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Process analytical technology (PAT) for biopharmaceuticals

Glassey, Jarka; Gernaey, Krist; Clemens, Christoph; Schulz, Torsten W.; Oliveira, Rui; Striedner, Gerald;
Mandenius, Carl-Fredrik

Published in:
Biotechnology Journal

Link to article, DOI:


10.1002/biot.201000356

Publication date:
2011

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Citation (APA):
Glassey, J., Gernaey, K., Clemens, C., Schulz, T. W., Oliveira, R., Striedner, G., & Mandenius, C-F. (2011).
Process analytical technology (PAT) for biopharmaceuticals. Biotechnology Journal, 6(4), 369-377.
https://doi.org/10.1002/biot.201000356

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Biotechnol. J. 2011, 6, 369–377 DOI 10.1002/biot.201000356 www.biotechnology-journal.com

Biotech Highlight

Process analytical technology (PAT) for biopharmaceuticals

Jarka Glassey1, Krist V. Gernaey2, Christoph Clemens3, Torsten W. Schulz3, Rui Oliveira4,5, Gerald Striedner6,
Carl-Fredrik Mandenius7
1 School of Chemical Engineering and Advanced Materials, University of Newcastle, Newcastle upon Tyne, United Kingdom
2 Center for Process Engineering and Technology, Department of Chemical and Biochemical Engineering, Technical University
of Denmark, Kgs. Lyngby, Denmark
3 Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim, Germany
4 Chemistry Department, FCT/Universidade Nova de Lisboa, Lisbon, Portugal
5 Instituto de Biologia Experimental e Tecnologica, Oeiras, Portugal
6 Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
7 Division of Biotechnology/IFM, Linköping University, Linköping, Sweden

Received 15 October 2010


Revised 7 February 2011
Keywords: CHO cells · Critical quality attributes · E. coli · Fed-batch process ·
Accepted 14 February 2011
Process analytical technology

Process analytical technology (PAT), the regulato- 1 Introduction


ry initiative for building in quality to pharmaceuti-
cal manufacturing, has a great potential for im- The term (and acronym) Process Analytical Tech-
proving biopharmaceutical production.The recom- nology (PAT) was introduced by the US FDA as an
mended analytical tools for building in quality, intiative to bring an improved understanding of
multivariate data analysis, mechanistic modeling, pharmaceutical manufacturing processes to in-
novel models for interpretation of systems biology crease the quality of their products [1]. The FDA
data and new sensor technologies for cellular uses the expression “to build in quality into the
states, are instrumental in exploiting this potential. pharmaceutical manufacturing process”, thereby
Industrial biopharmaceutical production has grad- implying that high product quality should ideally
ually become dependent on large-scale processes be created already at the design stage of the man-
using sensitive mammalian cell cultures. This fur- ufacturing process [1–3], contrary to traditional
ther emphasizes the need for improved PAT solu- processes that are often the result of empirical or
tions. We summarize recent progress in this area rule-of-thumb design. In addition, they also em-
based on an expert workshop held at the 8th Euro- phasize the need for improved on-line monitoring
pean Symposium on Biochemical Engineering Sci- and control methods to maintain high product
ences (Bologna, 2010), and highlight new opportu- quality during manufacturing operations. In the
nities for exploiting PAT when applied in biophar- biopharmaceutical industry PAT principles are
maceutical production. We conclude with recom- adopted with great care due to the fact that bio-
mendations for advancing PAT applications in the pharmaceuticals and their production systems are
biopharmaceutical industry. very complex. Compared to the small molecule
pharma industry the complexity of biopharmaceu-
tical proteins multiplies the analytical quality
issue.
Figure 1 illustrates a central concept of the PAT
Correspondence: Professor Carl-Fredrik Mandenius, IFM, Linköping philosophy: to identify and control the critical qual-
University, 581 83 Linköping, Sweden ity attributes (CQA) of the process based on moni-
E-mail: cfm@ifm.liu.se
toring and adjusting the critical process parame-
Abbreviations: CQA, critical quality attributes; CPP, critical process param-
ters (CPP).
eters; MVDA, multivariate data analysis; PAT, process analytical technolo- PAT forms a part of the Quality by Design (QbD)
gy; PCA, principal component analysis; PLS, partial least squares; concept, also a regulatory-inspired methodology
QbD, Quality by Design where PAT provides tools to enable the quality

© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 369


Biotechnology Biotechnol. J. 2011, 6, 369–377
Journal

Figure 1. The relationship of critical process parameters


(CPPs) and critical quality attributes (CQAs) in a bio-
pharmaceutical manufacturing process according to the
PAT concept.

goals [4, 5]. In QbD the acceptable ranges of the The first tier in the figure shows three cate-
CQAs and the CPPs are defined for the manufac- gories of methods for acquiring quality-related
turing process (Fig. 2). data from the pharmaceutical manufacturing pro-
A large number of analytical methodologies and cess: methods for (1) on-line sensing, (2) ‘omics’-
tools, here referred to PAT tools, are useful for re- based analysis, and (3) analysis of CQAs. These
alizing QbD. These PAT tools cover methodologies methods can show considerable overlaps based on
ranging from analytical chemistry, through control deeper process understanding.
theory and mathematical and statistical modeling In the second tier, the measurement data ob-
methods. In Figure 3 the most important of these tained in the first tier are processed using models,
methods and tools are compiled and related to their and thereby converted to useful process-related
role in building quality into the pharmaceutical information. Here multivariate data analysis mod-
manufacturing process. els, mechanistic models or any other modeling ap-
proach (e.g., neural network models as a typical
black-box model example) are highligthed.
The third tier in the figure shows alternative
control methods that can be applied with any of the
previous methods for data acquisition and analysis
in the first and second tiers, or by combining these
in appropriate ways.
In the most straightforward case it is an issue of
feeding back the information to the process to cor-
rect it. In QbD, we define the control space from
pre-knowledge created in separate experiments.
This pre-knowledge is in the best case optimized,
also using first tier methods.
The fourth tier represents a conceptually high-
er level of using the generated information. This
may be a human decision maker, an operator on the
plant, or a Quality Control (QC) officer deciding on
the release of a batch based on a well-defined set
of quality criteria. It may also be a more sophisti-
cated decision making mechanism – implemented
in an internet-based support system, e.g., using
historical data and statistical procedures.
Figure 3 illustrates the rich collection of suitable
Figure 2. The design space and control space as defined in QbD. alternatives for accomplishing the objectives of the
The axes represent the critical quality parameters. PAT initative for biopharmaceuticals.

370 © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim


Biotechnol. J. 2011, 6, 369–377 www.biotechnology-journal.com

Figure 3. Conceptual interrelations of


PAT tools and methods for biopharma-
ceutical processes structured on four
consecutive levels (tiers). The first tier in-
volves data acquisition tools, the second
tier data processing of these acquired
data. The methods of the third tier use
the processed data for controlling the
manufacturing process, and the fourth
tier uses the data for advanced data
analysis for further manufacturing
control.

In this article we highlight a few areas of recent new opportunities with on-line sensing.We also re-
progress and opinions on application of PAT late these to industrial requirements and practice,
methodologies of relevance for biopharmaceutical and conclude with an identification of future needs
production, based on a workshop held at the 8th Eu- to improve the impact of the PAT tools of benefit for
ropean Symposium on Biochemical Engineering biopharmaceutical production but also to biochem-
Sciences (Bologna, 5 September 2010). As typical ical engineering production in a more general per-
biopharmaceutical products we include therapeu- spective.
tic antibodies, regulatory proteins such as insulin
or growth hormone, enzymes with a pharmacolog-
ical effect such as thrombin or tissue plasminogen 2 Potential of MVDA in implementing PAT
activator, or vaccine components. But there can also on biopharmaceutical production
be other biopolymers with therapeutic effect, for
example, a gene therapy vector or a carbohydrate MVDA has the potential to play a central role in
polymer. PAT and can interact with several other methods
The quality issues for all these biopharmaceuti- and techniques that analyze the biopharmaceutical
cals are similar, although not identical. The main manufacturing process, leading to better under-
concerns are the purity of the protein and the de- standing of it and exerting control of its quality.
tection of impurities from the host organism, the The use of a range of established analytical
culture media or formation of adverse product techniques alongside more advanced methods,
forms. The host organism and the biomolecular such as near-infrared (NIR) spectroscopy, multi-
structure of the product have significant effects on wavelength fluorescence and electronic nose,
the prerequisites of applying PAT. Progress in PAT within the PAT framework typically leads to the
and an improved understanding of its applications generation of large multivariate data sets. To ex-
contribute to advanced manufacture of these com- tract useful information leading to deeper process
plex biopharmaceutical products. understanding, it is essential to employ appropri-
The article focuses on a few aspects of PAT: the ate data analysis techniques capable of dealing
furthering of multivariate data analysis (MVDA) with these multidimensional data. These data sets
for enhancing and building in quality into the bio- are highly heterogeneous, with varying frequency
pharmaceutical process, the exploitaion of mecha- of various measurements, typically with significant
nistic models as an additional support tool, the use delays in the off-line measurements. They are also
of systems biology data, the challenges of using often highly correlated, non-linear in nature and
mammalian cells in the processes, and examples of with high levels of redundancy and noise. Tech-

© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 371


Biotechnology Biotechnol. J. 2011, 6, 369–377
Journal

niques such as principal component analysis 3 Using mechanistic models as PAT tools
(PCA), partial least squares (PLS), parallel factor for predicting CQA in the
analysis (PARAFAC), unsupervised clustering biopharmaceutical process
methods and others, have long been used success-
fully by chemometricians for interpretation of An alternative modeling approach to MVDA is to
multidimensional data sets in various subject apply a mechanistic model description of the bio-
areas, and their usefulness has also been proven in pharmaceutical manufacturing system.
the area of biopharmaceuticals. A detailed descrip- PAT, and especially its application to QbD, can
tion of these techniques is beyond the scope of this only be realized in practice if sufficient process
contribution and can be found in a variety of text- knowledge is available to explain the effect of CPPs
books and manuscripts (e.g. [6–8]). Their ability to on CQAs. In this respect, mechanistic modeling has
reduce dimensionality by removing the redundan- gained renewed attention because a mechanistic
cy and noise leads to the identificaton of salient model can be considered as a structured represen-
features in the data. These features can subse- tation of the available process knowledge. Indeed,
quently be used in bioprocess monitoring, fault during the model-building procedure, the process
detection and process optimization, as has been knowledge is coded in a mechanistic model using
described extensively in the literature over the appropriate mathematical expressions [18–21].
years. Successful applications cover a range of Such a model therefore incorporates process-rele-
production systems from various microbial to cell vant input (critical process variables) – output
culture systems and a wide range of industrially (product concentration and product quality attrib-
relevant products. Identification of deviations utes) relationships, which can be used to establish
from nominal batch behaviour either in the seed or a proper design space. The mechanistic model
production cultivations (e.g. [9]), early detection of therefore has great value in planning experiments,
contamination or detection of faulty sensors are all or in determining which critical process variables
critical process decisions that have been improved necessitate tighter control [21, 22].
using MVDA techniques [2]. However, most impor- Recent applications of mechanistic models for
tantly, the PAT methodology, as defined by the FDA bio-based processes, such as biocatalysis [23] and
[1], requires effective control of CPPs affecting the fermentation [24] witnessed an interesting devel-
CQAs. This task is aided by the MVDA techniques opment. It should be emphasized indeed that the
enabling on-line estimation of such critical pa- application of mechanistic modeling is not only rel-
rameters as biomass, glucose and various other evant for the pharmaceutical industry, but also for
metabolites [10–12]. fermentation and biocatalytic processes. In fact,
Biopharmaceutical processes are predomi- many of the tools and techniques that are now
nantly operated in a batch mode, which leads to adopted by the pharmaceutical industry for the im-
further increase in the complexity of the resulting plementation of PAT were developed much earlier
data arrays. The analysis of such data structures by, or in close collaboration with, the fermentation
typically requires a modification of the traditional industry [25].
MVDA techniques or an application of non-linear One of the most frequently cited disadvantages
alternative methods. Multiway PCA and PLS have of using mechanistic models is excessive time and
been introduced in mid 1990 by Nomikos and resource requirements during the development
MacGregor [13] and used sucessfully to account phase. A systematic model development methodol-
for the major non-linearity of the batch processes ogy addresses this drawback [26] and is beneficial
[9]. Alternative non-linear data analysis tech- for a number of reasons: (i) model development is
niques, such as non-linear variants of PCA, PLS or more efficient (i.e., less time and resources re-
various forms of artificial neural networks, have quired), and (ii) communication and knowledge
also been shown to be effective in bioprocess mon- transfer among the various members of the multi-
itoring and control (e.g. [14, 15]). Whereas issues of disciplinary team (i.e., researchers, engineers, op-
regulatory approval of such ‘black-box’ data analy- erators, managers) typically involved in the devel-
sis techniques still represent a significant chal- opment and implementation of a PAT system are
lenge in their application in a manufacturing envi- facilitated. To this end, the matrix notation is com-
ronment, techniques such as autoassociative neu- monly used because it allows a compact and visu-
ral networks (AANN), self-organising maps (SOM) ally appealing description of a complex mathemat-
or support vector machines (SVM) can provide a ical model [20, 27].
more accurate representation of the fundamental The relatively large cost of developing a mech-
features contained in the available measurements anistic model is increasingly justified if model
[16, 17]. analysis techniques are applied to the mechanistic

372 © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim


Biotechnol. J. 2011, 6, 369–377 www.biotechnology-journal.com

model as part of good modeling practice (GMoP) ratio, has been established (to be published). Inte-
[28]. Moreover, mechanistic models also have great gration of comprehensive process data also yields
potential in Design of Experiment (DoE) applica- an increased process understanding and new
tions. GMoP comprises the application of a set of approaches for cell design [34]. In this work it was
mathematical and statistical techniques that allow also demonstrated that the reduction of the induc-
improvements in the use and the reliability of the tion level shows a significant increase of the solu-
model. Examples include the calculation of corre- ble recombinant protein fraction. Real-time pre-
lation coefficients and confidence intervals for es- diction of soluble and insoluble recombinant pro-
timated parameters to verify sufficient data quality tein provides access to a CQA with transcription
and quantity to allow reliable parameter estimation rate control as the CPP. This is just one example
[20]. Additional examples include uncertainty demonstrating a PAT solution with focus on prod-
analysis and sensitivity analysis [28–30]. Model uct quality aspects specific for bacterial-based pro-
analysis indeed provides answers to important duction processes.
questions such as: When is the time optimal for the Microbial production systems, especially E. coli,
collection of experimental data? Which variables were the host of choice in the early biopharmaceu-
should be measured? Which parameters can be es- tical processes. However, today mammalian cells
timated given an experimental data set and the have become the dominant system for the produc-
mechanistic model? tion of recombinant proteins mainly due to their
capacity of required protein folding and post-
translational modification. Thus, the resulting
4 Adapting the PAT tools to biopharma- quality and efficiency of glycosylated proteins, e.g.,
ceutical production with mammalian cells monoclonal antibodies, produced by recombinant
expression systems in mammalian cells can be
The actual application of the MVDA and mecha- considered to be superior to other expression sys-
nistic models depends to an extent on the particu- tems such as bacteria, plants and yeasts [35]. Mam-
lar host organism used in the manufacturing malian expression systems that are well known
process. Here we compare the two alternatives that since the licensure of tissue plasminogen activator
are so far dominant, E. coli and mammalian cells, in 1987 include Chinese hamster ovary (CHO) or
from a PAT perspective. Without a doubt, monitor- murine lypmphoid cell lines (e.g., NS0, Sp2/0).They
ing of living cells used as hosts, in an environment offer the potential of increased productivities,
involving a multitude of parallel reactions and which is one of the major driving forces for indus-
thousands of components as solid fraction in a mix- trial manufacturing. Wurm [35] reported that
ture of gas and liquid, is a very ambitious and chal- 60–70% of all recombinant protein pharmaceuticals
lenging task regardless of which organism is used. are produced in mammalian cells, usually following
As a consequence, on-line data acquisition has to a well-established production scheme. Moreover,
be individually designed for each organism used in Farid [36] stated that antibodies played an impor-
bioprocessing. In contrast to bacterial cells, where tant role in several of the important advances in
synthesis of recombinant proteins is strictly asso- pharmacotherapy that contributed to the treatment
ciated with cellular growth, product formation in of infectious diseases, cancer and autoimmune dis-
mammalian systems is more or less separated from eases.
growth. This fact leads to different process control This clinical and commercial success of mam-
strategies and specific monitoring requirements malian products, e.g., monoclonal antibodies, has
for each type of cell factory. Optimal exploitation of led to the need for large scale production with
bacterial systems can only be obtained by setting mammalian cell cultures. Furthermore, these in-
conditions that allow for recombinant gene expres- creased demands for therapeutic antibodies also
sion at high yet tolerable rates and simultaneous resulted in a rapid expansion of global manufac-
maintenance of cell viability and growth [31]. turing capacity, e.g., increasing size of reactor ca-
Growth rate, gene dosage and product titer are the pacity up to 10 m3. At the same time process effi-
central quality-related process variables. Real- ciency was improved to reduce manufacturing
time access to each of these variables is enabled by costs [37]. Clearly, besides the biological and qual-
the application of comprehensive on- and off-line ity-related advantages of the mammalian expres-
monitoring tools in combination with MVDA-based sion systems currently in use, economical aspects
predictions [32, 33]. For example, based on these also play an important role in the industrial pro-
results an improved transcription tuning concept, duction of monoclonal antibodies. Werner [38] il-
utilizing the real-time predicted cell dry weight lustrated that high therapeutic dosages of mono-
(CDW) for setting of a constant inducer to CDW clonal antibodies usually demand high capacity

© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 373


Biotechnology Biotechnol. J. 2011, 6, 369–377
Journal

needs, which in turn require significant capital in- stricts the choice to direct injection mass spec-
vestments, but also stimulate innovation for troscopy (DI-MS), Fourier transform infrared spec-
process improvements to decrease cost of goods troscopy (FT-IR) and (1H) NMR [42]. Among these,
(COG). DI-MS is considered the technique with the high-
est potential since it provides a fingerprint of the
complete exometabolome, is highly sensitive, re-
5 Integration of systems biology data from quires no sample treatment and is cheap, fast and
the host organisms of the bioprocess into high-throughput [41].
the PAT methodology Chemometrics plays a very important role in
PAT in MVDA, extraction of knowledge from large
This preference for mammalian systems in bio- datasets, modeling and statistical process control.
pharmaceutical manufacture has placed particular MVDA modeling is also widely applied in the
quality aspects, such as protein glycosylation het- analysis of ‘omics’ datasets to deduce the mecha-
erogeneity, charge distribution and polymorphism, nisms that support a given (observed) biological
at the forefront of research and development. function (the top-down approach) [43]. Systems bi-
Such CQAs are linked to molecular details pro- ology is concerned with the interpretation of data
duced by highly regulated intracellular processes to infer mechanisms (top-down) and to infer func-
that are not part of the mainstream carbon and ni- tion from known mechanisms (bottom-up). In fact
trogen fluxes. Although the dependency of, for ex- these two approaches can also be found in PAT
ample, protein glycosylation patterns on process modeling. The top-down approach is based on
operation parameters such as pH, temperature, chemometric modeling, while the bottom-up ap-
medium composition and carbon source feeding proach is based on mathematical (mechanistic)
rate has been demonstrated in several studies (e.g. modeling. In PAT, extensive challenges remain to
[39, 40]), systematization of knowledge and demon- be addressed in the integration of macroscopic
stration of controllability become impossible with- (process monitoring and control) models with sys-
out the consideration of intracellular processes. tems biology models [44, 45]. One important aspect
This is where systems biology can play an impor- is the efficient integration of mechanisms and
tant role in PAT, specifically in: (1) the generation MVDA.As new mechanisms are disclosed they rep-
of knowledge, (2) the elucidation of mechanisms, resent constraints to top-down MVDA (top-down
and (3) the modeling of the biological functions at and bottom-up meet halfway). Hybrid semi-para-
the basis of molecular level CQA. metric modeling may provide an adequate answer
Substantial efforts are made in academic and to some of these challenges. It represents a com-
industrial research in collecting ‘omics’ data sets at promise between rigorous mathematical modeling
various cultivation time to discover the fundamen- and empirical (chemometric) modeling, providing
tal regulation mechanisms of certain product a flexible framework to merge a priori mechanisms
CQAs, but also to find new ways to increase yield with heterogeneous datasets of the different layers
and productivity. In a PAT approach, it would be of of information about the cell and the process [45].
particular use to concentrate attention on the ex-
ometabolomics in the process.The exometabolome,
which consists of the total quantitative collection of 6 Challenges limiting routine industrial
small molecular weight compounds (metabolites) application of PAT
present in the extracellular medium, provides a
very informative “footprint” of cellular activity, from The development of efficient mammalian bio-
which it is possible to infer its intracellular state up processes in the biopharmaceutical industry has
to the proteomic and genomic levels [41]. Today led to increased product yields above 5 g/L mono-
cheap, fast and high-throughput techniques with clonal antibody. These achievements can be attrib-
little or even no sample preparation exist that en- uted to the use of high-producer cell clones with
able the measurement of the exometabolome. This enhanced cell productivity and to the optimization
opens an array of opportunities for advanced mon- of key process characteristics, such as advanced
itoring techniques that can support real-time con- process control and well-designed nutrient compo-
trol of critical intracellular processes at the basis of sitions, that are integrated into a platform technol-
the CQA. Mass spectrometry, NMR spectroscopy ogy for biopharmaceutical manufacturing process-
and vibrational spectroscopy are the main tech- es. However, to identify potential process parame-
niques currently used for metabolomics. The need ters that have an impact on CQAs, the process de-
for high-throughput, short analysis time compati- veloper first need to identify and understand a set
ble with at-line or even on-line measurement re- of CPPs.

374 © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim


Biotechnol. J. 2011, 6, 369–377 www.biotechnology-journal.com

When addressing QbD as described in the ICH the sensitive process parameters. In other words,
guidelines (ICH Q8: pharmaceutical development, the collected data are translated into process infor-
Q9: quality risk management and Q10: pharmaceu- mation and subsequently further transformed into
tical quality system), typical questions in the field real process knowledge using advanced analysis
of bioprocess development arise: Can we identify techiques, e.g., PCA, PLS or orthogonal PLS (OPLS)
CPPs and to what extent do these parameters have (Fig. 4). The generated process knowledge can be
an impact on an industrial bioprocess? Can we ad- subsequently used to monitor or control the critical
just these process parameters? Thus, as a first step sources of variability to ensure a consistent quality
in addressing those questions from an industrial for an advanced manufacturing process.
point of view, a ‘proposed workflow’ is presented The quality issues for all the biopharmaceuti-
with focus on new sensor techologies and advanced cals referred to in this contribution are similar, al-
data analysis for process data based on multivari- though not identical. The main concerns are the
ate projection techniques. purity of the protein and the detection of impurities
from the host organism, the culture media or for-
6.1 Industrial workflow to implement the QbD/PAT mation of adverse product forms. The host organ-
concept ism and the biomolecular structure of the product
have significant effects on the prerequisites of ap-
The implementation of advanced PAT technologies plying PAT.
into an already existing GMP manufacturing facil- Progress in PAT and an improved understand-
ity can be complex and faces many challenges. For ing of its applications contribute to advancing man-
example, new innovative process sensors for mam- ufacture of these complex biopharmaceutical prod-
malian suspension cultures need to be easy-to- ucts.
handle in a daily working routine, e.g., a simple cal-
ibration procedure is required. Moreover, PAT sen-
sors can be applied in a robust and applicable man- 7 Recommendations
ner for a broad range of process variants. This
allows the amount of valuable process data to be Based on the workshop, the following recommen-
increased and the corresponding know-how trans- dations for further developing PAT methodology
lated into a monitoring or control scheme to handle for biopharmaceuticals are suggested:

Figure 4. Proposed industrial workflow


to address the QbD/PAT concept using
multivariate projection techniques to
identify CPPs and their relationship to
CQAs.

© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 375


Biotechnology Biotechnol. J. 2011, 6, 369–377
Journal

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