, you make a change that is inherited by every single offspring of any child created from that egg.  That is called germline engineering -- meaning changing inherited genetic material.

And germline engineering of mitochondria crosses the line from using genetic engineering to fix our body parts into directly engineering the traits of our children.  It is a road that could lead, in the distant future, toward eugenics.

So should we celebrate or condemn this first step into reproductive cell or germline genetic engineering?

I think the price of experimenting on embryos to find a solution to disease, while high, is morally acceptable.  Creating embryos in the future by means of a mitochondrial transplant that will not be used to make babies on a limited basis seems to appropriately value children and adults over possible children and adults.

And while I, too, worry about where genetically engineering eggs might lead, I think doing so to find cures is ethically noble.  Those nations that say no to any form of germline engineering, including the U.S., should revisit those policies to permit research that is clearly intended as therapy.

The brave new world has now appeared in print.  We need to be brave enough to avail ourselves of the good it can bring.

Arthur Caplan is the head of the Division of Medical Ethics at NYU Langone Medical Center.

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A new technology can diagnose rare genetic disorders in critically ill newborns within a few days, rather than the weeks that are needed with current methods, researchers say. It involves sequencing the infant's genome, then using new software to identify the genes most likely to be disease culprits.

In a new study, researchers identified the genetic cause of a newborn's illness in three out of four babies tested. The whole process takes about 50 hours, they said.

The speed of the new test is what could make it useful for sick babies in neonatal intensive care units (NICUs), the researchers reported in the journal Science Translational Medicine. Currently, it can take weeks for doctors to diagnose a genetic disorder in an ill infant, and many babies die before their test results are available, said study researcher Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospital in Kansas City.

A faster diagnosis for genetic conditions would allow doctors to provide earlier treatments — if there are any — or to give parents an earlier warning, and potentially more time together with their child if the condition is untreatable and fatal, the researchers say.

Doctors already routinely screen newborns for a few genetic disorders that have effective treatments. But these tests look for single genes, rather than at the entire genome. About 3,500 diseases are known to be caused by mutations in a single gene.

"By obtaining an interpreted genome in about two days, physicians can make practical use of diagnostic results to tailor treatments to individual infants and children," Kingsmore said. As many as a third of babies admitted to a neonatal intensive care unit in the United States have some form of genetic disease. While treatments are currently available for more than 500 diseases, identifying them quickly has been a problem. 

However, critics point out that the diseases identified by new technology are rare, and extra genetic information is not always helpful. In fact, some are worried the genetic testing could deliver more information than researchers know what to do with.

Diagnosing genetic diseases

To begin a diagnosis with the new technology, the researchers take a drop of the baby's blood so that his or her genome can be sequenced. Next, a physician enters the patient's symptoms into a software program. The program scans the newborn's genome looking for genes that are likely to cause such symptoms.

The program identifies only diseases that are caused by a single genetic mutation. The researchers tested their program on 500 cases of children who had already been diagnosed, and found it was more than 99 percent accurate in finding the correct gene mutation that was causing the patient's symptoms.

The researchers also tested the technology on four NICU babies who had not yet been diagnosed with a condition. In one case, the researchers quickly identified a gene that causes epilepsy. Because the gene has been reported in only a few people in the world, "it would never have been on any physician’s radar," said Carol Saunders, director of the molecular genetics laboratory at Children's Mercy.

No treatments were available to help the child, and the child died. However, the parents can now undergo genetic testing to determine how likely it is they will have another child with the disease.

In a second newborn, the researchers found a new gene they believe causes heterotaxy, a condition in which some of the internal organs are on the wrong side of the body.

The testing is not always perfect. In the case of one newborn who died, the researchers were not able to identify the cause of death. They hope their testing will improve as they gather more information to add to the program.

The researchers tested two software programs developed at Children's Mercy, used in conjunction with a high-speed gene sequencer from Illumina called HiSeq 2500, which can sequence an entire genome in about 25 hours. The company helped pay for the study and company researchers took part in it. 

Criticism

While the new technology gives physicians another diagnostic tool, current newborn screening tests reveal most of the cases in which children would benefit from early treatment, said Dr. Jennifer Kwon, an associate professor of neurology and pediatrics at the University of Rochester Medical Center.

"I don't know that we're going to find as many cases where the rapid diagnoses lead to changes in management and treatment as the authors suggest,"  Kwon said.

"In addition, some of these diseases are so rare that we still do not understand the effects of a particular mutation or combination of mutations.  A certain mutation may be seen in a very sick child and the same mutation may be seen in a child who is doing relatively well," Kwon added.

Kwon pointed to a genetic condition called Krabbe disease, for which all newborns born in New York are routinely screened. Although fatal in some, the disease can be treated with a bone marrow transplant.  In the six years that the testing has been done, the state has seen five cases of children who would benefit from the bone marrow transplant, and 30 children who have the mutation and don't appear to be ill.

Kwon said she does not know whether these children will become ill at some point, and cannot tell parents what to expect. The new technology could create a large-scale version of this anxious situation, Kwon said.

The study is published today (Oct. 3) in the journal Science Translational Medicine.

Pass it on: A new technology can quickly identify rare genetic diseases in critically ill newborns.

Reuters contributed to this story.

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University of Washington

Dr. John A. Stamatoyannopolous, associate professor of genome sciences, in his lab. Stamatoyannopolous worked on the giant ENCODE project that is re-defining human biology.

In what many scientists say is a revolution in biology, a giant new project is rewriting our understanding not only of what causes diseases or what makes our eyes a certain color, but what makes us human. And it turns out scientists have been looking in the wrong place for a very long time.

The bounty of new discoveries, released in a batch of 40 research papers on Wednesday, shows the stretches of DNA that we call genes are only a very small piece of what makes the body work. Much more important is the stuff in between the genes – stuff once dismissed as “junk DNA”. It turns out that junk DNA is what is in control, they report in the series of papers in the journals Nature, Science and elsewhere.

“This has opened up whole new galaxies. It’s like having a bigger telescope,” says Dr. Bruce Stillman, president of Cold Spring Harbor Laboratory, which played a major role in the work. 

Scientists already knew in 2003, as they finished the giant Human Genome Project, that they did not have the understanding they had hoped for.  It turned out that humans had just a measly 22,000 genes – fewer than some animals and far fewer even than a plant such as rice. How could something as complex and advanced as a human be boiled down into something so simple?

“We understood precious little about the processes that turns genes on and off. In short we had more questions than answers about how the human genome works,” said Dr. Eric Green, director of the National Human Genome Research Institute, which conducted the study.

The next phase of work, called ENCODE for Encyclopedia of DNA Elements, shows there’s nothing simple about it. As many as 40 million different switches are controlling these genes, turning them on and off in complex and subtle ways.

“The genome is loaded with gene controlling switches. There are literally millions of these,” Dr. John Stamatoyannopoulos of the University of Washington, who worked on the studies, told reporters in a telephone briefing.

Dr. Francis Collins, director of the National Institutes of Health, calls the findings “awesome and elegant.”

“This is the first truly comprehensive view, of how the three billion letter instruction book for human biology actually carries out its work, across many tissues and over the course of development,” he told NBC News in an interview.

Stanford University genomic expert Michael Snyder says it looks like gene mutations -- the changes in DNA sequences that we associate with causing diseases -- may only affect rare diseases. Common diseases, like heart disease, cancer, and allergy, are probably controlled elsewhere. “We think that most of the changes that affect disease don’t lie in the genes themselves, but the switches,” Snyder says.

So treating these common diseases may lie in trying to affect the switches. “The pharmaceutical industry has largely given up on genomics and the genome in favor of older approaches,” said Stamatoyannopoulos. These new findings may reinvigorate new drug research, he said. “Now we have a huge amount of genetic data about human disease that we can actually put to work to find the right kind of genes and proteins to target,” he said.

This new data will also help doctors diagnose disease in the first place, predict which treatments will work best for patients, and monitor their progress. It  points the way to studies to determine the causes of hundreds of diseases including  all kinds of cancer, Alzheimer’s disease, schizophrenia, heart disease, type 1 and type 2 diabetes, lupus, rheumatoid arthritis and asthma.  It also may lead to a better understanding of how our genetics determine such non-disease factors as height, weight and expected life span.

Not only that, it also can help explain why humans and chimpanzees share 98 percent or more of our genes, yet are so different.

"Genes occupy only a tiny fraction of the genome, and most efforts to map the genetic causes of disease were frustrated by signals that pointed away from genes. Now we know that these efforts were not in vain, and that the signals were in fact pointing to the genome's 'operating system' -- the instructions for which are hidden in millions of locations around the genome," said Stamatoyannopoulos. "The findings provide a new lens through which to view the role of genetics and genome function in disease."

Another surprising finding was that the regulatory circuitry blueprints could be used to pinpoint cell types that play a role in specific diseases -- without requiring any prior knowledge about how the disease worked. For example, DNA changes associated with Crohn's disease (a common type of inflammatory bowel disease) are concentrated in the switches controlling two types of immune cells.

Researchers can use this same method to identify cell types not previously known to play a role in a particular disease, expanding our understanding of the disease process and potentially leading to new therapies.

"We now have a parts list of what makes us human," says Mark Gerstein of Yale university, who worked on the project. "What we are doing is figuring out the wiring diagram of how it all works."

The findings rewrite biology 101 for most of us.  Each gene, we were taught, provided the code for a single protein. The proteins were the building blocks of cells, and the products made by the cells, from compounds called growth factors to signal-carrying chemicals. An intermediary genetic structure called RNA carried this information. ENCODE shows this is not quite so straightforward, that RNA generates the 40 million switches that can affect how and when many things happen within the cells.

“This is another grand chapter in the ongoing and historic research story that is unraveling the details about how life works, and how disease occurs,” Collins said.

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Gary Garner, 32, of Great Falls, Mont., and his son, Skyler, 14. Garner used an Identigene drugstore paternity test kit to confirm that he's really Skyler's dad.

The company that made its name peddling drugstore paternity tests to uncertain spouses and skeptical kin now says that more than 1 in 10 adults in the U.S. has had reason to ask the question: Who’s your Daddy?

Twelve percent of men and 10 percent of women say they personally have been in a situation where paternity testing was "appropriate," according to a recent survey of 1,039 people conducted for Identigene, the Utah firm that markets direct-to-consumer DNA tests.

In addition, nearly 1 in 5 of those randomly surveyed said they have family members or close friends who’ve questioned paternity.

“There are a lot of situations where you can envision needing a paternity test,” said Steven Smith, president of Identigene, which has sold more than half a million kits for $29.99 a pop since 2008. “Somebody’s going through a divorce, child custody. Those things do come up.”

The survey, conducted late last year by the Los Angeles firm Impulse Research, is renewing debate about the touchy subject of confirming whether a child’s reported father is the real thing.

Smith said it proves there’s an unmet need for cheap, simple tests to solve crucial genetic questions.

But scientists who’ve studied what they call “misidentified paternity” say the actual proportion of faux fathers is much lower than the new survey would seem to indicate.

The population-based rate is probably closer to between 1 percent and 4 percent in western countries, with U.S. rates hovering between 2 percent and 4 percent, twice as high as Europe, said Michael Gilding, a professor of sociology at the Swinburne Institute for Social Research in Melbourne, Australia. He has spent years researching the issue.

“It is higher in the U.S. because there are more exnuptial births, less informal cohabitation and more divorce,” he wrote in an e-mail to msnbc.com.

(In other words, the U.S. has more babies born outside marriage and more couples living together.)

Whatever the actual rate, those who’ve used the tests say the results can be life-changing.

For 14 years, Gary Garner of Great Falls, Mont., has questioned his relationship with his wife’s oldest son, Skyler. He always believed he was the boy’s father, but another man’s name was on the birth certificate. Garner admits he and his wife, Rhonda, 33, have had a rocky history. They've been married to each other three separate times and once each to other people. The pair have three other children together, in addition to Garner's child with another woman. But the issue of Skyler’s paternity was always in question -- until Garner finally decided to buy an Identigene kit at a local Walgreens store late last year.

“Anywhere else, a DNA test is $2,500,” Garner said.

On Jan. 4, he took a swab of cells from his cheek and from Skyler’s cheek and sent both samples to the lab run by Sorenson Genomics of Salt Lake City for analysis. For the price of the drugstore kit plus a $129 lab fee, Garner had an answer within days.

“I saw they had the results and I didn’t even want to open up the e-mail,” said Garner, a heating and air conditioning technician.

“When I did, I was like, ‘YES!,’ I felt like I won the most epic battle known to man.”

The tests verify paternity with 100 percent accuracy, according to material on the Identigene site. Garner said telephone counselors told him it was “99.9 percent” accurate and that he couldn’t be excluded as Skyler’s dad.

Overall, nearly two-thirds of the paternity tests Identigene performs come back positive, company officials said. That rate is naturally higher than the population-based rate because those who take the tests are a select group with a reason to wonder about paternity.

It’s taken a while for the news to sink in for Garner -- and for his son.

“Both of us are hurt through this whole thing,” Garner said, adding that he’s planning a father-son trip to an arcade to celebrate the confirmation of what he always believed in his heart.

“Everybody’s just glad that we know now,” he said. 

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The claim by Ion Torrent on Tuesday that a reasonably affordable machine capable of mapping an individual’s complete genetic makeup for $1,000 will be ready by the end of the year has technology geeks in a tizzy.

The $1,000 genome has been hotly sought ever since a crude map of the human genome was first published in 2001. The Carlsbad, Calif. biotech company, part of Life Technologies, will sell its device to research labs and medical clinics for $99,000 to $149,000, compared to the current price of about $750,000 for existing sequencers, Reuters reported on its website Tuesday. According to Reuters, a doctor will be able to sequence a patient’s entire genome for $1,000, compared to the current rate of $3,000 just to test for breast cancer gene mutations, for example. And the company says its new machine can complete the genome analysis within a day, rather than the two months previously needed.

It's widely believed this type of genetic analysis will revolutionize medicine, that patients will learn their risk profile for potential diseases by having their DNA read right in the doctor's office. Drugs and vaccines will be designed to fit our genes, in order to maximize efficacy and minimize any side-effects. Newborn babies would have someone peek at their genes so parents could take steps to prevent genetic risks from becoming realities.

Sounds good. The company sure hopes Wall Street buys it.  And so do a lot of people hoping to sell you genetic tests. But I am not convinced.

We still don’t know all the significance of small variations in genes for health. Nor do we have studies of genetic risk factors involving large numbers of people or across a broad spectrum of racial and ethnic groups. Without that information, personalizing treatment to fit your genome is more a marketing slogan than meaningful medicine.

Besides, who is going to explain your test results?  Your doctor may have had only a couple of classes on genetics in medical school. There aren’t enough genetic counselors to meet even current demand.  And pharmacists are only now starting to be educated about the relationship between genes and drugs.

The biggest downer for those dreaming of all the good to come from cheap genetic testing may be simple human nature. It’s not clear that the average person will do anything about a known risk. As it is, about one-third of Americans are so obese they face high risks of chronic health problems such as diabetes and heart disease.

Will genetic information be any more motivating to get people to lose weight, stop smoking, reduce their stress, stay active, wear a seatbelt or a condom, than stepping on a scale or coping with a smokers’ hack?

Two cheers to scientists and businessmen for reaching the $1,000 genome. But, only two cheers.  There is a long way to go before the achievement gets translated into bottom line health results that we can put to practical use.

Art Caplan, Ph.D., is the director for the Center for Bioethics at the University of Pennsylvania.  Follow him on Twitter @ArthurCaplan.

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