Molecular Medicine Tri-Conference Wrap-up

February 15th, 2010 by Nancy Miller Latimer, M.S.

The 2009 Molecular Medicine Tri-Conference blasted off like a rocket with John Crowley’s  keynote, “When Drug Research is Personal.”  His family’s struggle is the inspiration for the motion picture Extraordinary Measures.  It was a profoundly moving experience to witness this father’s story of his family’s search for a cure for Pompe disease.  This journey eventually led to the founding of Novazyme Pharmaceuticals.    This is the kind of story that encourages us at both the human and scientific level.

I had a really tough time choosing which talks to attend but mostly settled on Molecular Diagnostics, Personalized Diagnostics, Cancer Profiling and Pathways, and Informatics Systems.  It was painful to miss the RNA Interfere, Cancer Biologics, and Translational Medicine sessions.  Many talks totally rocked.  Here are some of my favorites, in no particular order.  These talks come to mind because the material was fascinating, the delivery was exceptional, and they were all in areas for which I have a passionate scientific interest.

  • Single Molecule Real Time Biology: New technologies Enabling a More Complete Characterization of Disease Biology, Eric Schadt, Ph.D., Chief Scientific Officer, Pacific Biosciences
  • The Onco-SNP and Cancer Risk: microRNA Binding Site Polymorphisms as Biomarkers, Joanne B. Weidhaas, Ph.D., Assistant Professor, Therapeutic Radiology, Yale University
  • Expression Based Patient Stratification for Cancer Prognostics, Peter J. van der Spek, Ph.D., Department of Bioinformatics, Erasmus MC – Medical Faculty
  • Consumers and Their Genomes, Brian Naughton, Ph.D., Founding Scientist, 23andMe
  • Systematic Discovery of Cancer Gene Fusions using Paired End Transcriptome Sequencing, Chandan Kumar, Ph.D., Michigan Center for Translational Pathology, University of Michigan
  • Enterprise Scientific Workflow Environment Drives Innovation, Daniel J. Chin, Ph.D., Senior Principal Research Scientist, Roche Palo Alto

This year I presented a poster on biomarkers ala Pipeline Pilot™, attended talks, and caught up with professional colleagues.  The Outrageous Character awards affectionately (and respectfully) go to Eric Schadt and Peter van der Spek.  The Thank You award goes to Daniel for his kind words about our work together.  The Exquisite Explanation awards go Joanne and Chandan.  They did an amazing job of bridging any gaps in the audience’s varied background by presenting technical concepts in essential simplicity—truly beautiful.  Brian gets the award for my Favorite DTC Genetics Company.  I have spent many hours studying my own SNPs data (and that of my family members) thanks to 23andme.   I have derived much pleasure from connecting with relatives, all over the world, that I found through the 23andme site.   I am very grateful that I was able to get this type of genetic information AND the raw data, too.

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Great success at the Chemical & Biological Science & Tech Conference

December 1st, 2009 by Robert Walker

I started the Thanksgiving Week thankful that it was a short week. It needed to be short to recover from the action packed agenda at the 2009 Chemical and Biological Science and Technology Conference in Dallas the week prior. The conference was a huge success on many different levels. Although, the conference has been ongoing for the last few years, this was a first time combination of physical science and medicinal disciplines and to the credit of the conference organizers, it was well done! There were over 1400 people in attendance with over 600 poster presentations and countless oral presentations; however, even with the number of people and logistical challenges that existed, this was one of the best events I have attended (and I have attended a few).

I enjoyed the conference from the perspective that I was able to connect with former colleagues and make new friends (accomplices).  However, the most important aspect for me was hearing about some of the great work that is going into making our country safer. The science and technology is cutting edge and driving innovation in so many different disciplines.

As mentioned in a previous post we were honored to present two posters;

Nancy Miller Latimer presented a poster on “Using Data Pipelining to Analyze Biological Threats: A Biomarker Case Study”.

And

Dr. Nick Reynolds presented a poster on “Applications of nanoscale simulations methods for understanding the structure and mechanisms of chemical sensors”.

Both posters were well received and very applicable to the technology challenges that we face; Dr Reynolds and Ms. Miller Latimer directed and managed the traffic expertly (and there were a lot of people at the presentation).

Over the past few conferences that I have been to, data management and integration is becoming an increasing concern to all the Federal Agencies as more and more data intensive programs come into existence. From new drug and vaccine discovery to biometrics, the data produced for use and reuse is overwhelming legacy systems and there is increasing focus on how to address this challenge.

Addressing this challenge and back to Ms. Miller Latimer’s discussion on Data Pipelining;

She demonstrated “data pipelining”, using Pipeline Pilot™, in a biomarker case study for ALI (Acute Lung Injury). As part of this analysis, Pipeline Pilot was used to analyze and integrate mass spec proteomics data with gene expression data and sequences using data pipelining. Additionally, this study also showed how to automatically mine the literature analysis results for differentially expressed genes/proteins and then publish enterprise-wide interactive solutions via web portals.

To underscore the interest in this integrative and flexible capability, Ms. Miller Latimer’s work was recognized as the best poster overall (over 600 poster were presented). I was proud to be there as she received the award from Colonel Michael O’Keefe, Deputy Director, Chemical/Biological Technologies, Defense Threat Reduction Agency.  Accelrys is proud of Ms. Miller Latimer’s contribution. Well Done!!

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National Security & countering the threat of a chemical or biological threat

November 13th, 2009 by Robert Walker

Accelrys will be attending the 2009 Chemical and Biological Science and Technology Conference in Dallas TX, November 16 -20.

Two Accelrys posters have been selected to be presented during this conference:

Dr. Nick Reynolds will be presenting a poster on “Applications of nanoscale simulations methods for understanding the structure and mechanisms of chemical sensors.” The poster presentation will be on Wednesday, November 18 and will be part of the “Novel Material Science Approaches for CB Defense”

Nancy Latimer will be presenting a poster on “Using Data Pipelining to Analyze Biological Threats: A Biomarker Case Study.” The poster presentation will be on Wednesday, November 18 and will be part of the “Integrative Informatics, Systems, and Synthetic Biology Approaches for CB Defense”.

As is the research and development for new drug and vaccines continues to be important to the general health of our country, we need to be mindful that there is always the possibility of emergent threats that will require rapid response. September 11, 2001 was a painful reminder of this and since, there has been significant progress made in capability to counter these threats.

Accelrys is proud of its contribution to enabling innovative discovery and will continue to work closely with both commercial and federal agencies to ensure that the Unites States continues to be on leading edge.

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DTC Genetic Testing: Take 2

October 29th, 2009 by Nancy Miller Latimer, M.S.

I am trying to concentrate on creating a “Biomarkers” poster for the Chemical and Biological Defense Science and Technology Conference that I am attending  next month in Dallas.  However, I have a hard time resisting my email.  Just now, I received GenomeWeb Daily News that contained a blurb about:  Amway to Sell Interleukin Genetics Health Tests, October 29, 2009.

I thought, “Is this really the Amway that my neighbor tried to get me to sell 30 years ago by telling me how great their laundry powder was?”  Yes, it is.  Can anyone have any doubt that the genomic era has arrived?

An excerpt:

“The Weight Management Genetic Test is used in a program to determine if an individual is likely to lose weight more from low-calorie or balanced diets, or from increased exercise based on genotype.

The Heart Health Genetic Test uses variations in the IL1 gene in order to determine predisposition for inflammation, which has been implicated as a risk factor for heart disease, the company said.

The Nutritional Needs Genetic Test uses variations in genes related to B-vitamin metabolism and potential cell damage due to oxidative stress, and the Bone Health Genetic Test, which is expected to be available by the end of 2009, identifies susceptibilities to spine fractures and low bone mineral density associated with osteoporosis.”

This is not necessarily a new phenomenon and there are lots of folks that feel they need to protect the public from spending money on these DTC tests.  I find it interesting, however, that no one feels compelled to press the government or FDA to legislate the height of my red-spike high heels or how much my husband should be allowed to pay for them.  We know these shoes wreck havoc on my back and knees, yet my husband will happily pay hundreds of dollars if he can only get me to wear them!  And what about all those promises about the face cream that will make me look 10 years younger.

I am all for DTC genetic tests.  I am still waiting on a few specific SNPs to be incorporated in the report before I send my spit to 23andme.  Amway’s tests are very simple and, to me, are a new twist to DTC genetic testing.  It is not necessarily about medicine but choices that I as a consumer should be allowed to make.  I want to know how much will these tests cost?  I don’t gamble but I am certainly into recreational genetic tests.  Call me weird, call me Harriet, just make sure you call me eXXcited!  Bring on the soap, baby.  I’m ready.

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Do You Have Your Life Preserver?

September 28th, 2009 by Nancy Miller Latimer, M.S.

Scott Markel’s article, “Drowning Research Scientists, Meet Life Preserver,” found in the Sep 16, 2009 version of Drug Discovery & Development makes an impressive case for using pipelining technology in bioinformatics research community and in the broader biomarker and translational research communities. As he points out, there will never be a one-size fits all research approach for these scientific communities. The sheer volume of data sources and open source and third party integration opportunities just continue to grow and Pipeline Pilot, a leader in data pipelining, is uniquely capable of handling this challenge.

I loved his conclusion:
Rather than relying on standard templates, users should be able to configure what they want to see and how it is presented. This degree of flexibility leaves room for the innovation so vital to these initiatives, while still providing a framework for faster decision-making and ultimately faster results.

Scott is a Vice-President and member of the Board of Directors of the International Society for Computational Biology. Scott is also the head of ACCL’s talented biosciences R&D team and developer/architect extraordinaire. I get paid to work with him. Lucky me.

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Another Oncology Win in Personalized Medicine

June 1st, 2009 by Accelrys Team

header09_r1_c12At the World Biomarker Congress in Philadelphia this past week, I had a chance to catch up with a colleague, now a senior executive at a European-based global pharma company. Our conversation inevitably turned to Personalized Medicine, a shared interest of ours.

He updated me on some pre-release data that will be shown at Sunday’s meeting of the American Society of Clinical Oncologists (ASCO), concerning Iressa, Astra Zeneca’s lung cancer medication. Previously thought to be a commercial and scientific failure, Iressa is now at the vanguard of therapies “rescued by targeting.” iressa_logo

Targeted therapies are drugs that are shown to have a particular effectiveness in a subset of the overall population. “Targetting” in this context refers to the identification of a genetic difference which corresponds to better clinical outcomes for a particular group of patients. In the case of Iressa, the data that will be presented tomorrow shows that cancer progression is halted for over nine months in patients with the mutation, compared with 6 months for patients receiving chemotherapy (median values).

About one in ten cancer patients has this mutation. Overall, lung cancer kills 1.3 million people per year.  

But what if a patient doesn’t have the mutation? Then Chemotherapy is the better treatment option, which can hold back the cancer progression for five months, compared to only 1 month for Iressa (again, median values).

logo-herceptinIf these results are confirmed, Iressa will join the growing list of personalized medicine success stories in Oncology, which began with world’s first targeted therapy, Genentech’s Herceptin, in 1998. Since Herceptin, we’ve seen other highly publicized therapies with genetic targeting, such as Erbitux.

imcloneBut why so much genetic targeting in cancer, and not (yet) in other indications? Is it the serious nature of the disease or the quality of the data (high compliance in large populations) or something else? The Iressa story gives us a clue.

Astra Zeneca didn’t give up on it, and pursued semi-anecdotal findings of efficacy in some patients, even though it was not effective in the larger clinical trial population. Because of the large potential revenues resulting from effective cancer treatments, it becomes economic for companies to invest in risky clinical trials for treatments that might only be effective in 10% of the population.

Rittenhouse Square

Rittenhouse Square

As my colleague summed it up during lunch at a café on Rittenhouse Square in Philadelphia, “It’s about the money, of course. Cancer kills, and so cancer treatments cost.”

 

Oncology is clearly the vanguard for targeted therapies. But as scientists and marketing executives become more familiar and comfortable with a development process that results in a fragmented market, the techniques will inevitably be replicated in treatments that can only demand lower prices because they treat less serious diseases.

 

And that will make us all winners, no matter what mutations we have.

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More Personalized Medicine Surprises at ASCO Meeting?

May 12th, 2009 by Accelrys Team

am09-general1The abstracts for the semi-annual meeting of the American Society of Clinical Oncologists (ASCO) go up on their website this Thursday, May 14 at 6PM EST. This is a scientific conference that consistently reverberates on Wall Street, because so much of pharmaceutical sales is driven by cancer indications. Many of the largest mergers over the last six months had oncology as the subtext, such as Roche & Genentech and Eli Lilly & ImClone.  

 

kras1At a recent ASCO conference in January, 2009, “personalized medicine” went from a theoretical concept from science to a genuine business reality. At that conference, ASCO recommended a genetic test for a mutation in a crucial gene on human chromosome 12, called “KRAS,” that regulates cell division via signal transduction. If a colorectal cancer patient had the mutation, entire groups of therapies, called “anti-EFGRs,” were no longer recommended. This is not a rare mutation, as an estimated 40% of patients have the mutation. 

The result? Profound, immediate changes in market share potential for pharma companies offering the anti-EFGR monoclonal antibody therapies cetuximab and panitumumab.

In terms of pharmaceutical revenue, this is a very big deal. Each therapy carries a price tag that reflects the critical nature of the cancer indication, generally over $2000 per month. There are 150,000 new cases diagnosed in the US every year (resulting in 50,000 deaths). So just a simple calculation of the market shows that about $1.5 billion annual new business disappeared for makers of anti-EGFRs (40% of patients x $2,000 per month per patient x 12 months x 150,000 new patients per year), which of course excludes revenues from the estimated 400,000 current colorectal cancer patients.

And in terms of fighting this nasty scourge, the ASCO announcement was a very big deal. It personalized the treatment for 60,000 new patients annually (40% x 150,000) who would have otherwise placed their hopes for survival on a therapy that simply wouldn’t work for them.

The trade name for Cetuximab is Erbitux(FDA approval 2004), which is marketed in the US by ImClone & BMS, and in the rest of the world by Merck. Panitumumab is marketed by Amgen globally as Vectibix (FDA approval 2006).

Based on the stock market dip over the last 18 months (called the “Global Financial Crisis”), it is hard to discern definitively what effect the ASCO recommendation had on the stock prices of the companies involved.

But the bigger change will likely be observed internally at these companies, as they continue to commit resources to biomarker discovery and qualification. Biomarker activities around KRAS might have identified the lack of efficacy in the mutant form, which corresponds to not being effective in 40% of patients.

When it comes to post-hoc personalized medicine for blockbuster drugs, the pharma industry clearly doesn’t like surprises. Biomarker activities and translating those activities into clinical trials push those surprises into the research phase, where they belong.

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