Performance of Finnish biobanks in nationwide pulmonary carcinoid tumour research

Finnish hospital-integrated biobanks administer millions of formalin-fixed paraffin-embedded tissue samples collected within the clinical diagnostics. According to the Finnish Biobank Act, these samples can be coupled with patients’ clinical follow-up data and the data retrieved from national health registries. We collected a nationwide pulmonary carcinoid tumour series from Finnish biobanks to study prognostic factors as well as to explore how the number of tumours found in the Finnish biobanks corresponds to the number of tumours registered by the Finnish Cancer Registry (FCR). Finnish biobanks identified 88% of the tumours registered by the FCR and were able to deliver 63%. The main reasons for lacking samples were paucity of resected primary tumour tissue, incompatible primary diagnosis, and the absence of tissue blocks in the archives. The main bottleneck in the sample application process was retrieving patient data. Altogether, we received 224 tumour samples with appropriate patient data and identified six prognostic factors for shorter disease-specific survival: age over 56 years at the time of diagnosis, tumour size over 2.5 cm, atypical histology, Ki-67 proliferation index higher than 2.5%, hilar/mediastinal lymph node involvement at the time of diagnosis, and the presence of metastatic disease. In conclusion, the Finnish biobank infrastructure offers excellent opportunities for tissue-based research. However, to be able to develop the biobank operations further, involving more medical knowledge in the sample and data acquisition process is a necessity. Also, when working with tissue samples collected over decades, histological expertise is essential for re-evaluation and re-classification of the samples.Peer reviewe

LAS: a software platform to support oncological data management

The rapid technological evolution in the biomedical and molecular oncology fields is providing research laboratories with huge amounts of complex and heterogeneous data. Automated systems are needed to manage and analyze this knowledge, allowing the discovery of new information related to tumors and the improvement of medical treatments. This paper presents the Laboratory Assistant Suite (LAS), a software platform with a modular architecture designed to assist researchers throughout diverse laboratory activities. The LAS supports the management and the integration of heterogeneous biomedical data, and provides graphical tools to build complex analyses on integrated data. Furthermore, the LAS interfaces are designed to ease data collection and management even in hostile environments (e.g., in sterile conditions), so as to improve data qualit

Biobanks Go Global

Medical research increasingly relies on collections of donated human tissue, such as DNA samples, blood samples and solid organs and tissues. These collections of donated samples – referred to as biobanks, biorepositories or tissue banks – can be used in basic science experiments, population studies, or towards the refinement and personalisation of medical and surgical techniques. The practice of collecting and systematically organising biological samples is not new. Famous historical collections were put together by Carl Linnaeus (1707–78) in Sweden, Georges-Louis Leclerc, Comte de Buffon (1707–88) in France, and Joseph Banks (1743–1820) in England. In recent years, however, advances in experimental techniques (such as whole genome sequencing) and information technologies (such as “big data” storage and analytics) have massively increased the promise of biomedical research using collections of human biological samples. In order for the promise of biobanks to be fulfilled, large numbers of samples need to be collected, stored and analysed. Until recently, most biobanks were located within individual universities, research institutes or health facilities, and often tied to specific research projects. Increasingly, however, biobanks have become “networked” in an effort to become more sustainable and to increase their utility. Most often, these networks of biobanks draw together samples from within a country to create a single biobank that may be accessible to researchers based in different institutions and with different research interests. But even large domestic biobanks or biobank networks like these may still lack the statistical power to answer important research questions. For example, research into the genetics of rare or complex diseases often requires the analysis of samples that number in the hundreds of thousands, if not millions. Maximising the full potential of biobanks is therefore difficult within the confines of a single nation

Systematic review of birth cohort studies in Africa

In sub-Saharan Africa, unacceptably high rates of mortality amongst women and children continue to persist. The emergence of research employing new genomic technologies is advancing knowledge on cause of disease. This review aims to identify birth cohort studies conducted in sub-Saharan Africa and to consider their suitability as a platform to support genetic epidemiological studies

Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase

Performance of Finnish biobanks in nationwide pulmonary carcinoid tumour research

Finnish hospital-integrated biobanks administer millions of formalin-fixed paraffin-embedded tissue samples collected within the clinical diagnostics. According to the Finnish Biobank Act, these samples can be coupled with patients’ clinical follow-up data and the data retrieved from national health registries. We collected a nationwide pulmonary carcinoid tumour series from Finnish biobanks to study prognostic factors as well as to explore how the number of tumours found in the Finnish biobanks corresponds to the number of tumours registered by the Finnish Cancer Registry (FCR). Finnish biobanks identified 88% of the tumours registered by the FCR and were able to deliver 63%. The main reasons for lacking samples were paucity of resected primary tumour tissue, incompatible primary diagnosis, and the absence of tissue blocks in the archives. The main bottleneck in the sample application process was retrieving patient data. Altogether, we received 224 tumour samples with appropriate patient data and identified six prognostic factors for shorter disease-specific survival: age over 56 years at the time of diagnosis, tumour size over 2.5 cm, atypical histology, Ki-67 proliferation index higher than 2.5%, hilar/mediastinal lymph node involvement at the time of diagnosis, and the presence of metastatic disease. In conclusion, the Finnish biobank infrastructure offers excellent opportunities for tissue-based research. However, to be able to develop the biobank operations further, involving more medical knowledge in the sample and data acquisition process is a necessity. Also, when working with tissue samples collected over decades, histological expertise is essential for re-evaluation and re-classification of the samples.</p