FDA Inspection Sites and CDC Health Statistics
Welcome to the Map.
We built this map to identify current and future locations for cell
manufacturing. These facilities are our partners in capacity building
to translate promising concepts into accessible treatments.
Cell manufauring capacity rate-limits the commercialization of therapeutic breakthroughs.
[1]
Clinical trials used nealry a hundred trillion mesenchymal stromal cells (MSC) in 2017 and demand
has increased since.
[2]
The private sector can most significantly address this chokepoint by allocating and pivoting resources
towards current Good Manufacturing Practive (cGMP) production of MSC, including cell expansion, genetic engineering, and exosome harvesting.
The map shows cGMP facilities (as found using US-FDA inspection records)
and a heatmap of a leading degenerative disease, arthritis, to compare
manufacturing to public health need.
The facilities shown do not represent a comprehensie list, but a place to begin.
cGMP Facilities Identified from FDA Inspection Records.
The US FDA enforces current Good Manufacturing (cGMP) regulations by
inspecting facilites worldwide that make active ingredients and finished products.
[3]
Inspection records are publicly available through the FDA Compliance Dashboard.
[4]
The map below shows 342 facilities worldwide that passed FDA inspection in the past 5 years
that produce a biological product related to human tissue or gene vectors.
Patient Populations Mapped Using CDC Statistics.
The Center for Disease Control (CDC) publishes geolocated statistics of the
58.6 million people in the US with arthritis.
[5]
The map shows Arthritis-Crude Prevalence, which is the percentage
of an adult population in a given county with doctor-diagnosed arthritis.
The prevalance ranges from a minimum of 11.2% in Chattahoochee, Georgia,
to a maximum of 42.7% in Webster, West Virginia.
The average across all counties is 28.2%. Mouse over counties on the map
and the county name with the Arthritis-Crude Prevalence will display
in the upper right corner of the map.
The higher the prevalence, the more red the county will be appear.
MSC Capacity for Arthritis
Arthritis is of particular interest, because allogeneic MSC
show strong potential as a treatment due to their
anti-inflammatory proerties.
[6]
MSC therapies for arthritis have been approved abroad for a decade.
Stem cell therapeutic developer, Medi-Post commercialized
an allogenic MSC therapy to treat osteoarthritis, CartiStem,
which has been approved for use in Korea since 2012.
[7]
Even expensive therapies are viable.
The CDC estimates arthritis costs the US $303.5 billion each year through
medical expenses and lost wages.
[5]
The making of the map.
Objective:
Overlay the location of US-FDA inspected facilities
with a heatmap of arthritis in the United States.
Tasks:
- Workspace Set-up: Establish a folder structure for this project
and sync with a public GitHub repository. The repository contains
the source data downloaded from primary sources as cited,
code to process the data (python), and
code to create the website (html, css, and js). GitHub pages serve the site.
https://github.com/jesnyder/mapGMP
- Define Each US County:
Download a geoJSON file describing the shape of each US county
https://eric.clst.org/tech/usgeojson/
- Heatmap CDC Statistics per US County:
Download the Arthritis-Crude Prevalence statistics for the most recent year (2015).
https://www.cdc.gov/arthritis/data_statistics/state-data-current.htm
Coregister the downloaded CDC Statistics with geographic description of the
US county using the countyFID as a common idenifier.
Create a .js file where a unique variable is set equal to the county geoJSON with the cdc statistics.
- Retrieve FDA Inspection Records:
Download the US FDA inspection records.
Filter the results online before downloading.
Limit the "Project Area" to "Human Cellular, Tissue, and Gene Therapy", the "Product Type" to "Biologics", the Fiscal Year to
all years since and including 2015, and the facility passed inspection, meaning
the "Classification" is only "No Action Indicated (NAI)". The Data Dashboard returned more than 3000 results fitting the aforementioned criteria.
https://datadashboard.fda.gov/ora/cd/inspections.htm
- Map FDA Inspection Record as Flagged Locations:
Scrub the FDA facility list to remove locations working on
fertility, organ/tissue donation, blood donation, cornea implants,
medical offices, medical supply companies, dental implant manufacturers,
and most spine-focused projects.
These restriction filtered the list from more than 3000 records to 342 facilities of interest.
Prepare the FDA facility list to be mapped as a series of
annotated points. To do this, convert the FDA inspection site list, which is
a .csv converted to a pandas dataframe, to geoJSON and save as a .js file
that sets the geoJSON equal to a unique variable.
- Serve the Website:
Build the interactive website.
Leverage Leaflet tutorials to write the html, css, and js to build the website
using the county data coregistered with cdc statistics and the
fda facility list as a series of points.
The Leaflet Interactive Choropleth Map is especially helpful.
https://leafletjs.com/examples/choropleth/
On github, setup a Pages to serve the website from the docs file of the repo.
https://jesnyder.github.io/mapGMP/