Genomics is a Model for a Collaborative Scientific Environment

 :: Posted by American Biotechnologist on 10-22-2014

In an informative study conducted at the University of Michigan, researchers found that 92% of ecologists are reluctant to share their data for fear of being scooped by fellow scientists. Interestingly, the authors suggest that a much more collaborative effort exists among genomic researchers, which they use to explain the tremendous advances in that field (consider the Human Genome Project).

According to study co-author Georgina Montgomery:

Collaboration, rather than competition, is the best way to continue to advance science

Furthermore, Montgomery argues that

increased data sharing will allow more diverse people to actively participate in research, such as early-career scientists and those from underrepresented groups; scientists from smaller or historically less-influential institutions; citizen-scientists; and scientists from the Global South, scientists from Africa, South and Central America, and much of Asia who are often excluded from leading research.

It is quite heartening to hear that Montgomery et al. believe that genomics should be seen as a positive example of open collaboration. Certainly invaluable tools such as ExPASy would not be as successful as it is, (in fact it would not exist), had the world of molecular biology been bogged down by a cutthroat competitive culture. Sharing data is key to our success and I believe that molecular biologists can be proud of the collaborative environment that they have created. Furthermore, recent efforts to encourage scientists to publish their data in open-access journals will surely take the concept of collaboration one step further.

Nonetheless, our world is far from perfect. Regardless of what discipline you are in, the very nature of the grant process and of the tenured university environment, makes the “publish or perish” paradigm very prominent in all of our minds. It is important for us to come up with methods for further increasing shared knowledge which will surely benefit everyone involved.

Click here to read the original story from the University of Michigan.

Ballad of the Arrogant Professor

 :: Posted by American Biotechnologist on 10-21-2014

Easy Detection of Low Level Mutations

 :: Posted by American Biotechnologist on 10-20-2014

Bio-Rad Laboratories announced the launch of new PrimePCR Assays for Droplet Digital PCR (ddPCR™). This release expands Bio-Rad’s current offering of predesigned and fully wet-lab validated assays by an additional 100 assays for copy number variation (CNV) and 92 assays for mutation detection. Bio-Rad will also be adding 5,620 mutation detection assays that were created using the same algorithms and design rules as the wet-lab validated assays.

Bio-Rad’s ddPCR technology provides an absolute measure of target DNA molecules without the need for a standard curve. Together with PrimePCR Mutation Detection Assays, this technology enables detection of one mutant molecule in a background of 2,000 wild-type molecules. Measuring these extremely low levels of mutation abundance could lead to the development of new, less invasive and more sensitive diagnostics. In addition, the high precision and absolute quantification made possible by PrimePCR ddPCR Assays enable the quantitative discrimination required to resolve small fold changes in gene copy numbers for CNV analysis.

Highly studied gene targets
Among the genes that can now be targeted using PrimePCR ddPCR Assays is paired box gene 2 (PAX2), a CNV gene target that is suspected to have both oncogenic and tumor suppression functions in ovarian cancers. Another notable CNV assay released as part of this launch detects the neurexin-1-alpha gene (NRXN1), which has been linked to a range of neurodevelopmental disorders, including autism spectrum disorders, schizophrenia, and intellectual disability.

The new mutation detection PrimePCR ddPCR Assays include those for fms-related tyrosine kinase (FLT) mutations that are observed in acute myeloid leukemia (AML) patients. Mutations in the fms-like tyrosine kinase 3 (FLT3) gene represent one of the most frequently encountered and clinically challenging classes of AML mutations. This release also includes several assays that detect mutations in the neuroblastoma RAS (NRAS) gene, including the G12V mutation that has recently been linked to poor prognosis in malignant melanoma.

PrimePCR ddPCR Assays are compatible with all Bio-Rad Droplet Digital PCR Systems, including the QX200™ AutoDG™ Droplet Digital™ PCR System.

For more information on Bio-Rad’s PrimePCR products, please visit www.bio-rad.com/PrimePCRpr.

Saving 600,000 Children’s Lives With a Bar of Soap

 :: Posted by American Biotechnologist on 10-17-2014

University Nets Huge Grant to Analyze World’s Largest Collection of Brain Scans

 :: Posted by American Biotechnologist on 10-15-2014

In a rare distinction for one university, neuroimaging world leaders and USC Professors Arthur Toga and Paul Thompson will receive two major research center awards to advance their exploration of the human brain.

Toga and Thompson each will establish a Center of Excellence under a National Institutes of Health initiative to mine discoveries from the vast and exponentially growing amounts of data created by imaging science, genetic sequencing and many other biomedical fields.

The awards total $12 million and $11 million for Toga and Thompson, respectively, over four years. NIH is funding several Centers of Excellence, including the two at USC, under its Big Data to Knowledge initiative.

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