This week’s SNPpets include real-time visualization of Ebola spread, precision medicine informatics, big capacity for whole genomes, “genetobollocks” for a new description of media coverage of genomics papers, Neanderal pathogenic variants, and re-examining old problems on a couple of matters.
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…
Although I had other tips in my queue already, over the last week I’ve seen a lot of talk about the new Ebola virus portal from the UCSC Genome Browser team. And it struck me that researchers who have worked primarily on viral sequences may not be as familiar with the functions of the UCSC tools. So I wanted to do a tip with an overview for new folks who may not have used the browser much before.
There is great urgency in understanding the Ebola virus, examining different isolates, and developing possible interventions to help tackle this killer. Jim Kent was made aware of the CDC’s concerns from his sister–who edits the CDC’s “Morbidity and Mortality Weekly Report”, according to this story:
“It wasn’t until talking to Charlotte that I realized this one was special,” Jim Kent said. “It had broken out of the containments that had worked previously, and really, if a good response wasn’t made, the entire developing world was at risk.”
Jim Kent redirected his team of 30 genome analysts to devote all resources toward developing the Ebola genome. They worked through the night for a week to develop a map for other scientists to determine where on the virus to target treatment.
So the folks at UCSC have created a portal where you can explore the sequence information and variations among different isolated strains, annotations about the features of the genes and proteins, and they even added a track for the Immune Epitope Database (IEDB, which happened to be a video tip not long ago)–where antibodies have been shown to bind Ebola protein sequences. The portal also provides links to publications and further research related to these efforts.
The reference sequence that forms the framework for the browser is a sample from Sierra Leone: http://www.ncbi.nlm.nih.gov/nuccore/KM034562.1 It was isolated from a patient this past May, and I don’t see a publication attached to it–the submission is from the Broad’s Viral Hemorrhagic Fever Consortium. There are more details and thanks to the Pardis Sabeti lab for the sequence, you can read in the announcement email. So, as we keep seeing, we need to have access to the data long before publications become available. The work happens in the databases now, we can’t wait for traditional publishing.
In a side note, I also just learned that the NLM (National Library of Medicine) has a disaster response function, and they have a special Ebola section now because of the needs: Ebola Outbreak 2014: Information Resources. And for more of Jim Kent’s thoughts on Ebola, check out the blog that the UCSC folks have just started: 2014 Ebola Epidemic.
The goal of this tip was to provide an overview of the layout and features for folks who might be new to the UCSC software ecosystem. If you already know how to use it, it won’t be new to you. But if you are interested in getting the most out of the UCSC tools, you can also explore our longer training videos. UCSC has sponsored us to provide free online training materials on the existing tools, and this portal is based on the same underlying software. So you can go further, including using the Table Browser for queries beyond just browsing, if you learn the basics that we cover in the longer suites.
Karolchik D., G. P. Barber, J. Casper, H. Clawson, M. S. Cline, M. Diekhans, T. R. Dreszer, P. A. Fujita, L. Guruvadoo, M. Haeussler & R. A. Harte & (2013). The UCSC Genome Browser database: 2014 update, Nucleic Acids Research, 42 (D1) D764-D770. DOI: http://dx.doi.org/10.1093/nar/gkt1168
Gire S.K., A. Goba, K. G. Andersen, R. S. G. Sealfon, D. J. Park, L. Kanneh, S. Jalloh, M. Momoh, M. Fullah, G. Dudas & S. Wohl & (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak, Science, 345 (6202) 1369-1372. DOI: http://dx.doi.org/10.1126/science.1259657
Edit Nov 7, as publication of the browser paper was announced: Haeussler M , Karolchik D , Clawson H , Raney BJ , Rosenbloom KR , Fujita PA , Hinrichs AS , Speir ML, Eisenhart C, Zweig AS , Haussler D & Kent WJ & (2014). The UCSC Ebola Genome Portal, PLOS Currents Outbreaks., 1 DOI: 10.1371/currents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822