Canadian-based GPU maker Tycrid Platform Technologies has just announced the launch of the
Chris Heier, President of Tycrid Platform Technologies, stated in a release that "Alliance is being established to address a specific challenge that continues to impede the progress of scientific discovery – the lack of scalable, purpose-built appliances. I feel this is critical as we can virtually eliminate the need for scientists to become computer scientists. Our goal is to take a fresh, innovative approach to developing HPC solutions that do one thing really well – address specific computational challenges for bioinformatics.”
The team sequenced protein tyrosine kinase or PTK genes in 29 individuals with melanoma. Their search uncovered dozens of somatic mutations affecting the kinase domain of 19 different PTK genes. When they looked at the same 19 genes in another 79 melanoma patients, the researchers found that almost a fifth of those tested harbored mutations in ERBB4.
And, they reported, knocking down the mutated form of ERBB4 or using a drug that targeted the gene slowed the growth of melanoma cell lines, suggesting it might be useful to evaluate ERBB4 status in melanoma patients.
Researchers at the NIH Intramural Sequencing Center sequenced all 86 PTK family genes in tumor samples from 29 individuals with melanoma, picking out somatic mutations by comparing the tumor with matched normal tissue.
Overall, the team detected 30 somatic mutations affecting 19 different PTK genes. When the team sequenced the coding regions of these 19 genes in another 79 melanoma patients, they found 99 non-synonymous mutations.
In particular, 19 percent of the individuals had mutations affecting ERBB4 (also known as HER4), while ten percent carried PTK2B or FLT3 mutations.
Of these, the ERBB4 appeared to be the most severely mutated. As such, the team decided to investigate whether mutations in that gene influenced melanoma growth and/or treatment response, focusing on seven different missense mutations in ERBB4.
The researchers found that the growth of melanoma cell lines containing ERBB4 mutations was curbed when they knocked down the mutated form of the gene using small interfering RNA.
The team was also able to slow the growth of the melanoma cell lines by treating them with the ERBB4-inhibiting drug lapatinib, sold as Tykerb by GlaxoSmithKline.
"We have found what appears to be an Achilles' heel of a sizable share of melanomas," senior author Yardena Samuels, a researcher with the National
The team plans to do a clinical trial looking at whether lapatinib is effective for treating melanoma in patients who carry ERBB4 mutations. Steven Rosenberg, chief of surgery at the National Cancer Institute and a researcher with the NIH's clinical center will reportedly head the trial.
"We envision a day when each cancer patient will have therapies tailored to the specific genetic profile of his or her tumor," NHGRI Director Eric Green, said in a statement. "Ultimately, this should lead to more effective and less toxic approaches to cancer care." Green was not directly involved in the current study, but heads the NIH sequencing center that generated the sequence data.
Initial funding of more than US$200 million is being provided by the U.S. National Human Genome Research Institute (NHGRI) and the European Commission (EC).
Jane Peterson, associate director of extramural research at the NHGRI, said international collaboration is very important in advancing science, and that “the sum is more than the parts.” Participants in the IHMC have agreed in principle to the free and open release of data and resources, and the coordination of research plans, as well as to sharing innovative developments, she reported. Data from microbiome research already being conducted by the NIH Human Microbiome Project and the EC Metagenomics of the Human Intestinal Tract (MetaHIT) project will contribute an initial set of microbial genomes to the IHMC. Because the field is so young – less than three years old – there is much to be gained by collaboration, Peterson said.
Christian Desaintes, from the Research Directorate of the European Commission, said the IHMC’s goal for five years hence is to be sequencing 1000 microbiome genomes from over 1000 individuals’ body parts. The parts in question are the skin, mouth, nasal passages, gastro-intestinal tract, and urogenital tract.
Do you want to know more?For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank.
The conference will take place April 7-8, 2008 at the Natcher Conference Center on the main NIH campus in Bethesda, Maryland. For details on the meeting, see the conference Web site, at http://www.tech-res.com/GenBank25. The conference is open to the public and also will be available via live and archived webcast; the April 7 proceedings can be viewed at http://www.videocast.nih.gov/summary.asp?live=6670 and the April 8 proceedings at http://www.videocast.nih.gov/summary.asp?live=6671.
The conference will bring together a slate of world-renowned scientists in molecular biology, genetics, bioinformatics and other areas to discuss GenBank's applications, the discoveries it has enabled, its history, and future directions. Speakers include Rich Roberts, Ph.D., a Nobel Prize winner for his discoveries of split genes, and currently Chief Scientific Officer at New England BioLabs; Sydney Brenner, Ph.D., a Nobel Prize winner for his work on genetic regulation of organ development and programmed cell death, and currently a professor at the Salk Institute; Francis Collins, M.D., Ph.D., who led the Human Genome Project and is Director of NIH's National Human Genome Research Institute; and Craig Venter, Ph.D., who led the private-sector effort to sequence the human genome and is President of the J. Craig Venter Institute. More than a dozen other eminent scientists will be speaking; the full list of presenters can be viewed at the GenBank conference Web site.
"Each day, researchers across the world submit tens of thousands of sequences to GenBank and collaborating databases in Europe and Japan," said Donald A. B. Lindberg, M.D., Director of the National Library of Medicine. "Because of these contributions, GenBank has become an essential tool for molecular biology. The National Library of Medicine is proud to partner with the research community in making this valuable resource available."
Rich Roberts, Ph।D., Chief Scientific Officer at New England BioLabs, commented, "GenBank has provided a foundation upon which much of contemporary biology is now based. It is becoming almost impossible to conceive of any serious biological study of a new organism that does not begin with the determination of its DNA sequence, which of course must be stored in GenBank." Roberts, one of the early proponents of the database, added, "the availability of this wealth of sequence information in a single repository is something we could only dream about in 1979 at the Rockefeller Conference that led to its creation and which we could not imagine being without today."
