News and updates from NextBio
Genomics, HIPAA and Informed Consent
Andy Warhol talked about the fifteen minutes of fame of the future in 1968 and this quote captured everyone’s attention coming back again and again in a variety of forms and fashions. Those of us that work in health care and genomics can be just as captivated by the value of anonymity and privacy.
Patients and families turn to genomic medicine to treat cancer
Most of us probably associate being sick with the entire body- a fever, aches, chills and other broad symptoms. When it comes to a disease like cancer, we might take an organizational step or two down to think of a specific organ or tissue: breast, lung or brain cancer.
But increasingly, patient’s stories point clearly toward a finer resolution of cancer diagnosis, down to the level of a single gene. A report in the New York Times last week describes how a team of researchers worked to identify the genetic aberration underlying a colleague’s cancer, and helped treat his leukemia with an off-label drug currently used to treat kidney cancers.
Recent news articles discuss how NextBio scales technology to handle genomics data
As genomic data makes its way from specialized laboratories into routine healthcare evaluations, it is perhaps appropriate that announcements of the latest sequencers were made at the Consumer Electronics Show in Las Vegas rather than the upcoming Advances in Genome Biology and Technology conference.
New machines from Illumina and Life Technologies only strengthen the idea that 2012 is, in fact, the year of the $1000 genome. Led by a trickle of individual success stories, genome sequencing appears to be on the verge of altering the clinical landscape. While the FDA and regulatory bodies resolve the consumer issues of reimbursement and regulation crucial to patients, here at NextBio we tackle an intermediate problem: Making sense of the data. Read more…
Scientists present clinical trial results for the first bedside genetic test
How quickly can clinicians accurately determine the way a patient will respond to medication, or their chances of getting a disease? It might even begin the minute they walk in the door. ‘Genotyping by eye’, as Atul Butte from Stanford University phrased it at a recent Xconomy forum, can be as instantaneous as noticing a patient is obese, a factor that increases chances of diabetes more than any known genetic variant today.
More precise genetic tests are fast catching up to this idea of near-instant genotyping as well. Researchers from the University of Ottawa recently demonstrated the success of a ‘bedside’ genetic test to optimize treatments for patients undergoing coronary stent implantations. At the Transcatheter Cardiovascular Therapeutics symposium this week, the lead investigator, Dr. Derek So, presented the results of the RAPID GENE clinical trial, a point-of-care genetic test to identify carriers of a common genetic variant that reduces the efficacy of standard anti-platelet therapies. Read more…
If you’re a user of NextBio Basic, you’re probably aware that NextBio lets you access thousands of gene expression studies from sources such as GEO. NextBio has done the heavy lifting of importing, normalizing, and curating publicly available genomic data so that biologists can ask and answer biological questions completely in silico—even with little computational expertise.
Which makes our recent updates very exciting: We’ve made data from GWAS, CNV studies, and more freely available* through the NextBio Public site. These numbers update on a near-daily basis. Because our curators tag each imported study using a controlled vocabulary and custom disease ontology, you’ll easily be able to perform meta-analyses of multiple studies across different diseases through a simple, web-based interface.
Correlating genomic data from thousands of studies linked to different diseases, compounds, tissues, cells and more is complicated. We’re constantly trying to make the job a little easier, which is why we’ve also given the NextBio Public user interface a major overhaul.
Read more…
Remember when we said we had big news to share? It’s almost here! As we get closer to launching our public site, share in our excitement by entering the contests and prize drawings we’ll be announcing in this space over the next few weeks.
Join us every single week for another chance to win, or just drop by and participate when you like- there’s no obligation necessary (Either way, don’t miss the Official Rules first). And once our public site is up, come back for our biggest contest of the year: the NextBio Genomics Innovation Challenge.
At NextBio, we like to look at data with fresh eyes. We know that integrating diverse kinds of information with strong data mining strategies can yield fresh hypotheses, new insights and much more. With the data accessible and the most intuitive, user-friendly tools possible, brand new genomic discoveries are just waiting to be made. The NextBio Genomic Innovation Challenge is your chance to do it. And if intellectual satisfaction isn’t thrilling enough for you, there are big prizes to be won as well. Watch this space to find out more. And as you wait for the public site and bigger prizes, why not try your hand at a few other contests too?
For starters, we’ll keep it really simple- all you have to do is keep in touch! First, like us on Facebook and second, drop us a line. Leave us a comment either on this blog post or on our Facebook Wall, telling us about your research interests. Do both (Follow us on Facebook AND leave a comment) by August 5, 2011 August 10, 2011 and your name will be entered in a drawing for one of three gift cards ($10.00 each) from Starbucks, Amazon or iTunes (your choice!).
Using the internet for open science
A few days ago, PLoS hosted a talk by Michael Nielsen at their San Francisco offices. Nielsen, author of the book “Reinventing discovery”, due late this year from Princeton Press, is a strong-voiced proponent of the need for a change in the way we share data.
The Polymath project, his opening story, is one of the best examples of how and why open science works. Tim Gowers, a Fields medalist, posted a famous mathematical problem on his blog, an open invitation to anyone interested to try their hand at solving it. For the first 70 hours, nothing happened. Then a math professor left a comment, quickly followed by a high school teacher, another Fields medalist and so on. In the span of 37 days, over 800 comments collectively solved the problem. How many conferences and scientific papers, peer reviews boards and editorial revisions would it have taken to even get these diverse minds thinking together in the same space? Nielsen describes it as the difference between “driving and pushing your car”.
Read more…
More than 8,000 curated studies, a whole new look and thousands more users. If you’ve been wondering where we were, there’s your answer. We’ve had a lot going on, and now we’re back to share it all on this blog. So welcome back to news from NextBio!
Over the next few weeks, we hope to update this space with all the exciting happenings at NextBio. High on that list is the upcoming update of our public site, which will be made freely available to academic, government and non-profit users. Here’s a preview of what it looks like:
Read more…
Have you seen our new look? As of this week, the NextBio website has a great new design!
The foundation of the new design is more intuitive user interface. Take the new site for a test drive and see what you think – I know you’ll like it. Do a query for a disease, gene, compound or tissue and you’ll see the new way we are presenting search results. A search for “breast cancer” will take you to the Breast Cancer page which is easy to navigate and packed with information.
Personally, I really like the new vertical tabs for navigation on the left hand side. But the updated NextBio website is not just about aesthetics and ease of navigation – we’ve improved features and added new capabilities. My colleague Ilya Kupershmidt, one of the NextBio cofounders, likes to draw attention to the new “recommendation engine”. This exciting new feature makes use of NextBio’s unique ontologies to recommend studies, literature, clinical trials, and news items to users based on their interests. To see what NextBio suggests for you, sign in to your account and go to MyNextBio.
I am very excited about the new website! We’ve been working on it for a few months now and it great to finally see it come to life. Now that it is launched, I can’t wait to hear what other people think of the new NextBio. Please let me know what you think in the comment section.
- Lisa Green
I am quite excited to announce that I am the newest member of the Science and Technology Steering Committee for the Commonwealth Club of California!
The Commonwealth Club is an outstanding organization. It is the nation’s oldest and largest public affairs forum and has been fostering education through open public discussion for over a hundred years. If you aren’t familiar with the Commonwealth Club, you may want to take a look at their site to read about their history and look at all the interesting talks on the calendar.
Read more…