Dataset supporting the illustration of the accuracy of quantification using the Array-DASH process (Figure 9.zip)

This data set represents the estimation of the amount of the LSCAN 1 target in the mixtures based on both the peak height and peak area of the C allele signal in the Array-DASH profile from positions 8 and 25. See text file in the package for a further explanation.Please note the addition of a figure to the manuscript has caused the figure number to be increased by 1 compared to those in the file name. </div

Dataset supporting the illustration of the semi-quantitive nature of the Array-DASH approach (Figure 8.zip)

This data set contains ArrayDASH data from mixtures of synthetic oligonucleotides that differ at two specific locations such that one carries T bases and the other carries G bases resulting in an AC genotype call. The oligonucleotide carrying the G base is gradually decreased in the mixtures across the set to construct a standard curve to test the sensitivity of the system for this base combination to show the potential of the system.Please note the addition of a figure to the manuscript has caused the figure number to be increased by 1 compared to those in the file name. </div

The creation of an adaptable informed consent form for research purposes to overcome national and institutional bottlenecks in ethics review: experience from rare disease registries

BackgroundThe lack of harmonization of evaluation criteria by Ethics Committees in the European Union (EU) has led to inconsistent ethics reviews received by research sites participating in multicenter non-interventional studies. The European General Data Protection Regulation (GDPR) appears to be implemented at national level with a substantial degree of variance in interpretation. The European Reference Networks (ERNs) were struggling in setting an Informed Consent Form (ICF) for registries, allowing reuse of data for research purposes. The aim of this work is to develop an adaptable ICF for research purposes to be used in ERN registries.MethodsTo work on this challenge, a team was established within the European Joint Programme on Rare Diseases (EJP RD) to develop a patients’ registry ICF template allowing easy adaptation to ERNs, country, and site-level specificities. ERN and patients’ representatives validated the choice of developing a GDPR-compliant template for research purposes. The feedback received from 34 Ethics Committees on the Clinical Patient Management System ICF, including the submission of patients’ data to the ERN registries and the EU consent regulatory framework were analyzed along with existing ontologies for data access and reuse. An adaptable ICF was developed following iterative cycles of consultation and review by clinicians, research experts, ethics and regulatory advisors, and patients’ representatives. The development of pediatric material for minor participants was also undertaken.Results and ConclusionResearch oriented ICF templates for adults and for parents/legal representatives of patients were released in 26 national languages. This adaptable ICF aims to foster, according to patients’ preferences, the reuse of registries data for research purposes in compliance with the applicable laws and standards. Pediatric material is being finalized to collect minors’ assent. ICF machine-readability is also progressing to enhance data discovery and facilitate its access and reuse conditions

Dataset supporting the illustration of the effect of a non-reference base position on adjacent bases calls, in Array-DASH based re-sequencing (Figure 4.zip)

This is a dataset relating to the use of the Array-DASH method to two test oligonucleotide sequences that differed at 3 known positions. LSCAN 1 was the perfect reverse compliment of the reference sequence used to design the array while LSCAN 2 contained 3 known changes. See text files for more details.Please note the addition of a figure to the manuscript has caused the figure number to be increased by 1 compared to those in the file name. </div

Dataset supporting the discrimination of 4 Hypericum species using genotyping via Array-DASH. (Table 1.zip)

This dataset shows ArrayDASH genotyping profiles generated from ITS regions amplified from 4 Hypericum species and the identification of a set of probes that can be used to distinguish between them.Genotyping probes targeted specific sequences that are known to exist in the associated Hypericum species, rather than a set of 4 probes that only differ by their central position to represent the 4 possible bases (i.e., A, C, G and T

Dataset supporting the illustration of the effect of a heterozygous position on an Array-DASH profile (Figure 5.zip)

This data set consists of data obtained via the ArrayDASH from 6 mixtures of synthetic oligonucleotide sequences, which were the perfect reverse compliment to the reference sequence used to design the array except at 3 positions where the base was substituted to allow the constriction of mixtures that could represent all 6 possible di-allelic genotypes possible in a normal diploid genomePlease note the addition of a figure to the manuscript has caused the figure number to be increased by 1 compared to those in the file name. </div

Dataset supporting the re-sequencing of a HIV clone and a patient sample via Array-DASH, and the comparison of the results to those obtained from NGS (Figure 11.zip)

This data set contains ArrayDASH results obtained from the Protease and reverse transcriptase genes amplified from a control clone of HIV and a HIV patient.Please note the addition of a figure to the manuscript has caused the figure number to be increased by 1 compared to those in the file name. </div

Getting your DUCs in a row - standardising the representation of Digital Use Conditions

Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.</p

Common conditions of use elements. Atomic concepts for consistent and effective information governance

Myriad policy, ethical and legal considerations underpin the sharing of biological resources, implying the need for standardised and yet flexible ways to digitally represent diverse ‘use conditions’. We report a core lexicon of terms that are atomic, non-directional ‘concepts of use’, called Common Conditions of use Elements. This work engaged biobanks and registries relevant to the European Joint Programme for Rare Diseases and aimed to produce a lexicon that would have generalised utility. Seventy-six concepts were initially identified from diverse real-world settings, and via iterative rounds of deliberation and user-testing these were optimised and condensed down to 20 items. To validate utility, support software and training information was provided to biobanks and registries who were asked to create Sharing Policy Profiles. This succeeded and involved adding standardised directionality and scope annotations to the employed terms. The addition of free-text parameters was also explored. The approach is now being adopted by several real-world projects, enabling this standard to evolve progressively into a universal basis for representing and managing conditions of use.</p