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Chapter 15
Advanced Data Analytics Application inBiomanufacturing Processes
JunLuo, LinQiu, YangTang, GrantSumida, SidKundu, andYimingPeng
Abstract Biomanufacturing drug substance processes include cell culture (thaw,
seed train, inoculum, and protein production), harvest, and purication steps. Due to the living nature, the bioprocess inherently has higher variability when compared to chemical reactions. Ensuring consistent process performance and continuous process improvement are ongoing challenges for bioprocess.
Thorough characterization of process and product attributes using statistical design of experiments (DoE) during the process design (PD) stage is a proven means to establish the process and product knowledge. Recent accelerated develop­ment timelines are putting pressure and limitations on the extent of characterization during the PD stage, and, therefore, increasing the importance of a lifecycle approach to accumulate process and product knowledge during the post-approval stage of process validation (i.e., continued process verication).
Following telecoms, advertising, and insurance, the biopharma industry has started to embrace methods like Bayesian statistics and advanced data analytics (ADA) to gain additional process and product understanding, improved process control, and process performance. Using ADA may elucidate previously undetected relationships between process inputs and outputs, which hold promise as an addi­tional tool to augment traditional DoE as a means to gain actionable insights, pro­cess and product knowledge.
An internal multidisciplinary team (e.g., ADA) comprising data engineers, data scientists, bioprocess experts, and a translator /project manager is formed.
J. Luo (*) · G. Sumida Manufacturing Sciences, Genentech, Vacaville, CA, USA e-mail: luo.jun@gene.com
L. Qiu · Y. Peng Nonclinical Biostatistics, Genentech, South San Francisco, CA, USA
Y. Tang Nonclinical Biostatistics, Roche, Mississauga, ON, Canada
S. Kundu Cell Culture and Bioprocess Operations, Genentech, South San Francisco, CA, USA
K. Gadamasetti, S. A. Kolodziej (eds.), Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry,
https://doi.org/10.1007/978-3-031-62007-2_15
437© The Author(s), under exclusive license to Springer Nature Switzerland AG 2024
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J. Luo et al.
IT infrastructure to support ADA projects is established, the standard approaches to run the case studies are developed, and a library of models for bioprocess is built. An upstream process case study to improve upstream productivity and process robustness is discussed. The team is able to extract, cleanse, ingest, and process 800GB of data from 11 disparate data sources into a cloud environment to evaluate more than 100 hypotheses. Implementing the insights leads to improved process performance. Through the case study, the strategy to sustain the internal capability is developed. The importance of building ADA capabilities to enable more efcient and reliable bioprocesses is discussed.
Keywords Advanced data analytics · Machine learning · Cell culture · Process performance variation

15.1 Introduction

Biomanufacturing drug substance processes include cell culture (thaw, seed train, inoculum and protein production), harvest, and purication (chromatography, viral ltration, ultraltration dialtration, and freeze) steps. Due to the living nature, the bioprocess inherently has higher variability when compared to chemical reaction. To ensure consistent process performance and product quality, a bioprocess valida­tion lifecycle program is needed. The lifecycle includes three stages: PD (Stage 1), process qualication (PQ, Stage 2), and continued process verication (CPV, Stage
3) [1]. The data are collected and evaluated through all three stages of the lifecycle to generate process knowledge and establish scientic evidence that a process is capable of consistently delivering quality products.
Information used to characterize the process can be split as inputs and outputs of the process. For a specic step of mammalian cell culture processes, process inputs could be raw material, equipment, operational parameters (e.g., operator, operation sequence, operating parameters), and any measurements of the initial state, etc. Process outputs could be process performance indicators (PI, or KPI: key perfor­mance indicator) from the specic process step or any downstream steps, and prod­uct quality attributes (PQA or CQA: critical quality attributes). Process knowledge could be summarized in an equation or model to describe the correlation between inputs and output. Quantitative models for optimization commercial drug substance manufacturing processes have recently attracted increasing attention. Different data analysis methods may be used to build process knowledge during different process validation stages.
Per International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) quality guidelines ICH Q8 (R2), ICH Q9, and ICH Q10, the concept of quality by design is introduced. This concept includes quality-risk management systems and the implementation of Pharmaceutical Quality Systems. Key elements are critical process parameters (CPP), which affect CQAs, and DoE [2]. Thorough characterization of process and product attributes
15 Advanced Data Analytics Application inBiomanufacturing Processes
439
using statistical DoE during the PD stage is a proven means to establish process/ product knowledge. DoE-based approaches can provide a deeper understanding of how product quality attributes and process-related impurities change when several process operating parameters vary simultaneously for a given unit operation, and thus lead to increased process knowledge with respect to the robustness of a culture step or combination of culture steps. Prior to designing a DoE study, a risk assess­ment is typically conducted to rank the risk of process parameters regarding the impact on process performance and product quality. This is based on the previous knowledge from the platform process, rst principles, early development data, and literature review, etc. Based on the outcome of risk assessment, follow-up studies will be executed to identify the acceptable range for process parameters [3]. Since most bioprocess unit steps easily have more than four factors, the rst round of experiments typically uses the screening design (e.g., Plackett-Burman method) to identify the most important factors early in the experimentation phase when com­plete knowledge about the system is usually unavailable [4]. Once the important factors are identied, a follow-up DoE study (e.g., response surface designs or fac­torial design) to understand the interaction, and to rene the model. Note: Response surface design is recommended especially if there is suspected curvature in the response surface. Once the model is rened, the model could be used to predict worst-case conditions for certain process output, and the predicted worst-case con­ditions could be further tested in experiments. Separately, certain univariate studies could be performed to provide knowledge for ongoing manufacturing support. For example, a pH excursion study (effect of the short-term high/low pH) is typically executed to understand the effect of the pH probe spike issue occasionally observed in commercial manufacturing.
Many bioprocess companies have a CPV program that involves univariate trend­ing of quality attributes and process performance indicators, which are used to establish the evidence for process in control or identify process change/shift/excur­sion for further investigation. If process performance or capability is trending unfa­vorably, the ability to adaptively respond and adjust controls is contingent on the availability of documented causal relationships (i.e., models) between controllable inputs and important process/product outputs. With accelerating development time­lines, the accumulation of process knowledge during the CPV stage of process vali­dation is becoming increasingly important. Different statistical methods/models could be used to collect knowledge during the CPV phase in addition to performing experiments. For example, when the sample size is small, Bayesian statistics is a preferred method. With the increase of sample size, advanced data analytics (ADA) can be used.
Sample sizes of data in biomanufacturing drug substance processes are fre­quently quite small due to time, economic, and physical constraints. The effect of sample size on the interpretation of classical signicance tests has been emphasized [5]. The predictive model built upon a small number of samples may highly rely on the particular method for parameter estimation [6]. Under such circumstances, to enable meaningful model prediction and results interpretation, Bayesian statistics is usually preferred [7] because Bayesian methods incorporate both the observed data