Informatics Management of Tumor Specimens in the Era of Big Data: Challenges and Solutions

Zhang, Peifen; Zheng, Xiaohui; Li, Xi‐Zhao; Sun, Lin; Jia, Wei‐Hua

doi:10.1089/bio.2020.0084

Cited by 3 publications

(3 citation statements)

References 57 publications

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“…The management and traceability of the biobanked samples have proven to be demanding, with a real risk of mistakes and failure [ 41 ]. At the beginning of UPO Biobank activity, an in-house adapted system based on the REDCap database (REDCap, Vanderbilt University) was built to accommodate and track the storage of biological samples, as well as the pre-collection and post-storage operations (e.g., study management, informed consent, sample release, etc.).…”

Section: Resultsmentioning

confidence: 99%

UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research

Bettio,

Mazzucco,

Aleni

et al. 2023

JPM

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Biobanks are driving motors of precision and personalized medicine by providing high-quality biological material/data through the standardization and harmonization of their collection, preservation, and distribution. UPO Biobank was established in 2020 as an institutional, disease, and population biobank within the University of Piemonte Orientale (UPO) for the promotion and support of high-quality, multidisciplinary studies. UPO Biobank collaborates with UPO researchers, sustaining academic translational research, and supports the Novara Cohort Study, a longitudinal cohort study involving the population in the Novara area that will collect data and biological specimens that will be available for epidemiological, public health, and biological studies on aging. UPO Biobank has been developed by implementing the quality standards for the field and the ethical and legal issues and normative about privacy protection, data collection, and sharing. As a member of the “Biobanking and Biomolecular Resources Research Infrastructure” (BBMRI) network, UPO Biobank aims to expand its activity worldwide and launch cooperation with new national and international partners and researchers. The objective of this manuscript is to report an institutional and operational experience through the description of the technical and procedural solutions and ethical and scientific implications associated with the establishment of this university research biobank.

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Section: Resultsmentioning

confidence: 99%

UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research

Bettio,

Mazzucco,

Aleni

et al. 2023

JPM

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“…For biomedical ‘big data’, the lack of standardisation (in terms of ontology, terminology, data format, etc.) and the existence of (often incompatible) heterogeneous databases complicate the application of these data and prevent effective data sharing and data mining [ 58 , 59 ]. The Horizon 2020 programme STANDS4EU aims to “evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine” [ 60 ].…”

Section: Pillar 2—agile Regulationsmentioning

confidence: 99%

Phase-In to Phase-Out—Targeted, Inclusive Strategies Are Needed to Enable Full Replacement of Animal Use in the European Union

Marshall

Constantino

Seidle

2022

Animals

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In September 2021, the European Parliament voted overwhelmingly in favour of a resolution to phase out animal use for research, testing, and education, through the adoption of an action plan. Here we explore the opportunity that the action plan could offer in developing a more holistic outlook for fundamental and biomedical research, which accounts for around 70% of all animal use for scientific purposes in the EU. We specifically focus on biomedical research to consider how mapping scientific advances to patient needs, taking into account the ambitious health policies of the EU, would facilitate the development of non-animal strategies to deliver safe and effective medicines, for example. We consider what is needed to help accelerate the move away from animal use, taking account of all stakeholders and setting ambitious but realistic targets for the total replacement of animals. Importantly, we envisage this as a ‘phase-in’ approach, encouraging the use of human-relevant NAMs, enabling their development and application across research (with applications for toxicology testing). We make recommendations for three pillars of activity, inspired by similar efforts for making the shift to renewable energy and reducing carbon emissions, and point out where investment—both financial and personnel—may be needed.

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“…In the process of tumor progression, diagnosis, treatment and prognosis, bioinformatics has gradually played an important role with the continuous in-depth research of next-generation sequencing and big data centers ( Jacoby et al, 2015 ). Through the analysis and comparative study of big data gene chip information, to calculate differential genes and immune-infiltrating cell screening in colon cancer to provide important biological prediction data for tumorigenesis mechanism and prognosis ( Zhang et al, 2021 ). In our current research, we first explored the landscapes of chromatin regulators including differentially expressed genes, regulation network, correlations, and gene alterations in colon adenocarcinoma (COAD).…”

Section: Introductionmentioning

confidence: 99%

Development and validation of a chromatin regulator prognostic signature in colon adenocarcinoma

2022

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Aberrant expression of chromatin regulators (CRs) could lead to the development of various diseases including cancer. However, the biological function and prognosis role of CRs in colon adenocarcinoma (COAD) remains unclear. We performed the clustering analyses for expression profiling of COAD downloaded from The Cancer Genome Atlas. We developed a chromatin regulator prognostic model, which was validated in an independent cohort data. Time-intendent receiver operating characteristics curve was used to evaluate predict ability of model. Univariate and multivariate cox regression were used to assess independence of risk score. Nomogram was established to assess individual risk. Gene ontology, and Kyoto Encyclopedia of genes and genomes, gene set variation analysis and gene set enrichment analysis were performed to explore the function of CRs. Immune infiltration and drug sensitivity were also performed to assess effect of CRs on treatment in COAD. COAD can be separated into two subtypes with different clinical characteristics and prognosis. The C2 had elevated immune infiltration levels and low tumor purity. Using 12 chromatin regulators, we developed and validated a prognostic model that can predict the overall survival of COAD patients. We built a risk score that can be an independent prognosis predictor of COAD. The nomogram score system achieved the best predict ability and were also confirmed by decision curve analysis. There were significantly different function and pathway enrichment, immune infiltration levels, and tumor mutation burden between high-risk and low-risk group. The external validation data also indicated that high-risk group had higher stable disease/progressive disease response rate and poorer prognosis than low-risk group. Besides, the signature genes included in the model could cause chemotherapy sensitivity to some small molecular compounds. Our integrative analyses for chromatin regulators could provide new insights for the risk management and individualized treatment in COAD.

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Informatics Management of Tumor Specimens in the Era of Big Data: Challenges and Solutions

Cited by 3 publications

References 57 publications

UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research

UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research

Phase-In to Phase-Out—Targeted, Inclusive Strategies Are Needed to Enable Full Replacement of Animal Use in the European Union

Development and validation of a chromatin regulator prognostic signature in colon adenocarcinoma

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