Dataset Information

Automated Sample Storage in Biobanking to Enhance Translational Research: The Bumpy Road to Implementation.

ABSTRACT: The low reproducibility of biomarker research is a major holdback for the translation of research results to the bedside. Sample integrity has been identified as a key factor that contributes to improved reproducibility. The key mission of biobanks is to ensure that all activities and materials are managed according to standardized procedures and best practices to ensure and preserve sample integrity. When handling large numbers of biospecimens automation of sample handling and storage is often the method of choice to maintain and improve sample integrity. In December 2013, the centralized Biobank of the University Hospitals and the Catholic University of Leuven (UZ KU Leuven) decided to implement automated systems for sample storage and retrieval, one for storage at -20°C and one for storage at -80°C. Here we describe the extensive process of installation, acceptance, validation, and implementation of these two systems. Overall it took about 4 years to effectively take the systems into production. Multiple issues resulted in the delayed implementation, with labware change, quality of the initial installation, and misunderstanding of biobank concerns being the most impacting. Significant effort in terms of time and resources from both the automated store supplier as well as the biobank itself was needed to achieve a successful implementation. Within 15 months of actual integration in the biobank workflow, over 63 k samples were placed into the systems. Actual hands-on sample handling and retrieval times were substantially reduced, although this implied the shift of dedicated personnel time from the researchers' laboratories to the biobank. With the successful implementation of automated frozen sample storage systems, the centralized UZ KU Leuven Biobank is now also able to efficiently support large-scale translational research.

SUBMITTER: Linsen L

PROVIDER: S-EPMC6962113 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Automated Sample Storage in Biobanking to Enhance Translational Research: The Bumpy Road to Implementation.

Linsen Loes L Van Landuyt Kristel K Ectors Nadine N

Frontiers in medicine 20200109

The low reproducibility of biomarker research is a major holdback for the translation of research results to the bedside. Sample integrity has been identified as a key factor that contributes to improved reproducibility. The key mission of biobanks is to ensure that all activities and materials are managed according to standardized procedures and best practices to ensure and preserve sample integrity. When handling large numbers of biospecimens automation of sample handling and storage is often ...[more]

PMID: 31998730

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Project description:Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Designing effective individualized therapies for GBM requires quality fresh tissue specimens, and a comprehensive molecular profile of this highly heterogenous neoplasm. Novel neuro-surgical approaches, such as the automated resection NICO Myriad™ system, are increasingly used by neurosurgeons to better reach the invasive front of tumors. However, no information exists on how harvesting GBM tissue using this approach may impact the translational research value of the sample. Here, we set out to characterize matched specimens from 15 patients, where one tissue sample was obtained using traditional tumor de-bulking (herein referred to as "en bloc" sample), and the other sample was obtained using the MyriadTM System (herein referred to as "Myriad" sample). We investigated the fidelity of patient derived xenografts (PDXs) for each sample type to the corresponding human tissues and evaluated the added value of sequencing both samples for each patient. Matched en bloc and Myriad samples processed in parallel, were subjected to the following assays: cell viability, self-renewal, in vivo tumorigenicity using an orthotopic model of glioma, genomic sequencing, and pharmacological testing using PI3K-MTOR pathway inhibitors. Our results demonstrate that primary GBM cultures derived from matched specimens grew at similar rates (correlation coefficient R = 0.72), generated equivalent number of neurospheres, and had equivalent tumorigenic potential in vivo (mouse survival correlation coefficient R = 0.93). DNA Sequencing using the Illumina tumor panel amplicons revealed over 70% concordance in non-synonymous mutations between matched human GBM specimens. PDX genomic profiles were also highly concordant with the corresponding patient tissues (>70%). RNA sequencing of paired GBM samples revealed unique genomic variants and differential gene expression between the en bloc and Myriad specimens, with the former molecularly resembling the "tumor core" and the latter resembling the "invasive tumor front" signature. Functionally, we show that primary-derived GBM cells-obtained after fresh specimen's dissociation-are more effectively growth-inhibited by co-targeting non-overlapping mutations enriched in each sample type, suggesting that profiling both specimens more adequately capture the molecular heterogeneity of GBM and may enhance the design accuracy and efficacy of individualized therapies.

Project description:ObjectiveTo harmonize standard operating procedures (SOPs) and standardize the recording of associated data for collection, processing, and storage of fluid biospecimens relevant to endometriosis.DesignAn international collaboration involving 34 clinical/academic centers and 3 industry collaborators from 16 countries on 5 continents.SettingIn 2013, 2 workshops were conducted, followed by global consultation, bringing together 54 leaders in endometriosis research and sample processing worldwide.Patient(s)None.Intervention(s)Consensus SOPs were based on: [1] systematic comparison of SOPs from 18 global centers collecting fluid samples from women with and without endometriosis on a medium/large scale (publication on >100 cases), [2] literature evidence where available, or consultation with laboratory experts otherwise, and [3] several global consultation rounds.Main outcome measure(s)Standard recommended and minimum required SOPs for biofluid collection, processing, and storage in endometriosis research.Result(s)We developed recommended standard and minimum required SOPs for the collection, processing, and storage of plasma, serum, saliva, urine, endometrial/peritoneal fluid, and menstrual effluent, and a biospecimen data-collection form necessary for interpretation of sample-derived results.Conclusion(s)The Endometriosis Phenome and Biobanking Harmonisation Project SOPs allow endometriosis research centers to decrease variability in biofluid sample results, facilitating between-center comparisons and collaborations. The procedures are also relevant to research into other female conditions involving biofluid samples subject to cyclic reproductive influences. The consensus SOPs are based on the best available evidence; areas with limited evidence are identified as requiring further pilot studies. The SOPs will be reviewed based on investigator feedback, and through systematic tri-annual follow-up. Updated versions will be made available at: endometriosisfoundation.org/ephect.

Dataset Information

Automated Sample Storage in Biobanking to Enhance Translational Research: The Bumpy Road to Implementation.

Publications

Automated Sample Storage in Biobanking to Enhance Translational Research: The Bumpy Road to Implementation.

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