Imaging biobanks in oncology: European perspective

Standardizing digital biobanks: integrating imaging, genomic, and clinical data for precision medicine

Advancements in data acquisition and computational methods are generating a large amount of heterogeneous biomedical data from diagnostic domains such as clinical imaging, pathology, and next-generation sequencing (NGS), which help characterize individual differences in patients. However, this information needs to be available and suitable to promote and support scientific research and technological development, supporting the effective adoption of the precision medicine approach in clinical practice. Digital biobanks can catalyze this process, facilitating the sharing of curated and standardized imaging data, clinical, pathological and molecular data, crucial to enable the development of a comprehensive and personalized data-driven diagnostic approach in disease management and fostering the development of computational predictive models. This work aims to frame this perspective, first by evaluating the state of standardization of individual diagnostic domains and then by identifying challenges and proposing a possible solution towards an integrative approach that can guarantee the suitability of information that can be shared through a digital biobank. Our analysis of the state of the art shows the presence and use of reference standards in biobanks and, generally, digital repositories for each specific domain. Despite this, standardization to guarantee the integration and reproducibility of the numerical descriptors generated by each domain, e.g. radiomic, pathomic and -omic features, is still an open challenge. Based on specific use cases and scenarios, an integration model, based on the JSON format, is proposed that can help address this problem. Ultimately, this work shows how, with specific standardization and promotion efforts, the digital biobank model can become an enabling technology for the comprehensive study of diseases and the effective development of data-driven technologies at the service of precision medicine.

A Biobanking System for Diagnostic Images: Architecture Development, COVID-19-Related Use Cases, and Performance Evaluation

BACKGROUND

Systems capable of automating and enhancing the management of research and clinical data represent a significant contribution of information and communication technologies to health care. A recent advancement is the development of imaging biobanks, which are now enabling the collection and storage of diagnostic images, clinical reports, and demographic data to allow researchers identify associations between lifestyle and genetic factors and imaging-derived phenotypes.

OBJECTIVE

The aim of this study was to design and evaluate the system performance of a network for an operating biobank of diagnostic images, the Bio Check Up Srl (BCU) Imaging Biobank, based on the Extensible Neuroimaging Archive Toolkit open-source platform.

METHODS

Three usage cases were designed focusing on evaluation of the memory and computing consumption during imaging collections upload and during interactions between two kinds of users (researchers and radiologists) who inspect chest computed tomography scans of a COVID-19 cohort. The experiments considered three network setups: (1) a local area network, (2) virtual private network, and (3) wide area network. The experimental setup recorded the activity of a human user interacting with the biobank system, which was continuously replayed multiple times. Several metrics were extracted from network traffic traces and server logs captured during the activity replay.

RESULTS

Regarding the diagnostic data transfer, two types of containers were considered: the Web and the Database containers. The Web appeared to be the more memory-hungry container with a higher computational load (average 2.7 GB of RAM) compared to that of the database. With respect to user access, both users demonstrated the same network performance level, although higher resource consumption was registered for two different actions: DOWNLOAD & LOGOUT (100%) for the researcher and OPEN VIEWER (20%-50%) for the radiologist.

CONCLUSIONS

This analysis shows that the current setup of BCU Imaging Biobank is well provisioned for satisfying the planned number of concurrent users. More importantly, this study further highlights and quantifies the resource demands of specific user actions, providing a guideline for planning, setting up, and using an image biobanking system.

NAVIGATOR: an Italian regional imaging biobank to promote precision medicine for oncologic patients

NAVIGATOR is an Italian regional project boosting precision medicine in oncology with the aim of making it more predictive, preventive, and personalised by advancing translational research based on quantitative imaging and integrative omics analyses. The project’s goal is to develop an open imaging biobank for the collection and preservation of a large amount of standardised imaging multimodal datasets, including computed tomography, magnetic resonance imaging, and positron emission tomography data, together with the corresponding patient-related and omics-related relevant information extracted from regional healthcare services using an adapted privacy-preserving model. The project is based on an open-source imaging biobank and an open-science oriented virtual research environment (VRE). Available integrative omics and multi-imaging data of three use cases (prostate cancer, rectal cancer, and gastric cancer) will be collected. All data confined in NAVIGATOR (i.e., standard and novel imaging biomarkers, non-imaging data, health agency data) will be used to create a digital patient model, to support the reliable prediction of the disease phenotype and risk stratification. The VRE that relies on a well-established infrastructure, called D4Science.org, will further provide a multiset infrastructure for processing the integrative omics data, extracting specific radiomic signatures, and for identification and testing of novel imaging biomarkers through big data analytics and artificial intelligence.

Bridging gaps between images and data: a systematic update on imaging biobanks

BACKGROUND AND OBJECTIVE

The systematic collection of medical images combined with imaging biomarkers and patient non-imaging data is the core concept of imaging biobanks, a key element for fuelling the development of modern precision medicine. Our purpose is to review the existing image repositories fulfilling the criteria for imaging biobanks.

METHODS

Pubmed, Scopus and Web of Science were searched for articles published in English from January 2010 to July 2021 using a combination of the terms: "imaging" AND "biobanks" and "imaging" AND "repository". Moreover, the Community Research and Development Information Service (CORDIS) database ( https://cordis.europa.eu/projects ) was searched using the terms: "imaging" AND "biobanks", also including collections, projects, project deliverables, project publications and programmes.

RESULTS

Of 9272 articles retrieved, only 54 related to biobanks containing imaging data were finally selected, of which 33 were disease-oriented (61.1%) and 21 population-based (38.9%). Most imaging biobanks were European (26/54, 48.1%), followed by American biobanks (20/54, 37.0%). Among disease-oriented biobanks, the majority were focused on neurodegenerative (9/33, 27.3%) and oncological diseases (9/33, 27.3%). The number of patients enrolled ranged from 240 to 3,370,929, and the imaging modality most frequently involved was MRI (40/54, 74.1%), followed by CT (20/54, 37.0%), PET (13/54, 24.1%), and ultrasound (12/54, 22.2%). Most biobanks (38/54, 70.4%) were accessible under request.

CONCLUSIONS

Imaging biobanks can serve as a platform for collecting, sharing and analysing medical images integrated with imaging biomarkers, biological and clinical data. A relatively small proportion of current biobanks also contain images and can thus be classified as imaging biobanks.

KEY POINTS

• Imaging biobanks are a powerful tool for large-scale collection and processing of medical images integrated with imaging biomarkers and patient non-imaging data. • Most imaging biobanks retrieved were European, disease-oriented and accessible under user request. • While many biobanks have been developed so far, only a relatively small proportion of them are imaging biobanks.

Medical imaging clinical trials unit: A professional need

PURPOSE

To design and describe a management and control tool and the human resources needed to efficiently manage the imaging process within clinical trials for a better quality of care for the patient.

METHODS

A unit was created to efficiently organise the participation of our Medical Imaging Department in clinical trials. This entity was defined and monitored using a customized, flexible and modular software package that provides the necessary information to execute and monitor requests (appointments, protocols, reports, complaints, billing). Various indicators of activity and professional satisfaction were parameterised.

RESULTS

From 2016 to 2020, 367 trials were participated and monitored, 50% of all the hospital clinical trials. The budget of the Medical Imaging Department grew by 47% in this period. The coordination with other departments and principal investigators improved, as shown by surveys (62% fluid and 38% very fluid), with a high perception of collaboration (86%).

CONCLUSIONS

The implementation of a Medical Imaging Clinical Trials Unit involve identifying the tasks, personnel, organisational needs, workflow, monitoring and invoicing. The creation of this Unit has improved the control and traceability of clinical trials within the Department.

A deep look into radiomics

Radiomics is a process that allows the extraction and analysis of quantitative data from medical images. It is an evolving field of research with many potential applications in medical imaging. The purpose of this review is to offer a deep look into radiomics, from the basis, deeply discussed from a technical point of view, through the main applications, to the challenges that have to be addressed to translate this process in clinical practice. A detailed description of the main techniques used in the various steps of radiomics workflow, which includes image acquisition, reconstruction, pre-processing, segmentation, features extraction and analysis, is here proposed, as well as an overview of the main promising results achieved in various applications, focusing on the limitations and possible solutions for clinical implementation. Only an in-depth and comprehensive description of current methods and applications can suggest the potential power of radiomics in fostering precision medicine and thus the care of patients, especially in cancer detection, diagnosis, prognosis and treatment evaluation.

DICOM-MIABIS integration model for biobanks: a use case of the EU PRIMAGE project

PRIMAGE is a European Commission-financed project dealing with medical imaging and artificial intelligence aiming to create an imaging biobank in oncology. The project includes a task dedicated to the interoperability between imaging and standard biobanks. We aim at linking Digital imaging and Communications in Medicine (DICOM) metadata to the Minimum Information About BIobank data Sharing (MIABIS) standard of biobanking. A very first integration model based on the fusion of the two existing standards, MIABIS and DICOM, has been developed. The fundamental method was that of expanding the MIABIS core to the imaging field, adding DICOM metadata derived from CT scans of 18 paediatric patients with neuroblastoma. The model was developed with the relational database management system Structured Query Language. The integration data model has been built as an Entity Relationship Diagram, commonly used to organise data within databases. Five additional entities have been linked to the “Image Collection” subcategory in order to include the imaging metadata more specific to the particular type of data: Body Part Examined, Modality Information, Dataset Type, Image Analysis, and Registration Parameters. The model is a starting point for the expansion of MIABIS with further DICOM metadata, enabling the inclusion of imaging data in biorepositories.

Biobanks-A Platform for Scientific and Biomedical Research

The development of biomedical science requires the creation of biological material collections that allow for the search and discovery of biomarkers for pathological conditions, the identification of new therapeutic targets, and the validation of these findings in samples from patients and healthy people. Over the past decades, the importance and need for biobanks have increased considerably. Large national and international biorepositories have replaced small collections of biological samples. The aim of this work is to provide a basic understanding of biobanks and an overview of how biobanks have become essential structures in modern biomedical research.

From Medical Imaging to Radiomics: Role of Data Science for Advancing Precision Health

Treating disease according to precision health requires the individualization of therapeutic solutions as a cardinal step that is part of a process that typically depends on multiple factors. The starting point is the collection and assembly of data over time to assess the patient’s health status and monitor response to therapy. Radiomics is a very important component of this process. Its main goal is implementing a protocol to quantify the image informative contents by first mining and then extracting the most representative features. Further analysis aims to detect potential disease phenotypes through signs and marks of heterogeneity. As multimodal images hinge on various data sources, and these can be integrated with treatment plans and follow-up information, radiomics is naturally centered on dynamically monitoring disease progression and/or the health trajectory of patients. However, radiomics creates critical needs too. A concise list includes: (a) successful harmonization of intra/inter-modality radiomic measurements to facilitate the association with other data domains (genetic, clinical, lifestyle aspects, etc.); (b) ability of data science to revise model strategies and analytics tools to tackle multiple data types and structures (electronic medical records, personal histories, hospitalization data, genomic from various specimens, imaging, etc.) and to offer data-agnostic solutions for patient outcomes prediction; (c) and model validation with independent datasets to ensure generalization of results, clinical value of new risk stratifications, and support to clinical decisions for highly individualized patient management.

Integrating radiomics into holomics for personalised oncology: from algorithms to bedside

Radiomics, artificial intelligence, and deep learning figure amongst recent buzzwords in current medical imaging research and technological development. Analysis of medical big data in assessment and follow-up of personalised treatments has also become a major research topic in the area of precision medicine. In this review, current research trends in radiomics are analysed, from handcrafted radiomics feature extraction and statistical analysis to deep learning. Radiomics algorithms now include genomics and immunomics data to improve patient stratification and prediction of treatment response. Several applications have already shown conclusive results demonstrating the potential of including other “omics” data to existing imaging features. We also discuss further challenges of data harmonisation and management infrastructure to shed a light on the much-needed integration of radiomics and all other “omics” into clinical workflows. In particular, we point to the emerging paradigm shift in the implementation of big data infrastructures to facilitate databanks growth, data extraction and the development of expert software tools. Secured access, sharing, and integration of all health data, called “holomics”, will accelerate the revolution of personalised medicine and oncology as well as expand the role of imaging specialists.

AI-based applications in hybrid imaging: how to build smart and truly multi-parametric decision models for radiomics

INTRODUCTION

The quantitative imaging features (radiomics) that can be obtained from the different modalities of current-generation hybrid imaging can give complementary information with regard to the tumour environment, as they measure different morphologic and functional imaging properties. These multi-parametric image descriptors can be combined with artificial intelligence applications into predictive models. It is now the time for hybrid PET/CT and PET/MRI to take the advantage offered by radiomics to assess the added clinical benefit of using multi-parametric models for the personalized diagnosis and prognosis of different disease phenotypes.

OBJECTIVE

The aim of the paper is to provide an overview of current challenges and available solutions to translate radiomics into hybrid PET-CT and PET-MRI imaging for a smart and truly multi-parametric decision model.

Imaging biomarkers in upper gastrointestinal cancers

In parallel with the increasingly widespread availability of high performance imaging platforms and recent progresses in pathobiological characterisation and treatment of gastrointestinal malignancies, imaging biomarkers have become a major research topic due to their potential to provide additional quantitative information to conventional imaging modalities that can improve accuracy at staging and follow-up, predict outcome, and guide treatment planning in an individualised manner. The aim of this review is to briefly examine the status of current knowledge about imaging biomarkers in the field of upper gastrointestinal cancers, highlighting their potential applications and future perspectives in patient management from diagnosis onwards.

Biobanking in health care: evolution and future directions

BACKGROUND

The aim of the present review is to discuss how the promising field of biobanking can support health care research strategies. As the concept has evolved over time, biobanks have grown from simple biological sample repositories to complex and dynamic units belonging to large infrastructure networks, such as the Pan-European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Biobanks were established to support scientific knowledge. Different professional figures with varied expertise collaborate to obtain and collect biological and clinical data from human subjects. At same time biobanks preserve the human and legal rights of each person that offers biomaterial for research.

METHODS

A literature review was conducted in April 2019 from the online database PubMed, accessed through the Bibliosan platform. Four primary topics related to biobanking will be discussed: (i) evolution, (ii) bioethical issues, (iii) organization, and (iv) imaging.

RESULTS

Most biobanks were founded as local units to support specific research projects, so they evolved in a decentralized manner. The consequence is an urgent needing for procedure harmonization regarding sample collection, processing, and storage. Considering the involvement of biomaterials obtained from human beings, different ethical issues such as the informed consent model, sample ownership, veto rights, and biobank sustainability are debated. In the face of these methodological and ethical challenges, international organizations such as BBMRI play a key role in supporting biobanking activities. Finally, a unique development is the creation of imaging biobanks that support the translation of imaging biomarkers (identified using a radiomic approach) into clinical practice by ensuring standardization of data acquisition and analysis, accredited technical validation, and transparent sharing of biological and clinical data.

CONCLUSION

Modern biobanks permit large-scale analysis for individuation of specific diseases biomarkers starting from biological or digital material (i.e., bioimages) with well-annotated clinical and biological data. These features are essential for improving personalized medical approaches, where effective biomarker identification is a critical step for disease diagnosis and prognosis.

What the radiologist should know about artificial intelligence - an ESR white paper

This paper aims to provide a review of the basis for application of AI in radiology, to discuss the immediate ethical and professional impact in radiology, and to consider possible future evolution.Even if AI does add significant value to image interpretation, there are implications outside the traditional radiology activities of lesion detection and characterisation. In radiomics, AI can foster the analysis of the features and help in the correlation with other omics data. Imaging biobanks would become a necessary infrastructure to organise and share the image data from which AI models can be trained. AI can be used as an optimising tool to assist the technologist and radiologist in choosing a personalised patient's protocol, tracking the patient's dose parameters, providing an estimate of the radiation risks. AI can also aid the reporting workflow and help the linking between words, images, and quantitative data. Finally, AI coupled with CDS can improve the decision process and thereby optimise clinical and radiological workflow.

Radiomics and liquid biopsy in oncology: the holons of systems medicine

Abstract

Radiomics is a process of extraction and analysis of quantitative features from diagnostic images. Liquid biopsy is a test done on a sample of blood to look for cancer cells or for pieces of tumourigenic DNA circulating in the blood. Radiomics and liquid biopsy have great potential in oncology, since both are minimally invasive, easy to perform, and can be repeated in patient follow-up visits, enabling the extraction of valuable information regarding tumour type, aggressiveness, progression, and response to treatment. Both methods are in their infancy, with major evidence of application in lung and gastrointestinal cancer, while still undergoing evaluation in other cancer types. In this paper, the main oncologic applications of radiomics and liquid biopsy are reviewed, and a synergistic approach incorporating both tests for cancer diagnosis and follow-up is discussed within the context of systems medicine.

Teaching Points

• Radiomics is a process of extraction and analysis of quantitative features from diagnostic images.

• Most clinical applications of radiomics are in the field of oncologic imaging.

• Radiomics applies to all imaging modalities.

• A cluster of radiomic features is a “radiomic signature”.

• Machine learning may improve the efficacy of radiomics analysis.

Biobanking in oncology and radiology

The first biobank in Russia was created in 1998 to investigate post-Chernobyl thyroid tumors. The number of biobanks in the world is growing. Infrastructure and collaboration are improving. Ethical, legal and methodological guidelines for biobanking have been developed and are regularly reviewed. Biobanking objects are now not only biological samples of patients but also their dynamic biomedical characteristics. Comparison of genetics, proteome and tumour metabolism and in vivo radiological visualization is necessary to improve personalized diagnostics, treatment and its effectiveness. The article focuses on international evidence-based experience of sample preparation and cryopreservation of biological samples, information logistics, and integration solutions in biobanking. Guiding principles and the model of a modern biobank, integrating up-to-date technologies of digital personalized medicine and telemedicine in oncology and radiology are reported. The article may be of interest to a wide range of experts in biomedicine, especially oncologists, radiologists, pathologists, geneticists, and IT specialists.

Digital liver biopsy: Bio-imaging of fatty liver for translational and clinical research

The rapidly growing field of functional, molecular and structural bio-imaging is providing an extraordinary new opportunity to overcome the limits of invasive liver biopsy and introduce a "digital biopsy" for in vivo study of liver pathophysiology. To foster the application of bio-imaging in clinical and translational research, there is a need to standardize the methods of both acquisition and the storage of the bio-images of the liver. It can be hoped that the combination of digital, liquid and histologic liver biopsies will provide an innovative synergistic tri-dimensional approach to identifying new aetiologies, diagnostic and prognostic biomarkers and therapeutic targets for the optimization of personalized therapy of liver diseases and liver cancer. A group of experts of different disciplines (Special Interest Group for Personalized Hepatology of the Italian Association for the Study of the Liver, Institute for Biostructures and Bio-imaging of the National Research Council and Bio-banking and Biomolecular Resources Research Infrastructure) discussed criteria, methods and guidelines for facilitating the requisite application of data collection. This manuscript provides a multi-Author review of the issue with special focus on fatty liver.