Accelerating the Development and Validation of New Value-Based Diagnostics by Leveraging Biobanks

Review of Indicators in the Context of Biobanking

Background: Biobanks that intend to serve as high-performing and stable elements of an innovative research ecosystem must have an established system for regular measurement and evaluation using appropriately set indicators. The main objective of this study was to provide a comprehensive overview of indicators in the context of biobanking, with new perspectives to highlight the existence of numerous options and introduce indicators that could help overcome problems associated with the difficult assessment of the impact of biobanks. Methods: A literature review was performed to identify publications relevant to the topic of indicators in biobanking. The Web of Science Core Collection and PubMed databases were searched using specific keywords. In addition, three articles that focused on indicators designed for the evaluation of research infrastructures were included in the review. Results: Based on the scientific literature for the biobanking field, many types of quantitative and qualitative indicators exist. They are mainly related to the quantity and quality of data and samples, their distribution, the monitoring of research projects, and subsequent publication outputs. The indicators identified in the biobanking literature primarily focus on the outcome, not the impact. Conclusions: Indicators identified in the biobanking literature may be further expanded with suggestions designed for other types of research infrastructures, while considering the context where biobanks operate and the needs of individual biobanking stakeholders. The establishment of a comprehensive monitoring system that captures all necessary elements is crucial for modern biobanks.

Follow-up of the manganese-exposed workers healthy cohort (MEWHC) and biobank management from 2011 to 2017 in China

Background

Long-term excess exposure to environmental manganese (Mn) can lead to multi-system damage, especially in occupational populations. Therefore, we established a manganese-exposed workers healthy cohort (MEWHC), focusing on the systemic health effects related to Mn exposure. Here, we aimed to describe the follow-up activity for the MEWHC study and establish a standardized biological sample bank for the scientific management of high-quality biospecimens and the attached data from 2011 to 2017.

Methods

Baseline examinations for onsite workers were conducted, and the biobank for the MEWHC was first established in 2011; follow-up examinations occurred four times between July 2012 and November 2017. All questionnaires, clinical data and biological samples were routinely collected during each follow-up activity. Additional workers were recruited in 2016, which further enriched the resources of the biobank.

Results

A total of 2359 onsite workers and 612 retired workers at a ferromanganese refinery were enrolled in the prospective cohort, and their biological samples were obtained in the preliminary baseline survey and the follow-up investigation, including 2971 blood and urine samples from the cohort. In addition, 1524 hair samples, 1404 nail (toe and finger nails) and 1226 fecal samples were also collected. All specimens were preserved in the biobank, and the data were scientifically managed using a computer system.

Conclusions

The MEWHC study in China provides an effective way to obtain biological samples such as plasma, DNA, hair and urine for storage in a biobank for further study. The standardized management of various samples is crucial for accessing high-quality biospecimens.

Electronic supplementary material

The online version of this article (10.1186/s12889-018-5880-0) contains supplementary material, which is available to authorized users.

Genetic Analysis of Venous Thromboembolism in UK Biobank Identifies the ZFPM2 Locus and Implicates Obesity as a Causal Risk Factor

BACKGROUND

UK Biobank is the world's largest repository for phenotypic and genotypic information for individuals of European ancestry. Here, we leverage UK Biobank to understand the inherited basis for venous thromboembolism (VTE), a leading cause of cardiovascular mortality.

METHODS AND RESULTS

We identified 3290 VTE cases and 116 868 controls through billing code-based phenotyping. We performed a genome-wide association study for VTE with ≈9 000 000 imputed single-nucleotide polymorphisms. We performed a phenome-wide association study for a genetic risk score of 10 VTE-associated variants. To assess whether obesity is a causal factor for VTE, we performed Mendelian randomization analysis using a genetic risk score instrument composed of 68 body mass index-associated variants. The genome-wide association study for VTE replicated previous findings at the F5, F2, ABO, F11, and FGG loci. We identified 1 new locus-ZFPM2 rs4602861-at genome-wide significance (odds ratio, 1.11; 95% confidence interval, 1.07-1.15; P=4.9×10^-10) and a new independent variant at the F2 locus (rs3136516; odds ratio, 1.10; 95% confidence interval, 1.06-1.13; P=7.60×10^-9). In a phenome-wide association study, a 10 single-nucleotide polymorphism VTE genetic risk score was associated with coronary artery disease (odds ratio, 1.08; 95% confidence interval, 1.05-1.10 per unit increase in VTE odds; P=1.08×10^-9). In a Mendelian randomization analysis, genetically elevated body mass index (a 1 SD increase) was associated with 57% higher risk of VTE (odds ratio, 1.57; 95% confidence interval, 1.08-1.97; P=0.003).

CONCLUSIONS

For common diseases such as VTE, biobanks provide potential to perform genetic discovery, explore the phenotypic consequences for disease-associated variants, and test causal inference.