Science Market Update

The Parkinson's Disease Biomarkers Program (PDBP) is a recently-formed NIH initiative to advance research into biomarkers for the disease in order to better understand its progress and develop treatments. Some funded projects will focus on statistical analysis tools and data sharing among researchers. Others will examine early clinical manifestations of PD in patients. Still more will involve lab studies, including identification of genetic biomarkers as well as antibodies in the blood and changes in body chemistry. All projects "must inform the etiology, pathogenesis or treatment of PD," according to grant program guidelines. Research supported by the PDBP is being carried out at the 11 Morris K. Udall Centers of Excellence in Parkinson's Disease Research (logo right), directed by the National Institute of Neurological Disorders and Stroke (NINDS) within the NIH.

An historic collaboration between the University of California Davis and China's BGI, the world’s largest genomics organization, has dramatically increased the University's genome sequencing capabilities and promises to open up altogether new research opportunities in the life sciences community with genomic studies of plants, animals, humans and microbes. The new joint endeavor is called BGI@UC Davis and will benefit both UCD and China's first citizen-managed, non-profit research institution. 

For both dairy and beef production, cows are an important part of the US economy and food supply. When they get sick, it's bad for business (and not too pleasant for the cow). The most common illness in cattle is Bovine Respiratory Disease (BRD), which accounts for losses of more than $690M annually in the US alone. To combat this threat to bovine health and productivity, the USDA has recently awarded a $9M 5-year grant to researchers at Texas A&M University's College of Veterinary Medicine and Biomedical Sciences, in collaboration with colleagues at the University of Missouri, to study genetic selection for breeding more disease-resitant stock. A second $5M grant will go towards research into feed efficiency, again with the aim of breeding heartier, healthier, and more profitable animals.

Oregon State researchers recently discovered DNA in a nematode, a type of roundworm, that may provide an insight into the mechanisms of human aging. The researchers found a specific portion of DNA within the mitochondria of the nematode which displayed the characteristics of "selfish" DNA, in other words, DNA which actually hurts the animal's chances of survival. Scientists have previously found instances of selfish DNA occurring in plants, but this is the first example found in an animal. “We weren’t even looking for this when we found it, and at first we thought it must be a laboratory error,” said Dee Denver, Oregon State associate professor of zoology (photo left courtesy of OSU). "Selfish DNA is not supposed to be found in animals."

A study by researchers at the Fred Hutchinson Cancer Research Center has revealed that a fast DNA sequencing technique called high-throughput sequencing (HTS) can greatly improve cancer relapse detection in patients.

We're finding out that there's a lot more to malnutrition among infants and children than just not getting enough to eat, or enough high-quality food. Individuals may develop malnutrition as a result of what is or isn't growing in their gut, where food gets processed. It's a fascinating insight with significant implications for treating a deadly world problem. In addition to getting sufficient good food, malnutrition could be addressed with novel dietary and microbial therapeutics, effectively optimizing a person's ability to draw nutrients and calories from the food and drink they take in, as well as making sure the immune system is being supported rather than compromised in the process.

The National Human Genome Research Institute (NHGRI) is a branch of the NIH, and they administer the ENCODE project, which stands for Encyclopedia of DNA Elements. Established in 2003, the goal of ENCODE is to create a comprehensive catalog of functional genomic elements. Towards that end, they have just awarded a further $10.5M in grants to 10 research institutions with investigators working in three main areas:

Discovery of Functional Elements

The 1000 Genomes Project is an international genomic research and data collection effort that has produced "a deep catalog of human genetic variation" for public research use. Now, thanks to Amazon Web Services (AWS) and the White House's recently-announced Big Data Research and Development Initiative, the 1000 Genomes data is available gratis on the AWS cloud.  In reality, there are over 1700 genome profiles in the demographically-diverse study, and all that data takes up about 200 terabytes of memory, according to a New York Times article on the cloud bonanza. So even though researchers could download the data free to their own computers from 1000 Genomes directly before, it's something you really don't want to do, even if you have that kind of memory (re: 200TB).  Instead, you'll likely be better off accessing the data through AMS and paying them to crunch numbers for you, which probably explains why AWS has decided to engage in this bit of philanthropy.  Future profit, plus their preeminence as a computational resource in the brave new world of Big Data.

Last year in a blog of ours on the future of genome sequencing we referenced a July appeals court ruling that protected Utah's Myriad Genetics' patent on two genes known to be indicators of breast cancer risk.  Now, in a recent Supreme Court ruling on that same case, the previous ruling has been overturned and the case returned to the lower court for rehearing.  This decision follows another important high court ruling on the patentability of genes: Mayo vs. Prometheus Labs (San Diego), which also just ruled against a company's right to hold patents on human genes, and which was quoted as a precedent in the latest Myriad judgement.

Science researchers at Washington University School of Medicine in St. Louis are offering to sequence the DNA of 99 patients with rare genetic diseases in order to find the genetic alterations that made them ill. The new effort, known as the Rare99X Clinical Exome Challenge, will allow patients’ DNA to be decoded at the university’s Genomics and Pathology Services (GPS) at no cost to the patients or advocacy groups who represent them.