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NGS Leaders Blog

Guest Post: To Sequence or Not to Sequence is No Longer the Question

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Mary Ann Brown July 21, 2011

Mary Ann Brown (Executive Director, Conferences, Cambridge Healthtech Institute) : I was once asked, “Why do you organize conferences?” My answer: In my own way I am advancing scientific research. Specifically I design conferences to bring researchers together. All of my conference participants have different backgrounds, from academic research centers to start-up entrepreneurial companies to established research firms from biotech and pharma. These attendees are focused and excited about their research. It is evident by the energy and discussions that take place either from the scientific podium, during the question and answer sessions, at the poster sessions, in the exhibit hall, or just in the hallway. From my perspective, bringing the right researchers together and setting aside the time to focus on a specific research topic creates a collaborative community to advance science.

As an example, the NGx Applying Next-Generation Sequencing and the Next-Generation Sequencing Data Management meetings this September 26-28 in Providence, Rhode Island are noted for advancing NGS technologies into the clinic specifically in the areas of personalized medicine and cancer. The companion data management meeting completes the picture with analyzing these NGS data sets. They are also affectionately known as the Providence NGS meetings.

Recently, I had the pleasure of interviewing three speakers from the meeting: Toby Bloom, Director, Informatics, Genome Sequencing Platform, at the Broad Institute; David Smith, Professor, Lab Medicine & Pathology, Mayo Clinic, and Gholson Lyon, Research Scientist, Center for Applied Genomics, Children’s Hospital of Philadelphia.

In these interviews, I asked about their experiences with NGS and how they are benefiting from the data bonanza. Toby discusses The Broad’s current and future data management infrastructure to support a major sequencing center’s data outpoint. David addresses his role in setting up a sequencing laboratory at a major cancer clinic and Gholson highlights his use of the software VAAST to discover rare Mendelian disorders.  

It has been a pleasure to watch the next-generation sequencing field explode over the last six years. When I first started organizing NGS meetings, it was difficult to even find a sequencing paper in PubMed let alone find a research scientist that was willing to part with their brand new sequencer to attend a meeting and share insights. A lot has changed since then. This disruptive technology has changed the research landscape and the landscape of research possibilities. NGS now allows rapid and in depth interrogation of the genome from DNA sequence to DNA regulation to transcription to determine the genomic underpinnings of health and disease. To sequence or not to sequence is no longer the question...

Click here to listen to the podcasts... Enjoy!

 

What Single Event Could Most Positively Impact the Future of NGS?

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Editor’s Note: Bio-IT World has just published a comprehensive market study on the future of next-gen sequencing and NGS Leaders invited Allison Proffitt, from Bio-IT World, to give us her perspective on the report, which you can download for free. In addition, we invite you to join the discussion and add your comments or questions about the study. - Janine Holley   study cover 

July 14, 2011
Allison Proffitt (Managing Editor, Bio-IT World) : What single event could most positively impact the future of NGS?  One response sums it up: “Uniformity in standards, analysis, more trained informaticians. The cost of sequencing is moot, now the data deluge is coming and none of the experiments are reproducible because of data storage and sharing data issues.”

When the results came in from the three surveys that make up The Future of Next-Gen Sequencing report, I was anxious to read through them—and it certainly was an undertaking! With over 1,400 respondents and more than 18,000 words worth of write-in responses, the full study represents a wealth of information and the message from respondents was loud and clear: there is a huge need for standards in the industry.

When we asked directly about standards, respondents were split over the best way to develop industry reference points for data management. Very few respondents thought the government should intervene, but researchers and informaticians generally favored user-driven directives while those IT professionals who support core facilities and manage and store data preferred that vendors include standards in their products. Perhaps that breakdown is predictable.

Though any solution will certainly evolve as the user community grows and more researchers have experience with the NGS workflow, the survey shows that it is already a problem worth addressing. Where are standards needed besides the inevitable question of how long and which data to keep? Should the standards be different for research data and clinical data? If our end goal is personalized medicine, is there really a distinction between the two? How do we balance standards that ensure reproducibility while still allowing for maximum creativity in dealing with a relatively new data type?

One respondent suggested “the development of industry standards that guarantee that only processed NGS data need to be stored (small footprint) and that those data are stored in a consistent format that is appropriate for any downstream analyses researchers from a variety of backgrounds may require.”

A tall order, indeed.

Over the next several months there will be much discussion here on NGS Leaders about what all of this loquacity actually means, and if you didn’t get to participate in the surveys on the first three rounds, there will be plenty of opportunities still to join the conversation. 

On the Road to the $1,000 Genome

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Davies_pic April 18, 2011                  

 Kevin Davies :  In May, I was privileged to be a guest speaker at the second annual conference on personalized medicine hosted by Larry Gold, professor at the University of Colorado (“CU”) and founder/CEO of protein biomarker company SomaLogic.


The GoldLab symposium brings together an impressively wide variety of speakers discussing trends in all facets of ‘omics research, personalized medicine and healthcare. Gold is an advocate of what he calls “longitudinal ‘omics,” the idea that personal health can (and eventually will) be monitored via a recurring series of simple blood tests using a sophisticated molecular techniques to detect fluctuations in select groups of protein biomarkers that predict the onset of cancer, cardiovascular disease, and many other conditions.


All of the videos from the 2011 GoldLab Symposium are now available on YouTube. Particular standouts in my mind, quite unrelated to next-gen sequencing, include Brandeis University professor Greg Petsko on the coming epidemic of neurological disorders and New York fashion photographer Rick Guidotti’s astonishing work on behalf of an organization called Positive Exposure, instilling extraordinary self-esteem in children with neglected disorders through the power of photography.

 

As for my own talk, with University of Colorado Nobel Laureate Tom Cech in the front row, I thought it only fitting to begin by congratulating the CU faculty and student body for its superb accomplishment in taking prime position in the latest ranking of North American party schools, published in that esteemed journal Playboy. From there, it was best to move on and talk about the technology and pioneers paving the road to the $1,000 genome:

 

 

OCT
10
I-Study: Genomic Interpretation - Who Will Pay?
During this webinar, members of the study review team present preliminary findings of the I-Study, conducted at the Harvard Medical School's 2011 Personalized Medicine Conference.
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