The Number of Adverse Event Reports filed into the FDA's AERS / MedWatch Program Rose 45% Quarter over Quarter

The most recent release of Adverse Event Data from FDA's AERS / MedWatch database[1][2] shows the biggest jump in total number of reports submitted ever (if you count by absolute number of reports submitted). It's also one of the biggest percent increases (44.8%) in Adverse Event submissions since the AERS program began. I wish I knew what caused the jump. It's safe to assume that it was unrelated to the Supreme Court's recent ruling [pdf] about Adverse Event reporting related to Zicam as the jump we see in AERS reports took place from July to September of 2010, even before the case was argued before SCOTUS.

Q1 2009 AERS data released today

FDA released the Q109 AERS data today.

Initial upload into FDAble looks like everything was okay.

Interestingly, there are ~111,000 reports in this release compared to ~121,000 for the previous quarter. Not sure how significant this decrease is (is it seasonal? is it just noise? is FDA weeding out duplicates?). Will take closer look later....

The Food and Drug Administration isn't able to reliably determine how much money it needs

WOW. Sister-in-law sent this to me...

By JENNIFER CORBETT DOOREN

WASHINGTON -- The Food and Drug Administration isn't able to reliably determine how much money it needs to regulate medical products because, among other things, its staff can't track all the adverse-event reports it handles, according to the Government Accountability Office.

Full story here.

"More Eyeballs on AERS"

That's what the Nature Biotechnology editors titled it.

Our correspondence to Nature Biotech regarding AERS data came out yesterday. I can't post the article due to copyright restrictions, but I'm sure you can pick up a copy at your local newsstand.

FDAble's Side Effect Check now available in iTunes App Store

Can be had here.

FDA Dings Zicam & Matrixx

FDA just issued an advisory about a potential link between certain Zicam products and the loss of sense of small (anosmia).

What's flabbergasting about this is that this information has been around for more than 4 years in the AERS system.

Here you can see that there have been 390 cases of anosmia reported to FDA where Zicam was also mentioned.

Here you can see that, by 2008, adverse event cases for Zicam reported anosmia ~1,000-fold more often than anosmia was reported in all other cases for all other drugs.


This signal is present as far back as Q3 of 2004.

AERS & VAERS Reporting Frequency has Approximately Tripled since their Inceptions

A little bit of navel gazing today, but I decided to plot the # of reports submitted to the AERS and VAERS systems vs. Time today. There are small bits of information in the graphs shown below that might warrant further examination.

e.g., The # of reports submitted to AERS has almost tripled from 1998 to 2008 (11 years).

Is this a big increase?

I can't really say with any certainty, but it feels like an inadequate increase given the concomitant increases in the use of information technology over that period (e.g., the interwebs).

[Aside: Wolfram Alpha is being of no use in trying to find the change in internet usage over the years to serve as a comparison---okay wikipedia is telling me that internet usage from 1997 to 2007 has gone up almost 6 fold in the developed world...so I think my feeling is probably correct.]

Also...what's going on with those dips in the # of reports in the early 2000s?

Note that 1997 only includes data for Q4 of that year so it's artificially low.

VAERS
As far as VAERS is concerned, it looks mostly like a flat-line from 1991 to 2006 (okay it doubled, but that's over 16 years) and then there's a HUUUUGE spike over the past 2 years.

Is VAERS being "marketed" better all of a sudden, or is it The Jenny McCarthy/ Autism effect? Or both?

FDA AERS Data & Quality Control

FDA just released its Q4 2008 AERS data (yes, it’s May 13, but that’s another story altogether).

This post is about Quality Control of AERS data. It seems that every quarter, there’s some type of SNAFU with the data release (last year they released AERS data partially contaminated with a previous quarter's data).

This quarter, we have the classic newline-characters-where-they-don’t-belong error that's screwing up my AERS parser.

A little Background:
FDA releases its data in 2 forms (ASCII and SGML). ASCII is the one that I use and each ASCII file consists of row after row after row of $-delimited Adverse Event Records.

2 sample rows might look something like this:

$12345$abcdef$somestuff here$blah$more blah$blah $34321$blahblah$doscum$etcetc$vixerunt$gaius$cicero

Each row should represent one particular database record and my parser dutifully goes through each row extracting all the little bits of information between the dollar $ign$.

But with this latest quarterly release FDA released its Drug data file (aka DRUG08Q4.txt) with 4 significant quality control errors (see sample screenshot below).

[For those who want gruesome details, the following lines in the DRUG.txt file contain errors: 537-538, 258909-258910, 281285-281286, 408948]

The gist of the issue is that whoever entered the data for these 4 drug-records forgot to remove the newline characters (“carriage returns”) and so the record is actually split across 2 or more lines.

While this doesn’t seem like a big deal, if your parser isn’t “smart” it could inadvertently stuff the wrong data into the wrong slots in your database.

And so, you have to design your parser to look for these types of errors--and then you have to have a human look at the problem just to assure yourself that there wasn’t a bigger error. This wastes time...especially when the file you’re looking at has 416,000 records.

‘t would be nicer if FDA did more quality control on their data releases.

FAERS - AERS, but Fancier

Someone at FDA sent this to me recently (see below). It's an email sent around from within the FDA announcing a new Adverse Event Reporting system (sort of).

Emphases are mine. Editorial comments are mine, too.

Spoiler alert: They forked over $$$$$ and went with Oracle.

Bioinformatics Board (BiB) News

Post Market Safety BRB Announces Selection of Vendor[We've decided to shop at Barney's. Can't tell you what we're buying just yet, but it's gonna be FAB!] for New Enterprise Adverse Event System

The Bioinformatics Board (BIB) News provides FDA employees with an update on the activities and progress of the BiB. This month’s news focuses on the Post Market Safety BRB and the selection of the Adverse Event System Vendor. For more information about the BiB or the contents of this message, please contact your BiB representative or email the Bioinformatics Board, bioinformatics@fda.hhs.gov.

Post Market Safety Business Review Board Announces Selection of Vendor for New Enterprise Adverse Event System FDA’s Bioinformatics Board and the Post Market Safety Business Review Board are pleased to announce a significant milestone for the Agency. After an extensive analysis of FDA scientific needs for the management and analysis of post market product safety reports, and an evaluation of leading industry tools, the FDA Adverse Event Reporting System (FAERS) Program has selected Oracle AERS[$$$] (Adverse Event Reporting System) as the new tool for FDA staff[guess who's not getting access to the data juuuust yet...?] to efficiently[you wouldn't believe what we were doing before] analyze post market safety reports in order to identify potential product safety problems.

Selection of the new FAERS tool represents a significant landmark for the Agency. With the selection of an advanced tool that all centers and offices can leverage, the Agency can now focus on implementing processes for sharing post market safety data across our product centers as well as advancing the science of post market report analysis. Achievement of this milestone represents the efforts of numerous individuals from across the Agency over several years[wow. just...wow]. While in many ways this is just a beginning, it is important to recognize our progress towards meeting the goal of providing modern tools necessary to address many post-market surveillance needs. Selection of Oracle AERS[What? no love for MySQL? They're about to be subsumed by Oracle, too, ya know.] positions the Agency for success in this complex and dynamic arena.

We expect the initial users in CDER and CBER to receive training and begin using the new system as early as fall 2009[but don't quote us on that] with additional users being trained and brought on over time. CDRH users are expected to begin using the tool in 2010, and additional centers and offices expected shortly thereafter.

FDA Search Firefox Add-on

Just tried to publish my Firefox add-on, titled FDA Search 0.1.0. What I didn't realize is that Firefox keeps your add-on in purgatory until some FF regulars actually review it, and only then can you nominate your add-on for inclusion in the public repository. Thanks to James Cook and his add-on, which I used as a template for mine.

VAERS Update...this time with feeling

The FDA (or is it the CDC? Or is it Health & Human Services? Can't really tell....) just updated its Vaccine Adverse Event Reporting System (VAERS) dataset (April 13, 2009).

What they haven't bothered to note is that they've also changed the structure of their dataset.

VAERS data used to come packaged as 2 CSV files--one called VAERSData.csv and one called VAERSVaccine.csv.

VAERSData.csv used to contain 20 slots per row for symptoms associated with each vaccine adverse event.

In the database world, one says that there is a 1-to-many relationship between a VAERS report and the Symptoms associated with that report.


And day 1 of any remedial Database management course will inform you that because of the 1-to-many relationship, you should separate the VAERS record from the Symptoms records and link each symptom back to its report via a foreign key.

The reason for doing this is that 20 slots for symptoms *may* seem like more than enough slots for any case that you'll ever come across, but at some point, some hypochondriac is going to slip in 21 symptoms and totally screw with your file.

Well, 19 years later, the VAERS folks have finally given the Symptom data its own csv file, appropriately titled VAERSSymptoms.csv. They didn't bother to tell anyone that they did this...and I had to tinker with my parsing algorithm last night to adjust for the changes, but the discerning pharmacovigilantes among us were able to figure it out when we asked ourselves

"Why are there 3 csv files per year now when there used to be 2? And why haven't they updated their file explaining the structure of the VAERS files?" As of this writing, the most recent revision of the VAERS explanation is June 2007.

Ah yes...lest I forget...as of this writing, the Zip file containing all of 2008's VAERS data is contaminated with 2009 data. I think that's just to keep everyone on their toes.