Test-Driven Development and GAMP

In the world of software development, there's a development methodology called, "Test-Driven Development" aka ("TDD") where you basically write the test BEFORE you write the actual functional code.  There are other tenants of TDD, but the notion that you write the test first is the main focus here.

By writing the test first, it forces you to look to see where your "goal posts" are.
 
I actually have no opinion on TDD other than to point out that it exists, and there are some principles with strong parallels in the FDA-regulated markets with respect to computer system validation.

The V-Model refers to the way in which (software) systems are validated and verified:

The only reason (I can think of) for why this is called a "V-model" is because someone is being clever with the Verification and Validation.  But I digress.

The point of the V-model is that someone actually went through and documented what the users/stakeholders wanted.  Then, they went through and figured out what functions match with those user/stakeholder desires.  THEN, they went through and figured out how to make those functions happen:

• User Requirement Specification (URS)
• Functional Specification (FS)
• Detailed Design Specification (DDS)

That's the downstroke of the V.

The upstroke is the part where you go about proving that what you designed actually made it into the actual system.  And the functions you said are available are actually available:

So in the world of computerized system validation (CSV, not comma-separated variable), the Installation Qualification (IQ) is what verifies that the items of the detailed design got into the system.  So the battery of tests that prove the correct software configuration was inputted.  

Operational Qualification (OQ) is the battery of tests that prove that the functions specified perform as specified.  For example, if your functional specification says that your impeller speed has to operate between 60 to 255 rpm, you should have a test in your OQ that runs the impeller at the boundary and within that operating range.

• Installation Qualification
• Operational Qualification

So what does any of this have to do with test-driven design?  Well, anyone who has validated a computer system knows that for the most part, the V is executed exactly as it's drawn: first the downstroke, then the upstroke:

You first write the URS, then the FS, then the DDS.  After this planning phase is over, there's the testing phase during which time you draft the IQ, OQ (and sometimes PQ).  And by the time you get to executing these tests, you may find nonsensical tests or deviations.  

And the reasons may be that you ran into these issues is because you didn't start with the tests (IQ/OQ) first.  

The TDD methodology is saying that you start with the URS (what the stakeholders/users want).  Then you skip ahead and write what a passing test looks like (IQ and OQ).  Then you go backwards and fill out the specification and perform the build.

The thinking seems backwards on first-pass, but it isn't without merit.

ZOOMS 2 - Fastest Way to View Trends

So in addition to biologics manufacturing commentary, it turns out that Zymergi is actually a for-profit business that provides software, consulting and technical support.

For 2014, we're pretty much booked on the technical support side, but I wanted to take some time to talk about our software products.

Our flagship product is ZOOMS, which is an acronym for Zymergi Object-Oriented Metadata Search.  And in 2014 - thanks to Edward Snowden, more people know what metadata is than in 2008 when we started ZOOMS (v1.0)

So why are we interested in searching metadata? Well, let's take a step back. When working the front lines of campaign monitoring and process support, we noticed that viewing trend data (i.e. tag values plotted against time) was the principal component of process understanding. The more trends a person reviewed, the more process knowledge they gained and the more they understood normal from abnormal.

And in all that time, very few people actually learn to speak "Automationese."

"Hey, did you see that weird thing going on with T100.GLOBAL.CLX.AI05.PV?"
- No one ever

In the automation world, everything is a tag. In the Manufacturing Sciences world, everything is about a measurable parameter within the process. So when you listen to the process scientists and engineers talk, it's always about some parameter (e.g. "Optical Density") in some unit (e.g. "Tank 100"). That right there is the metadata of a tag.

The tag takes care of the Y-axis on the trend. What about the X-axis?

The X-axis deals with time-windows: start times and end times and the metadata around the time-windows are called, "batches." Specifically using S88 terminology, people involved with campaign support are interested in Unit Procedures, a.k.a. "unitbatches."

I'll leave the formal definition of "unit procedure" up to the automation gurus, but to a Manufacturing Sciences data engineer, a unit procedure is a process that happens on a piece of process equipment.

So say you're making rituximab in production bioreactor T100 using the version 1.1 process and batch R2D201 ran from 20-Dec-2013 to 28-Dec-2013... that there is a unit procedure:

batchid	unit	product	procedure	start time	end time
R2D201	T100	rituximab	production culture version 1.1	20-Dec-13	28-Dec-13

The metadata around this time-window (i.e 12/20/2013 to 12/28/2013) are as follows:

• R2D201
• T100
• rituximab
• production culture version 1.1

So it stands to reason that if an internet user who knows nothing about a subject can type keywords into Google and get the most relevant results on that subject; that in 2014, a process citizen who doesn't know too much about the process ought to be able to type some keywords into a webpage and get some process trends.

And now they can: Introducing ZOOMS 2:



Learn More

Unnecessary Testing in cGMP World

by Oliver Yu

In the world of soaring medical costs, we have unnecessary medical tests and procedures sapping precious healthcare dollars.

The thing about these medical tests is that they are necessary for someone under some circumstances, just not for most people under most circumstances.

So is the case in the world of GMP biologics manufacturing. There are

Image courtesy of the Chemical Heritage Foundation Collections.

plenty of tests that need to happen to produce a releasable lot. There are in-process tests; there of Certificate of Analysis (CofA) tests.  There are analytical tests you for engineering runs; there are tests you perform on contaminated lots, but not others.

But regardless of what test you are performing, the litmus test for performing the test or analysis is:

Does the result of the test help me make a decision?

Consider the following snippet from a computer program:

   if ( testResult == PASS )
   {
      forwardProcessBatch();
   }
   else
   {
      forwardProcessBatch();
   }

In this case, if I run a test and pass, I get to forward process the batch. If the test fails, I still get to forward process the batch. So if in either case, I get to forward process the batch, why should I bother doing the test? The result of the test does not do anything to serve the outcome!

Another good way to approach the question of whether or not to perform a test is to see if you can write down a plan for what to do with the test result. If you can write down a reasonable plan and stick with the plan prior to getting the test results, then there's a good reason to perform the test; otherwise, you're simply on a fishing expedition and making it up as you go along.

FIO Samples

There exists "For Information Only" samples that are specified into the process.  For example, concentrations of ammonium (NH₄⁺), sodium (Na⁺), pO₂ and pCO₂ are measures of cell culture metabolism that are useful for long-term process understanding.  They likely never be used to make a forward-process decision, though they can be used for retrospective justification of discrepancies or as variables during multivariate data analysis.

In my experience, these routine FIO samples are contentious.  On one hand, they serve the purpose of long-term, large-scale process understanding as well as sporadic justification for discrepancies.  On the other hand, if FIO samples get used enough to close discrepancies and release lots, over time the FDA and other agencies will pressure you into making these FIO tests into in-process or lot-release tests.

Defensibility

In the end, your actions in deciding to perform a test need to be defensible.  You need to defend the costs to do the test to management.  You need to defend not doing the test to the FDA.  And your situation may be different than the biologics manufacturer down the street.

That defense ought to rest on whether or not you can do something with the result of the test.

Pareto Principle at work in Biotech

In the latest FDAzilla post, guest blogger and regulatory professional - Greg Hattoy - talks about 5 ways to prepare for a regulatory audit.

The first idea is that small things can build into big things and that management needs to have a pulse on what's going on. It isn't so much that there's something small out there that's wrong with your plant (like rust on the bottom of the fermentor) that that it becomes big (like your fermentor gets a hole in the bottom of it from the rust).

I've seen this in action where immediate- and short-term fixes are executed in a way that causes long-term maintenance chores. For example:

• The intended design of post-inoculation additions was among the suspect causes of bioreactor contamination.
• In the name of mitigating this potential risk via process of elimination, post-inoc additions were changed away from the intended design.
• True cause of microbial contamination was later deemed to be something else.
• Due to "don't fix what ain't broke" and heavy workload, the modified additions were never changed back.

You get enough of these decisions and a well-engineered plant encumbers itself and slips farther away from good engineering practices.

His second idea is that there are "Big Wins." This is absolutely consistent with the Pareto Principle where 80% of the effects can be explained by 20% of the causes, and though Greg states that it my fly in the face of the "small things add up" thesis, it actually doesn't. Here's why:

Every biotech professional from worker bee on up to the top of management has their list of 100 to-do's. Everybody is loaded down and their email inbox just looks like a constant scroll.

There actually aren't 100 different problems that need to be solved. It's actually something like 12 real problems. The majority of the effect/response (80%) is caused by a minority of the causes/factors (20%).

There are people who tackle this list according to priority: #1...done. #2...done. #3....done. And by the end of the day, the top 10 items get subtracted off the list (and another 10 get added).

Then, there are people who look at the list and go, "Gosh, #3, #7, #13, #49, #62, #85 are all related. If I spend time tackling the true root cause, I can hit six birds with one stone!" And when you go about solving problems in this manner, you can use the Pareto principle in your favor:

You can solve 80% of your problems by fixing 20% of what's wrong.

Obviously, there are times when you need to tackle the list sequentially. But this ought to be a minority of the time compared to tackling your to-do list strategically.

Critics of the sensible approach say that walking away from regulatory inspections has more to do with the personality of the inspector.  For that, there are ways of gathering regulatory intelligence.   But for the rest of us, following defensible plan is the most sensible approach for preparing for a regulatory audit.

Drain Water vs. Clean Air - Drain Design for Bioreactor Contamination

UPDATE: The point isn't to install air-breaks at all costs.  The point is to use the correct BioSafety Level for your process, recognizing that a lot of facilities are overly-conservative for the processes they run.

On multiple consulting assignments, we are seeing an alarming trend where CIP manifolds and process piping are piped directly to drain.  We have identified direct piping to floor drains as contamination risks.  And our experience mitigating floor drain contamination risk is to cut the piping.

The main objection to this recommendation is that it would compromise the Class 100,000 clean room status of the process space.

With the cut in the piping, the worry is that contaminants from the drain are now able to enter the processing suite and will send your viable airborne particles beyond your environmental monitoring action limits.

But of the unfavorable options available, there's one that's obvious to us.

Your choices are as follows:

• Keep the bioreactor sipping drain water, but hey, you've got a Class 100,000 processing suite.
• Cut the pipes and get your bioreactor sipping fresh, 20 air-changes-per-hour filtered air.

It turns out that that we aren't the only ones who think this is true.  In a 2006 article on biocontamination control, @GENBio reported the "original views" of chemical engineer, Jim Agalloco:

...Trying too hard to protect the bioreactor environment can adversely affect the ability to sterilize equipment. For example, a steam sterilizer normally requires an atmospheric break between its drain and the facility drain, but some biotech companies object to that layout because it compromises the controlled environment.

Somehow, the viable airborne particles of the environment matter more than the ability to sterilize equipment.  They further state:

Eliminating the atmospheric break introduces more piping and surfaces, which leads to more opportunities for microbes to grow. To protect the outside of the tank, they purposely risk contaminating the inside.

Which is exactly our position on the matter.

We're aware that managing perceived action is as important as managing action.  But taking the action that keeps cell cultures from contamination is always defensible even if it flies in the face of perception.

Zymergi Bioreactor Sterility Consulting

How to Institutionalize Tribal Knowledge

Is your knowledge going to walk out the door when key old-timers begin retiring?

Biotechnology was invented in the 1970's by Bob Swanson and Herb Boyer. Commercialization of this stuff (large-scale biologics manufacturing) started taking off in the 1980's.

We're closing in on 30-years since biotech manufacturing started. If you joined as a junior employee (in your 20's), you're now in your fifties. If you joined as a more senior employee (in your 30's), you're about to retire.

Chances are, a lot of your core competency is sloshing around in the brains of these folks. And when those guys are long gone, all that's left will be hard drives full of spreadsheets and documents.

How do you institutionalize tribal knowledge?

Zymergi has solved this problem for biotech companies with the help of Google. Prior to Google Docs and Google Mail for the enterprise, Google sold their search engine as a physical appliance. Customers purchase their machine, slide it into a server rack and configure it to crawl your web-enabled network drives.

(The process is iterative since there's quite a number of files on public network drives that ought not be there)

From here, you basically get an intranet site that looks and feels like Google, except now, instead of searching the internet, you're searching critical enterprise documents, powerpoint slides and PDFs.

The limitation with the out-of-the-box solution is that scope is limited to files on a network drive. Yet in an enterprise environment, your usable knowledge may be stored in back-end relational databases used by systems like SAP or TrackWise. How do you liberate the knowledge stuck behind the front-end application that has been engineered to run a business process (as opposed to serve data)?

ZST is Zymergi's answer. ZST is a web-application that does one thing: make web-pages out of relational database data. Coded in the .NET Framework, the ZST runs in the Windows environment, and when configured, can expose your relational data to search engines for indexing.

With QA discrepancy data and engineering change order data juxtaposed with scientific memos, anyone with authorized access can learn your business the way they learn other subjects: using Google and on the... intranet.

Want to see all discrepancies, change orders, process flow diagrams, campaign summaries, science memos about CD11a production culture pH?



Want to know about all contaminations at the seed train scale across the entire manufacturing network?

by Oliver Yu

Managing the biologics manufacturing workforce of the future will require institutionalizing tribal knowledge.  One way to tech transfer from tribal elders to young blood is with ZST and an intranet search engine.

OSI PI Historian Software is Not only for Compliance

by Oliver Yu

In October 1999, I joined a soon-to-be licensed biotech facility as Associate (Fermentation) Engineer. They had just got done solving some tough large-scale cell culture start-up problems and were on their way to getting FDA licensure (which happened in April 2000).

As the Manufacturing Sciences crew hadn't yet bulked up to support full-time commercial operations, there were 4 individuals from Process Sciences supporting the inoculum and production stages.

My job was to take over for these 4 individuals so they could resume their Process Science duties. And it's safe to say that taking over for 4 individuals would've not been possible were it not for the PI Historian.

The control system had an embedded PI system with diminished functionality: its primary goal in life was to serve trend data to HMIs. And because this was a GMP facility and because this embedded PI was an element of the validated system, the more access restrictions you could place on the embedded PI, the better it is for GMP and compliance.

Restricting access to process trends is good for GMP, but very bad for immediate-term process troubleshooting and long-term process understanding, thus Automation had created corporate PI: a full-functioned PI server on the corporate network that would handle data requests from the general cGMP citizen without impacting the control system.

Back in the early-2000's, this corporate PI system was not validated... and it didn't need to be as it was not used to make GMP forward-processing decisions.

If you think about it: PI is a historian. In addition to capturing real-time data, it primarily serves up historical data from the PI Archives. Making process decisions involves real-time, data, which was available from the validated embedded PI system viewed from the HMI.

Nonetheless, the powers that be moved towards a validating the corporate PI system, which appears to be the standard as of the late-2000's. 

Today, the success for PI system installations in the biotech/pharma sector is measured by how flawlessly the IQ and OQ documents were executed.   Little consideration is really given to the usability of the system in terms of solving process issues or Manufacturing Sciences efficiency until bioreactor sterility issues come knocking and executive heads start rolling over microbial contamination.

Most PI installations I run into try to solve the compliance problem, not a manufacturing problem, and I think this largely the case because automation engineers have been sucked into the CYA-focus rather than value-focus of this process information:

• Trends are created with "whatever" pen colors.  
• Tags are named the same as the instrumenttag that came from the control system.  
• Tag descriptors don't follow a nomenclature
• Data compression settings do not reflect reality...
• PI Batch/EventFrames is not deployed
• PI ModuleDB/ AF is minimally configured

The key to efficiencies that allow 1 Associate Engineer to take over the process monitoring and troubleshooting duties of 4 seasoned PD scientists/engineers lie precisely having a lot of freedom in using and improving the PI Historian.  

If said freedom is not palatable to the QA folks (despite the fact that hundreds of lots were compliantly released when manufacturing plants allowed the use of unvalidated PI data for non-GMP decision), the answer is to bring process troubleshooters and data scientists in on at the system specification phase of your automation implementation.

If your process troubleshooters don't know what to ask for upfront, there are seasoned consultants with years of experience that you can bring onto your team to help.

Let's be clear: I'm not downplaying the value of a validated PI system; I'm saying to get user input on system design upfront.

Continuous Improvement of Bioreactor Sterility

In a lot of bioreactor contamination investigations, the root cause is never found, that is: the cause of bioreactor contamination is not conclusively determined.

This is quite disappointing in a cGMP environment because the way problems get fixed is that you find the root cause, the technical folk propose a solution, you write it up in a CAPA and push it through the "change implementation team" and you never have to deal with that problem again.

But if root cause is never found, there is no corrective action; there certainly is no preventative action and the chain reaction of cGMP improvement never takes place.

One reason the true the proverbial smoking gun is never found is because there are too many other "smoldering guns" at the crime scene. As they say of a theory that cannot be confirmed, but also cannot be denied on Discovery Channel's show Mythbusters, "It's plausible."

• It is plausible to tilt your system to be more susceptible to contamination after you've sent thousands of liters of untreated, un-decontaminated cell culture down the drain.
• It is plausible that floor drains with no air-breaks are the source of your microbial contaminations.
• It is plausible that after several dozen pure cultures that the status-quo valve sequence on your feed-delivery line was pulling a vacuum and that sucks non-sterile fluid into your bioreactor.
• It is plausible that misaligned or misfit elastomers was the sterility breach that failed to keep out microbial contaminants.
• It is plausible that you were using the wrong type of steam for sterilization.

One reason these plausible sterility risks exist was because you didn't know about them. (if so, call me).

Another reason these plausible sterility risks exist was because they weren't worth fixing because the system wasn't "broke." You had bigger fish to fry and it's hard justifying that precious budget dollars should be spent on a system that was "working" fine.

That reasoning works until you get back-to-back contaminations and your biotech manufacturing plant is perceived to be out-of-control.

Now, you're staring down a laundry list of potential causes, all of which are plausible, many of the solvable, none of which you can cross off your list as the true root cause.

Which gets me to the point of this missive. You're not going to be mired in contamination for your entire career. You're going to have periods of success. All the sterility risks you can address during that time will ensure that your periods of failure in the future are short-lived.

Bringing In The Big Guns

In the biotech world, perception can be (and often is) reality. The perception that you brought in the big guns matters as much as the reality that you brought bullets.

It actually reminds me of that scene from the movie, Men In Black where Tommy Lee Jones' character is arming Will Smith's character with this puny gun:

In the movie, this gun is called the "Noisy Cricket" and turns out to pack an enormous punch. However, the gun's small sizes makes it look like, at best,  a weak weapon.  Look at Will Smith's face.

What does this have to do with bioreactor sterility or cell culture consulting?

Well when you have a rash of contaminations or when your production campaign is on track for failing to meet ATP, you have actually TWO problems:

1. Solving the actual problem
2. Looking like you're solving the problem

A customer once told me, "Oliver, I need both action and PERCEIVED action."

He's right, and here's why:

by Oliver Yu

In claiming to have solved a problem, the first thing people will usually ask is how you solved the problem. If you tell them the solution and the solution is credible (perceived to be viable), then great, problem solved and let's move on.

If you tell them the solution and the solution seems dubious even though it worked, you will get lingering questions and second-guesses.

Managing the perception is as important as managing the reality.

Amgen Singapore : I stand corrected

by Oliver Yu

In a previous post, I indicated that biotech manufacturing facilities in Singapore costing 200M is cheap.

It turns out that that's par for the course.

My original statement is false, but becomes true when edited thusly:

I think the [Lonza-built] Roche plant cost 290 million and the [Genentech-built] Roche plant cost 500 210 million, so if Amgen gets it done for 200 million, that's pretty cheap par for the course.

I got the 290 million figure from multiple sources:

• Pharmaceutical-Technology.com
• Roche.com.Sg

But then I mis-read the $500 million figure from the Roche Singapore About page where it says:

With a combined investment of approximately USD500 million, the site is comprised of two state-of-the-art facilities which use two different production technology platforms to manufacture biologic medicines.

(emphasis mine).

So doing the math.... both facilities cost approximately 500 million USD.  One costs 290M, so the other must cost $210M.

Thanks to a savvy reader for this correction.

Biotech Manufacturing in Singapore

Note: The original post has been corrected; this post is the result.  OLY/Jan31,2013

Amgen is going to build their first Asia plant in Singapore. Here's the link from Amgen.

The current list of Singapore Biotech Companies includes:

• Pfizer
• Roche - Built by Genentech then acquired^{OLY 1/31/13}
• Novartis
• Schering-Plough
• Genentech (Lonza built this)^{OLY 1/31/13}

All these plants are clustered in the Tuas Biomedical Park on the west side of Singapore:

(image from Google Maps)

Zooming in, you can see that these plants are basically right next to each other.

... and right next to Malaysia.

I think the Genentech plant cost 290 million and the Roche plant cost 500 million, so if Amgen gets it done for 200 million, that's pretty cheap^{OLY 1/31/13} par for the course.

CGMP.CO (without the M)

Anyone that engage(s) in the manufacture, preparation, propagation, compounding, or processing of a drug or drugs shall register and submit a list of every drug in commercial distribution [to the FDA]

The above statement is the text of 21 CFR section 207 and appears to be the way the FDA gets a list of all drug facilities they need to inspect.  Incidentally, the FDA provides a way to search that here.

Search for Lonza Biologics:



and you get this:



Whoop-dee-do.

Now check this out.  Here's the same query over at cGMP.co:

http://cgmp.co/biotechpharma/directory/search?q=lonza+biologics

Click into the Hopkinton, MA result and you see wayyyyy more information:




Quite frankly, you can cross-reference the address with Google Maps to get a picture of where this place is.

You can cross-reference this facility with the list of FDA inspections that happened there.  Perhaps a list of 483s or warning letters that was issued there.

You can see all the other facilities that are owned by Lonza as well as the other cGMP companies located in Hopkinton.

So what's this have to do with Zymergi?

Well, for one, this was built with our software: Zymergi SQL Tool.  We eat what we bake.

For two, I'm interested in finding more leads that I can turn into customers.

For three, I'm interested in owning web-properties that can help connect cell culture/fermentation/cGMP folks.

Let me know how I can improve it.

disclosure: cGMP.co is owned and operated by Zymergi LLC.

Cell Culture Engineers are #Keynesians

by Oliver Yu

It occurred to me today that the cell culture/fermentation engineers are to genetically engineered cells what Keynesian economists are to the modern economy.

This is not to say that cell culture/fermentation engineers are charlatans... but if you were a CHO cell, you'd certainly suspect that cell culture engineers don't exactly have your best interests in mind.

You see, the purpose of large-scale cell culture is not, in fact, to sustain a viable biological system.

We know this because at the end of every production culture, the cells are sent down the drain and suicided in the waste kill system. After outliving their usefulness, the cells are... in fact... waste.

The fact of cell culture is that we are replicating a biological system in a stainless steel tank - a phony environment... stimulating the culture with nutrient-rich media so that the cells can engage in the phony economy of secreting the active pharmaceutical ingredient.

We start with eugenics in the seed cultures. This is where we maintain a high copy count of the genes that produce the active pharmaceutical ingredient. Should an offspring be unable to produce enough API, it will die off from being in selective media. The genetic composition of the cell population is thereby controlled.

We then start a series of stimulate/bailout where we transfer the culture into successively larger volumes. When they've consumed their finite resources and polluted their environment, we bail them out into a larger volume.

The ultimate endgame happens at the production scale where we grow the cells beyond the carrying capacity of the culture - crashing their economy and population - so that we can harvest the fruits of their labor.

As cells don't have feelings or livelihoods, I don't feel so badly as a fermentation engineer. These cells were engineered by us for exactly one reason and the end result tends to be life-saving molecules to treat and cure human disease.

But were I a modern economist advising a stimulate/bailout path-forward so the politicians can get re-elected, I'd be a bit more responsible.

The catastrophic collapse of a population and its economy is as predictable as it is scientifically repeatable.  

Free #FDA 483s Offer Is Over. But @FDAzilla Has Opened A 483 Store

Bad News.  The Free 483s Dropbox Folder Offer has ended.

Earlier this year, I found out that FDA483s.com was offering all of the FDA.gov's free 483s in an organized format in a Dropbox:

http://blog.zymergi.com/2012/03/all-fdagov-483s-for-free_6895.html

My biggest problem using these files was:

• Click through 7 separate pages to see what was free
• When you downloaded the file, it was some gibberish like ucm191924.pdf

So when FDAzilla went through and curated it all and put it in a Dropbox, I was really happy to get access.

Afterall, commercial cell culture that produces API in the US is regulated by the FDA and that means you are subject to FDA inspection... most of which my customers are.

Good News.  FDAzilla has opened a 483 store where you can purchase 483s cheaply, instantaneously and anonymously.

Tony tells me that qualifying purchase will grant you access to the Dropbox.

@CellCultureDish On Eliminating Animal-Derived Components - ಠ_ಠ

by Oliver Yu

In a recent article on key improvements for improving the quality of biopharmaceutical manufacturing, the author, "The Dish" states:

Many problems with respect to contamination are a result of problems with raw materials and too often these raw materials are sourced from animals. Animal-derived products always carry a risk of contamination from adventitious agents, such as viruses and prions. Not only are animal sourced products a safety risk, but also they simply are no longer necessary ingredients in manufacturing.

While I agree that eliminating animal-derived sources will improve the process, this claim is rather spurious.

Let's go through this one claim at a time:

Animal-derived products always carry a risk of contamination from adventitious agents, such as viruses and prions.

This is certainly true... there is always a risk, albeit small.  Peptones and other animal-derived media components are heat-inactivated.  Automation engineers code recipes into the PLC or DCS to make certain this happens.  After the animal-derived media components are added during cell culture media preparation, the entire media is virally-inactivated with a process similar to pasteurization.  Whatever risks were there are significantly diminished before the bioreactor is even batched.

In the case of antibody manufacture, the Protein A chromatography is the step that binds the antibody and throws everything else away.  To present the risks of viruses or prions in the final product as a risk - given the viral barriers and purification capabilities of modern biotechnology - is extremely irresponsible.

What about this claim?

Not only are animal sourced products a safety risk, but also they simply are no longer necessary ingredients in manufacturing.

Is it true that we fully understand the components of animal-derived ingredients?  I'm not aware that this is true.  Perennially, miniferm experiments confirm that cultures that use animal-derived sources produce higher titers than "veggie" media or fully-defined media.

There's that je ne sai quoi in animal-derived media that the cells seem to like.  Some think it is the shear-reduction capabilities; others think it is some magic ingredient that we have yet to fully characterize, but these process R&D managers aren't stupid.  If your process titers are low, and using animal-derived media can increase titers so that you can commercially manufacture the API... you use animal-derived media.  It's that simple.

All this said, The Dish is correct about eliminating animal-derived media components... but for the wrong reasons.

Elimination of undefined media sources will reduce process variability because you've eliminated a potentially huge source of variability.  I've seen titers swing 300% from year to year with no change in the manufacturing formula, no change in manufacturing execution, no change in anything but the lots of ingredients that we get. Using defined media will simply eliminate the lingering question of, "Is it the peptone lot?"

On top of that, variability reduction increases process capability.  Even if using fully-defined media loses out 25% yield to the best performing undefined media, you gain from the predictability of your process.

Now, you can schedule campaigns with greater confidence.  You can manage the supply chain.  You can be assure that there will be fewer disturbances to your manufacturing process... you can keep less inventory... and you can ultimately save in costs.

Variability reduction is the reason you want to eliminate animal-derived media components... not risk of viral or prion contamination.

Process R&D managers that "get it" understand that optimizing titer must be balanced with optimizing process capability.

Single-Use Bioreactors (there's the Mobius by @EMD_Millipore)

Mobius CellReady Single-Use Systems

The concept of throwing away your bioreactor after a single use is quite foreign to me. My professional career grew up on stainless steel bioreactors that sat majestically in these uber-clean processing space in these plants.

But the disposable bioreactor concept appears to be gaining traction.

The idea is this:

You sterilize a plastic bag and you fill it with media. You can mix the contents of the bag. You can control temperature. You have pH and dO2 sensors hooked into a control system that maintains pH and dO2. You have everything that a stainless steel bioreactor has to maintain cell culture. Except when you're done with the operation, you get to throw away the bioreactor, whip out a new sterile bag and repeat.

What's the Advantage?

The most obvious thing is that you don't need to clean-in-place (CIP) or steam-in-place (SIP) the bioreactor... these bags come sterile. This means that you don't have CIP and SIP validation and the associated quality costs.

This also means that you don't have the piping, the valves, the boilers, the steam traps... all the infrastructure that goes into maintaining CIP and SIP systems.

CIP and SIP consumables don't need to be purchased. WFI systems can be smaller. Your Waste Kill isn't taking on all that acid, alkali and rinse solutions.

Staffing overhead to maintain and troubleshoot these systems don't need to be hired. The PLC logic or DCS recipes don't need to be coded. Control loops don't need to be tuned, so your automation engineers aren't as busy.

What about contaminations? Everyone knows from miniferm experiments that tube welding has low associated contamination risks. Everyone know that your failure rates go up the larger your tank. Is it true that success rates are higher with these single-use bioreactors?

What Stays The Same?

by Oliver Yu

You're still going to need to execute, so your production organization ought to stay the same. You're still going to need to troubleshoot the process, so your Manufacturing Sciences process support stays the same. You still need scheduling, you still need downstream recovery and purification. All that stays the same.

I Still Have A Few Questions...

• Do Single-Use Bioreactors (SUBs) decrease my plant shutdown times?
• What is the turn-around time (from dirty to prepped) on a SUB?
• What commercial products are manufactured with SUBs?
• At what scale are SUBs proven?
• What is the Total Cost of Ownership of SUBs?

If you want to know more, Dan over at EMD Millipore has some answers.

Contact Dan For More Info

Dang @Novartis, 9 #FDA 483s Since 2009!? You Should Get With @fdazilla

I was reading this FiercePharmaManufacturing's Article on Novartis' CEO under a Regulatory Cloud.

So I got to thinking... how many FDA 483s are these guys getting?

It turns out, Novartis - across all their businesses has gotten at least nine 483s since 2009.

• 17 observations made at the Liverpool UK site in 2011
• 14 observations at the Emeryville site in 2010
• 8 observations at the Vacaville site in 2011 after 5 observations from 2009
• 5 observations at Suffern NY in 2010 after 4 observations from 2009
• 1 observation at Brea in 2011
• 13 observations issued in 2011 after 2 observations at Lincoln, NE in 2010 

As Eleanor Roosevelt once said, "Learn from the mistakes of others.  You can't live long enough to make them all yourself."

Fierce is doing a good job tracking Novartis' quality problems. I'm just letting you know how to get your hands on their 483s.

Double Block and Bleed - Contamination

When filling up a bioreactor with media (colloquially called, "batching"), the media is delivered through a dedicated pipe.  When the batching is complete, there needs to be a way to contain the bioreactor... which is why there is a "near-to" block valve.

And the excess media (not required per specification) is sent to drain via a bleed valve that is on the non-sterile side of the block valve.



Figure 1: Single Block and Bleed

This is pretty standard for fermentors and bioreactors... in the 1980's.

After the media line has delivered the media, it is dirty because the nutrient-rich media has coated the pipes and will promote growth unless cleaned.

And if you have single-block-and-bleeds, your cleaning and rinse solutions are going to pound against that block valve.  Should it fail, you're going to have a contaminated bioreactor.

Modern plants... those with the luxury of building from scratch install two blocks and two bleeds, hence

Figure 2: Double Block and Bleed

by Oliver Yu

In this scenario, when the media is delivered, both block valves shut simultaneously and both bleed valves are opened simultaneously.  The excess media is sent to drain via the valves farther away from the bioreactor.

Subsequent manipulations to that line (e.g. post-use integrity tests, cleaning, sterilization) are isolated from the bioreactor by two block valves... prophylaxis for disturbances to the sterile envelope.

Read About A Successful Contamination Response

Cell Culture Database - Batch Information

You work in biopharma. Maybe you're a fermentation guru... or a cell culture hot shot. Whatever the case...
We muggles don't have the luxury of waving our wands and having protein fold themselves mid-air. There's usually a container where the process happens.
A time-window (starttime to endtime) is when processes happen.

Operators execute process instructions; these procedures is how the process happens.
The execution of process instruction results in an output. The output of the process step is the product and constitutes the what.
Lastly, the process (step) is given a name describing who the batch is.
It stands to reason that the who, what, how, when, where of a batch is characterized by:

• batchid
• product
• procedure
• starttime - endtime
• unit

and fully describe batch information for cell cultures and fermentation.

Organize Your Cell Culture Data

#FDA Inspector Just Showed Up... @fdazilla

It’s Friday. 8:30am. You’re looking forward to a long, nice weekend. Then, you get a call from one of your associates. An FDA inspector is waiting in the lobby. She’s unannounced, she’s experienced, she’s eager, and she’s ready to go.

Do you know the feeling?