In an upswing for scientists studying embryonic stem cells, a federal appeals court announced today that it would set aside a ruling from a lower court last August barring federal funds for the research. As I noted in a story last year, the surprise ruling threw the field into a state of uncertainty--few had even known about the lawsuit, brought by two scientists studying adult stem cells—and brought grant reviews at the nation's largest funding agency, the National Institutes of Health (NIH), to a halt.

According to an article from ABC news on the latest ruling,

The court found that the law--the Dickey-Wicker Amendment enacted in 1996--is "ambiguous" and that the NIH has "reasonably concluded" that while the law bans federal funding for the destructive act of deriving cells from an embryo "it does not prohibit funding a research project in which an hESC will be used."

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"Today's ruling is a victory for our scientists and patients around the world who stand to benefit from the groundbreaking medical research they're pursuing," said Nick Papas, a spokesman for the White House.

...Sam Casey, an attorney representing Sherley and Deisher said he was "disappointed but not surprised" by the ruling. He says he is considering whether to appeal the decision to the full court.

"This is a victory not only for the scientists, but for the patients who are waiting for treatments and cures for terrible diseases," said Arnold Kriegstein, director of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, in a statement from the university. "This ruling allows critical research to move forward, enabling scientists to compare human embryonic stem cells to other forms of stem cells, such as the cell lines which are derived from skin cells, and to pursue potentially life-saving therapies based on that research." Kriegstein was one of two University of California scientists to file a Declaration in September 2010 in support of the UC Board of Regents' motion to intervene in the August lawsuit, Sherley v. Sebelius.

The ruling is a victory for the Obama Administration. Soon after becoming president, Obama had signed an executive order ending a restrictive policy enacted in 2001 by President Bush that had blocked federal funds from being used to study most human embryonic stem cells.

If the federal government does shut down this weekend, clinical trials will stop enrolling new patients and researchers at the National Institutes of Health (NIH) will have to put their studies on hold. Internal research at the agency involves thousands of scientists and hundreds of lab and animal facilities and consumes about ten percent of the NIH's $31 billion budget. Whether the involuntary hiatus will prove to be an inconvenient blip or a serious impediment to clinical research will depend on just how long the standstill lasts. Federally funded scientists working outside of NIH are unlikely to be greatly affected by a short shutdown.

But patients with fast-progressing diseases, such as some types of cancer, who had hoped to enter new clinical trials don't have says to spare. According to a blog from ABC news, there are currently seven new procedures scheduled to start next week at the NIH Clinical Center that will not begin if the government shuts down over the weekend.

Ongoing studies at the NIH Clinical Center will not admit new patients, according to John Burklow, associate Director for Communications and Public Liaison at NIH, which "will delay the completion of all studies currently active at the Clinical Center."

Burklow says there are approximately 640 clinical trials (and 1,443 variations, or protocols, within those clinical trials) at the Clinical Center that will stop admissions of new patients.

Of the 640 clinical trials that will stop admitting new patients 285 are for patients with cancer and 60 involve children with cancer.

One new patient -- a child from a poor family with a rare disease -- was supposed to visit NIH on Monday to be added to a clinical trial, and had made special arrangements including traveling to NIH on a Miles for Kids program on Sunday. But none of this will happen if there's a shutdown: no new patients, after all.

NIH is quietly preparing for the shutdown by designating employees who will be allowed to come to the facility to care for animals or protect ongoing research, such as tissue cultures, from damage.

According to an article on ScienceNow;

NIH Deputy Director for Intramural Research Michael Gottesman e-mailed ScienceInsider yesterday that each of NIH's 27 institutes and centers is identifying people who would be "excepted" from the shutdown. That includes clinical staff; fire, security, and animal care personnel; and a few employees "who are protecting research investments."

But the details are sketchy. Any public discussion of the contingency plans is forbidden "for political reasons," says one high-level official, explaining that the government can't look like it's preparing for a shutdown. Even internal e-mails are now verboten, this source said; instead, planning has been done the old-fashioned way, by word of mouth.

That said, "there seems to be a coherent plan," a lab chief said. A few months ago, PIs submitted lists of essential personnel, including most physicians, animal caretakers, and others who will maintain experiments or cell lines that can't be shut down. The numbers ScienceInsider heard ranged from 50% of a group that does nonprimate work and clinical trials to just 10% of one institute's entire intramural program. But there's no word whether those lists have been approved.

The uncertainty is stressful, says one PI, who was allowed to designate only himself and one other lab member to maintain lab animals and cell cultures for a pause of indefinite length. "A great deal of treasure will be lost if this shutdown happens" because experiments may be damaged, he predicted.

It's been ten years since Science and Nature, the two most prestigious science journals in the world, published the first detailed look at the sequence of the human genome. Both journals are commemorating the event with special sections looking back at the progress the field has made over the last decade and the hurdles that still remain.(Check out our January issue for TR's take on the genome ten years later, our understanding of inheritance, and the implications for cancer .)

A series of short essays in Science, authored by Francis Collins, who oversaw the Human Genome Project and now runs the National Institutes of Health, Desmond Tutu, archbishop emeritus of South Africa, and many others, explore the facets of the genome.

Collins describes one of the field's successes: the case of a 6-year-old Wisconsin boy who had suffered for years with a severe form of inflammatory bowel disease.

Despite numerous tests and more than 100 surgeries, doctors remained at loss for a diagnosis and the little boy grew sicker. Then, researchers at the Medical College of Wisconsin carried out whole-exome sequencing, examining the protein-coding regions of every gene in Nic's genome. They identified a mutation in his XIAP gene. XIAP mutations were not previously associated with bowel symptoms, but had been linked to a severe blood disorder that is curable through bone marrow transplantation. The medical team raised the possibility of a transplant, which would not have been considered without a firm diagnosis. It was performed in July 2010, using stem cells from the cord blood of a matched, healthy donor. Seven months later, Nic appears to be on the road to recovery. While he is still on immunosuppressants, doctors report the new stem cells are stably engrafted, blood counts are good, and there's been no return of bowel disease (http://journals.lww.com/geneticsinmedicine/Documents/GIM200819_Revised.pdf). More important to Nic, he can finally eat solid foods!

Craig Venter, a genomics pioneer who ran the private arm of the genome race, outlines a major missing chunk of information that is necessary to interpret the meaning of the genome.

Among the many improvements that are needed in human genome research, the most important is the collection of human phenotypes (according to agreed-upon parameters and standards), in conjunction with tens of thousands of accurate human genome sequences. Such data sets will be the foundation for accurately predicting clinical outcomes from DNA sequence information. This is true not only for diagnosis but also in foreseeing and avoiding drug side effects, as well as monitoring stem cell genome mutations and/or variations before cell therapies.

Desmond Tutu, who had his genome sequenced as part of a study of human genetic diversity, writes about how important it is to understand the genomes of all the world's peoples.

As a nation, however, we need to continue to fight against racial inequalities and socioeconomic disparities on a daily basis. My participation in the Southern African Genome Project was a step in this direction, generating the first Southern African Genome to be sequenced—exactly 9 years after the publication of the human genomes.

My reasoning was simple. Southern Africans are victims of many devastating diseases whose eradication requires immediate attention and international resources. My hope is that my genetic code may provide a voice for the region and serve as the starting point for a map of DNA variation significant for Southern African peoples, to be used for medical research efforts and effective design of medicines. I implore the scientific community to continue what I hope was just a first step to further medical research within the region.

Kari Stefansson, chief executive officer of DeCode Genetics, a leader in the study of genomics and disease, points out that what we call a complete genome is not truly complete.

However, still today, we do not have "the complete sequence" of the reference human genome as parts (such as the centromeres or regions of copy number variation) are still incomplete. The suboptimal quality of the reference sequence is one of the limiting factors in the work of those who are using whole-genome sequencing to understand human biology. Hence, this is an anniversary of a moment in the history of our quest for an instrument (the reference sequence) to use in better understanding ourselves.

Eric Schadt, chief scientific officer of Pacific Biosciences of California, one of several companies racing to develop cheaper and faster sequencing technology, describes how complex the genome has revealed itself to be.

We have learned that the human genome is much more dynamic than previously thought. Elucidating its complexity will require a more systems-level approach, including comprehensive integration with other data dimensions, such as RNA, metabolite, protein, and clinical data. For me, although this past decade has exposed many amazing aspects of the genome, it has revealed the existence of a world about which we know very little. We will have to become masters of information if we ever hope to go from the big data sets coming to dominate biology to knowledge and to understanding.

On Thursday, Nature will feature a piece by Eric Green, current director of the National Human Genome Research Institute, outlining the institute's vision for the next ten to 20 years. Check back Thursday for a Q&A with Green.