USPTO Opens Patent Data For Cancer Purposes

Yesterday the U.S. Patent and Trademark Office (USPTO) announced a Cancer Moonshot Challenge.  It runs from now until 5 p.m. Eastern on September 12.

The Challenge involves using a curated data set of nearly 270,000 patent documents going back to 1976.  The goal is to analyze, sift and visualize this data to see what insights might be there to speed up progress on cancer cures.  Entrants will develop a visualization to represent these insights, along with a story (1,000 words or less) that supports the visualization and access to the visualization for testing purposes.

Submissions will be judged on five criteria (each weighted equally):

  • Creativity and Innovation – how unique is the approach to the issue and/or the issue itself
  • Evidence Base and Effectiveness – the strength of the evidence and the impact the story has on cancer R&D and/or the public policy process
  • Value to Public – how much value is provided to policymakers and stakeholder communities
  • Usability – visualization should encourage engagement by policymakers and the public
  • Functional Product – visualization should be interactive and function as described

Non-Travel Zika Emergence In Florida Likely To Increase Your Cynicism

Yesterday the Florida Department of Health announced that there was a high likelihood that four cases of the Zika virus in the Miami-Dade County area were due to local transmission.  This marks the first time that non-travel related cases were found in the continental United States.  There are currently just under 400 cases of Zika confirmed in the state that are travel-related (contracted due to travel in areas outside of the continental United States).  The Health Department will continue to update its Zika virus information each weekday at 2 p.m. Eastern time.

At this time the area of transmission is quite small – roughly one square mile.  However, two of the infected individuals live in neighboring Broward County.  The Department has instituted a serious canvass effort in the transmission area to determine if there are additional cases that have not caught the attention of medical personnel (which was the situation for the four cases reported to date).  As the mosquito bites that transmitted the virus took place in early July, additional cases seem likely.  However, the Centers for Disease Control and Prevention (CDC) does not anticipate widespread transmission at the present time.

As of July 27, there were 1,658 cases of Zika in the continental United States and Hawaii, all of which were travel related (thought some cases were spread via sex or in one case, a laboratory accident).  However, the situation in Puerto Rico is serious, with over 5,500 cases in the commonwealth as of July 7.  The CDC has been working with Puerto Rican health agencies for months, but its impact has been limited.

As Congress is not in session (and won’t be until September), the anemic federal response (mainly redirecting unspent money for the Ebola virus) will continue.  Members of Congress from Florida have been diligent in advocating for funding, and the Obama Administration had provided $8 million before the President informed Governor Scott that another $5.6 million was on the way.  It’s a lot less than what share Florida would receive under the various Zika aid packages that Congress tried and failed to pass earlier this year.

That said, I would expect the newly reported cases would spur some action, even if it’s only campaign rhetoric in connection with the upcoming elections.  Florida is once again expected to be a major battleground in the presidential race, and it would not surprise me to see one or both of the major party candidates to try and wring some advantage from the situation.  Whether it will be well informed remains to be seen, but the campaign to date leaves me skeptical.

The change in action following the Florida cases, however slight, will also point out the dramatic difference in attention that our outlying territories receive compared to the states.  Congressional representation matters, especially in situations like this.

What About The Privately Owned Research Chimps?

In 2015 The National Institutes of Health ended its support for invasive research on chimpanzees, continuing the retirement of federally owned research chimpanzees it started in 2013.  In 2015 the Fish and Wildlife Service reclassified research chimpanzees as endangered, further restricting chimpanzee research under a permitting system.

The research chimpanzees retired by the NIH (a process that has not gone well) have been guaranteed spots in a Louisiana sanctuary.  Research chimpanzees not held by the government do not have such a guarantee, but a reserve in Georgia has been redeveloped to fill that need.  It’s not the only option for those 300 or so chimps that need a home.  They could retire in place, or be transferred to other research centers or zoos.

Project Chimps spearheaded the effort, which should help address this need.  The sanctuary has taken its first group of chimps, and expects to host over 250 animals.

Congressional Inaction Doesn’t Stop FDA, NIAID And CDC From Dealing With Zika

Congress managed once again to do nothing when something was necessary, this time with a funding bill to deal with the Zika virus.  The executive branch, however, does not have the luxury of inaction, especially with a lack of resources.  And once Congress returns, the combination of a chronically broken appropriations process and the November elections makes it nearly certain that instead of a new budget there will be a continuing resolution.  Such a resolution would continue spending at the prior year’s levels, which typically means new proposals like Zika funding are shut out.

The Food and Drug Administration (FDA), the National Institute of Allergy and Infectious Diseases (NIAID) and the Centers for Disease Control and Prevention (CDC) have been active in the vacuum of Congressional leadership.  The FDA has taken steps on protecting the blood supply, supporting potential diagnostic tests, dealing with potential Zika-related fraudulent devices and addressing the mosquitoes that carry the virus.  But as of this writing there are no FDA-approved diagnostic tests, vaccines or treatments in the advanced stages of development.

The CDC has been active in developing resources for state and local health agencies, as well as various stakeholders.  They are assisting the Utah Department of Health in a case of virus transmission, and may assist other states as the number of U.S. cases grows.  The NIAID has been active in researching the virus since before the current outbreak, but started expanding that work in the beginning of 2016.

However, without additional resources (using Ebola funds that have not yet been spent could be counterproductive), the impact of this work will be necessarily limited.  With almost 800 pregnant women with Zika in the United States, perhaps the microcephaly associated with Zika births will motivate Congressional action.  But I’m not optimistic.

 

 

PCAST Breaks Pattern By Meeting On A Wednesday

Today the President’s Council of Advisers on Science and Technology (PCAST) met in Washington, D.C., breaking its usual pattern of meeting on Fridays.  As is customary, a webcast is available.

The public agenda was focused primarily on ongoing projects, with presentations on studies PCAST is conducting on forensics and biological defense.  PCAST also heard from members of the National Academies Committee on Accessible and Affordable Health Care for Adults.  PCAST issued a letter report on innovation in hearing technologies in late 2015, and the Academies released its report last month.  As you might expect, the Academies’ report is longer, with more detailed research and recommendations than the PCAST letter report.

For once, there was some detail about the private session that PCAST (likely) held with the President.  Per the Federal Register, PCAST was to meet with the President for an hour to discuss a report on “Action Needed to Protect Against Biological Attack.”  The meeting was to be held in a secure location and the contents of that report may not be made public due to national defense or security interests.  (Pardon the verb tense, as I’m not sure whether the scheduled meeting took place, and may never know given the security concerns.)

The next meeting of PCAST is likely in September.  And yes, you may have noticed that I haven’t posted about the May meeting of PCAST.  I will rectify that shortly.

FDA Releases Proposed Guidances For Next Generation Sequences

Last week the Obama Administration released one of its periodic fact sheets announcing recent actions on the Precision Medicine Initiative (PMI).  The PMI is trying to build tools and gather data to make it easier to target therapies and other medical treatments for specific individuals.

Part of this latest fact sheet is the announcement that the Food and Drug Administration (FDA) is releasing draft guidance on oversight for what’s called next generation sequencing (NGS).  This category of tests measures a much higher number of genetic variants than current sequencing.  The agency believes that these draft guidances – one on standards for analytical validity of NGS tests and another on using evidence from public genome databases to demonstrate the clinical validity of NGS tests – can be sufficiently flexible for a family of tests that is emerging and notably distinct from existing sequencing and related tests.  This is a situation where the agency likely believes that establishing some boundaries for a new testing field can support the development of such tests.

If you’re interested in providing comment on either draft guidance (or both), you will need to submit them by October 6.

Possible Zika Death In Utah; Still No Congressional Support

On Friday the Salt Lake County Health Department held a press conference on a recent death that may be linked to the Zika virus.  The person died in late June, and post-mortem tests confirmed that they were carrying the virus.  However, the person also had a separate health condition and it is unclear to what extent the Zika virus may have contributed to that death.

This would be the first Zika-related death in the continental United States, following a case in Puerto Rico were a man passed from a condition that resulted from antibodies to the Zika virus attacking his platelets.

As of July 6, there have been over 1100 cases of Zika virus infection in the continental United States reported to the Centers for Disease Control.  More than 2500 have been reported in U.S. territories.  By comparison, back in February there were all of 45 cases reported in the entire U.S.  Nearly all of the cases in U.S. territories are locally acquired, while none of the cases – including the person who passed in Utah – in the continental U.S. were locally acquired.  Congress remains unable to pass a funding bill for fighting the virus, which places additional demand on resources currently dedicated to fighting Ebola.  I’m skeptical that a possible fatality related to Zika would move members to act, but would be happy to be proven wrong.