Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis
Abstract Background Novartis and the University of Oxford’s Big Data Institute (BDI) have established a research alliance with the aim to improve health care and drug development by making it more efficient and targeted. Using a combination of the latest statistical machine learning technology with...
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2021
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oai:doaj.org-article:d43dee580b834d6ca85817e178bae9182021-11-14T12:39:26ZAdvancing data science in drug development through an innovative computational framework for data sharing and statistical analysis10.1186/s12874-021-01409-41471-2288https://doaj.org/article/d43dee580b834d6ca85817e178bae9182021-11-01T00:00:00Zhttps://doi.org/10.1186/s12874-021-01409-4https://doaj.org/toc/1471-2288Abstract Background Novartis and the University of Oxford’s Big Data Institute (BDI) have established a research alliance with the aim to improve health care and drug development by making it more efficient and targeted. Using a combination of the latest statistical machine learning technology with an innovative IT platform developed to manage large volumes of anonymised data from numerous data sources and types we plan to identify novel patterns with clinical relevance which cannot be detected by humans alone to identify phenotypes and early predictors of patient disease activity and progression. Method The collaboration focuses on highly complex autoimmune diseases and develops a computational framework to assemble a research-ready dataset across numerous modalities. For the Multiple Sclerosis (MS) project, the collaboration has anonymised and integrated phase II to phase IV clinical and imaging trial data from ≈35,000 patients across all clinical phenotypes and collected in more than 2200 centres worldwide. For the “IL-17” project, the collaboration has anonymised and integrated clinical and imaging data from over 30 phase II and III Cosentyx clinical trials including more than 15,000 patients, suffering from four autoimmune disorders (Psoriasis, Axial Spondyloarthritis, Psoriatic arthritis (PsA) and Rheumatoid arthritis (RA)). Results A fundamental component of successful data analysis and the collaborative development of novel machine learning methods on these rich data sets has been the construction of a research informatics framework that can capture the data at regular intervals where images could be anonymised and integrated with the de-identified clinical data, quality controlled and compiled into a research-ready relational database which would then be available to multi-disciplinary analysts. The collaborative development from a group of software developers, data wranglers, statisticians, clinicians, and domain scientists across both organisations has been key. This framework is innovative, as it facilitates collaborative data management and makes a complicated clinical trial data set from a pharmaceutical company available to academic researchers who become associated with the project. Conclusions An informatics framework has been developed to capture clinical trial data into a pipeline of anonymisation, quality control, data exploration, and subsequent integration into a database. Establishing this framework has been integral to the development of analytical tools.Ann-Marie MallonDieter A. HäringFrank DahlkePiet AardenSoroosh AfyouniDaniel DelbarreKhaled El EmamHabib GanjgahiStephen GardinerChun Hei KwokDominique M. WestEwan StraitonSibylle HaemmerleAdam HuffmanTom HofmannLuke J. KellyPeter KruscheMarie-Claude LarameeKarine LheritierGreg LigozioAimee ReadieLuis SantosThomas E. NicholsJanice BransonChris HolmesBMCarticleMachine learningData managementData anonymisationClinical trialMedicine (General)R5-920ENBMC Medical Research Methodology, Vol 21, Iss 1, Pp 1-11 (2021) |
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DOAJ |
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EN |
| topic |
Machine learning Data management Data anonymisation Clinical trial Medicine (General) R5-920 |
| spellingShingle |
Machine learning Data management Data anonymisation Clinical trial Medicine (General) R5-920 Ann-Marie Mallon Dieter A. Häring Frank Dahlke Piet Aarden Soroosh Afyouni Daniel Delbarre Khaled El Emam Habib Ganjgahi Stephen Gardiner Chun Hei Kwok Dominique M. West Ewan Straiton Sibylle Haemmerle Adam Huffman Tom Hofmann Luke J. Kelly Peter Krusche Marie-Claude Laramee Karine Lheritier Greg Ligozio Aimee Readie Luis Santos Thomas E. Nichols Janice Branson Chris Holmes Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| description |
Abstract Background Novartis and the University of Oxford’s Big Data Institute (BDI) have established a research alliance with the aim to improve health care and drug development by making it more efficient and targeted. Using a combination of the latest statistical machine learning technology with an innovative IT platform developed to manage large volumes of anonymised data from numerous data sources and types we plan to identify novel patterns with clinical relevance which cannot be detected by humans alone to identify phenotypes and early predictors of patient disease activity and progression. Method The collaboration focuses on highly complex autoimmune diseases and develops a computational framework to assemble a research-ready dataset across numerous modalities. For the Multiple Sclerosis (MS) project, the collaboration has anonymised and integrated phase II to phase IV clinical and imaging trial data from ≈35,000 patients across all clinical phenotypes and collected in more than 2200 centres worldwide. For the “IL-17” project, the collaboration has anonymised and integrated clinical and imaging data from over 30 phase II and III Cosentyx clinical trials including more than 15,000 patients, suffering from four autoimmune disorders (Psoriasis, Axial Spondyloarthritis, Psoriatic arthritis (PsA) and Rheumatoid arthritis (RA)). Results A fundamental component of successful data analysis and the collaborative development of novel machine learning methods on these rich data sets has been the construction of a research informatics framework that can capture the data at regular intervals where images could be anonymised and integrated with the de-identified clinical data, quality controlled and compiled into a research-ready relational database which would then be available to multi-disciplinary analysts. The collaborative development from a group of software developers, data wranglers, statisticians, clinicians, and domain scientists across both organisations has been key. This framework is innovative, as it facilitates collaborative data management and makes a complicated clinical trial data set from a pharmaceutical company available to academic researchers who become associated with the project. Conclusions An informatics framework has been developed to capture clinical trial data into a pipeline of anonymisation, quality control, data exploration, and subsequent integration into a database. Establishing this framework has been integral to the development of analytical tools. |
| format |
article |
| author |
Ann-Marie Mallon Dieter A. Häring Frank Dahlke Piet Aarden Soroosh Afyouni Daniel Delbarre Khaled El Emam Habib Ganjgahi Stephen Gardiner Chun Hei Kwok Dominique M. West Ewan Straiton Sibylle Haemmerle Adam Huffman Tom Hofmann Luke J. Kelly Peter Krusche Marie-Claude Laramee Karine Lheritier Greg Ligozio Aimee Readie Luis Santos Thomas E. Nichols Janice Branson Chris Holmes |
| author_facet |
Ann-Marie Mallon Dieter A. Häring Frank Dahlke Piet Aarden Soroosh Afyouni Daniel Delbarre Khaled El Emam Habib Ganjgahi Stephen Gardiner Chun Hei Kwok Dominique M. West Ewan Straiton Sibylle Haemmerle Adam Huffman Tom Hofmann Luke J. Kelly Peter Krusche Marie-Claude Laramee Karine Lheritier Greg Ligozio Aimee Readie Luis Santos Thomas E. Nichols Janice Branson Chris Holmes |
| author_sort |
Ann-Marie Mallon |
| title |
Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| title_short |
Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| title_full |
Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| title_fullStr |
Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| title_full_unstemmed |
Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| title_sort |
advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis |
| publisher |
BMC |
| publishDate |
2021 |
| url |
https://doaj.org/article/d43dee580b834d6ca85817e178bae918 |
| work_keys_str_mv |
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