Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem.

We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing uncertainty about permissible re-use of shared data. Here we discuss clarifications and subsequent updates to the Consent Codes (v4) based on new areas of application (e.g., the neurosciences, biobanking, H3Africa), policy developments (e.g., return of research results), and further practical considerations, including developments in automated approaches to consent management.

GA4GH Passport standard for digital identity and access permissions.

The Global Alliance for Genomics and Health (GA4GH) supports international standards that enable a federated data sharing model for the research community while respecting data security, ethical and regulatory frameworks, and data authorization and access processes for sensitive data. The GA4GH Passport standard (Passport) defines a machine-readable digital identity that conveys roles and data access permissions (called "visas") for individual users. Visas are issued by data stewards, including data access committees (DACs) working with public databases, the entities responsible for the quality, integrity, and access arrangements for the datasets in the management of human biomedical data. Passports streamline management of data access rights across data systems by using visas that present a data user's digital identity and permissions across organizations, tools, environments, and services. We describe real-world implementations of the GA4GH Passport standard in use cases from ELIXIR Europe, National Institutes of Health, and the Autism Sharing Initiative. These implementations demonstrate that the Passport standard has provided transparent mechanisms for establishing permissions and authorizing data access across platforms.

Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article.

Registered access: authorizing data access.

The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.

The availability of high-throughput molecular profiling techniques has provided more accurate and informative data for regular clinical studies. Nevertheless, complex computational workflows are required to interpret these data. Over the past years, the data volume has been growing explosively, requiring robust human data management to organise and integrate the data efficiently. For this reason, we set up an ELIXIR implementation study, together with the Translational research IT (TraIT) programme, to design a data ecosystem that is able to link raw and interpreted data. In this project, the data from the TraIT Cell Line Use Case (TraIT-CLUC) are used as a test case for this system. Within this ecosystem, we use the European Genome-phenome Archive (EGA) to store raw molecular profiling data; tranSMART to collect interpreted molecular profiling data and clinical data for corresponding samples; and Galaxy to store, run and manage the computational workflows. We can integrate these data by linking their repositories systematically. To showcase our design, we have structured the TraIT-CLUC data, which contain a variety of molecular profiling data types, for storage in both tranSMART and EGA. The metadata provided allows referencing between tranSMART and EGA, fulfilling the cycle of data submission and discovery; we have also designed a data flow from EGA to Galaxy, enabling reanalysis of the raw data in Galaxy. In this way, users can select patient cohorts in tranSMART, trace them back to the raw data and perform (re)analysis in Galaxy. Our conclusion is that the majority of metadata does not necessarily need to be stored (redundantly) in both databases, but that instead FAIR persistent identifiers should be available for well-defined data ontology levels: study, data access committee, physical sample, data sample and raw data file. This approach will pave the way for the stable linkage and reuse of data.

Manipulating walking path configuration influences gait variability and six-minute walk test outcomes in older and younger adults.

This study determined whether manipulations to walking path configuration influenced six-minute walk test (6MWT) outcomes and assessed how gait variability changes over the duration of the 6MWT in different walking path configurations. Healthy older (ODR) and younger (YNG) (n=24) adults completed familiarisation trials and five randomly ordered experimental trials of the 6MWT with walking configurations of; 5, 10 and 15m straight lines, a 6m by 3m rectangle (RECT), and a figure of eight (FIG8). Six-minute walk distance (6MWD) and walking speed (m.s(-1)) were recorded for all trials and the stride count recorded for experimental trials. Reflective markers were attached to the sacrum and feet with kinematic data recorded at 100 Hz by a nine-camera motion capture system for 5m, 15m and FIG8 trials, in order to calculate variability in stride and step length, stride width, stride and step time and double limb support time. Walking speeds and 6MWD were greatest in the 15m and FIG8 experimental trials in both groups (p<0.01). Step length and stride width variability were consistent over the 6MWT duration but greater in the 5m trial vs. the 15m and FIG8 trials (p<0.05). Stride and step time and double limb support time variability all reduced between 10 and 30 strides (p<0.01). Stride and step time variability were greater in the 5m vs. 15m and FIG8 trials (p<0.01). Increasing uninterrupted gait and walking path length results in improved 6MWT outcomes and decreased gait variability in older and younger adults.

Consent Codes: Upholding Standard Data Use Conditions.

A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA).

Impact of enzalutamide on quality of life in men with metastatic castration-resistant prostate cancer after chemotherapy: additional analyses from the AFFIRM randomized clinical trial.

BACKGROUND: To present longitudinal changes in Functional Assessment of Cancer Therapy-Prostate (FACT-P) scores during 25-week treatment with enzalutamide or placebo in men with progressive metastatic castration-resistant prostate cancer (mCRPC) after chemotherapy in the AFFIRM trial. PATIENTS AND METHODS: Patients were randomly assigned to enzalutamide 160 mg/day or placebo. FACT-P was completed before randomization, at weeks 13, 17, 21, and 25, and every 12 weeks thereafter while on study treatment. Longitudinal changes in FACT-P scores from baseline to 25 weeks were analyzed using a mixed effects model for repeated measures (MMRM), with a pattern mixture model (PMM) applied as secondary analysis to address non-ignorable missing data. Cumulative distribution function (CDF) plots were generated and different methodological approaches and models for handling missing data were applied. Due to the exploratory nature of the analyses, adjustments for multiple comparisons were not made. AFFIRM is registered with ClinicalTrials.gov, number NCT00974311. RESULTS: The intention-to-treat FACT-P population included 938 patients (enzalutamide, n = 674; placebo n = 264) with evaluable FACT-P assessments at baseline and ≥1 post-baseline assessment. After 25 weeks, the mean FACT-P total score decreased by 1.52 points with enzalutamide compared with 13.73 points with placebo (P < 0.001). In addition, significant treatment differences at week 25 favoring enzalutamide were evident for all FACT-P subscales and indices, whether analyzed by MMRM or PMM. CDF plots revealed differences favoring enzalutamide compared with placebo across the full range of possible response levels for FACT-P total and all disease- and symptom-specific subscales/indices. CONCLUSION: In men with progressive mCRPC after docetaxel-based chemotherapy, enzalutamide is superior to placebo in health-related quality-of-life outcomes, regardless of analysis model or threshold selected for meaningful response. CLINICAL TRIAL NUMBER: NCT00974311.

DbVar and DGVa: public archives for genomic structural variation.

Much has changed in the last two years at DGVa (http://www.ebi.ac.uk/dgva) and dbVar (http://www.ncbi.nlm.nih.gov/dbvar). We are now processing direct submissions rather than only curating data from the literature and our joint study catalog includes data from over 100 studies in 11 organisms. Studies from human dominate with data from control and case populations, tumor samples as well as three large curated studies derived from multiple sources. During the processing of these data, we have made improvements to our data model, submission process and data representation. Additionally, we have made significant improvements in providing access to these data via web and FTP interfaces.

The effect of abnormal colour vision on the ability to identify and outline coloured clinical signs and to count stained bacilli in sputum.

AIM: To determine if medical practitioners with congenital colour vision deficiencies (CCVD) are less able to identify and delineate the extent of coloured abnormal signs than those with normal colour vision. METHOD: Twenty-two medical practitioners with CCVD and 17 with normal colour vision, matched for age and gender, were shown 10 photographs. They were asked to identify and outline the extent of the clinical sign in eight that were of vomit or stool (six of these showing fresh blood), one of a skin rash and for one to mark the position of bacilli in sputum stained by the Ziehl-Neelsen method. RESULTS: There were statistically significant differences between the CCVD practitioners and those with normal colour vision in their ability to outline abnormalities in five of the six photographs that showed fresh blood, in the photograph of a rash and in marking the position of bacilli in the photograph of a stained slide. CONCLUSION: Medical practitioners with CCVD are handicapped in their evaluation of the presence and extent of coloured clinical signs. Medical schools should ensure that students with CCVD are aware of their deficiency and know its severity, so they can take special care in clinical practice.

The description of physical signs of illness in photographs by physicians with abnormal colour vision.

BACKGROUND: Physicians with congenital colour vision deficiency (CCVD) have reported difficulties recognising certain physical signs of illness, for example, jaundice, red rashes and pallor, and interpreting coloured charts, diagrams and slide projections. However, there has been little study of the effects of CCVD on the performance of medical practitioners. AIM: The aim of this study was to look for evidence of the effect of CCVD on the ability of physicians to recognise and describe physical signs of illness that have colour as either the main or an important feature. METHOD: Twenty-three general practitioners with CCVD were shown 11 colour photographs depicting colour signs of illness and were asked to describe the signs they saw and rate their confidence in making their descriptions. Their responses were compared to those of 23 age-matched general practitioners with normal colour vision. RESULT: General practitioners with CCVD compared to those with normal colour vision had less ability and confidence in detecting physical signs in the photographs and naming the colours. CONCLUSIONS: The results of this study support other evidence that physicians with CCVD have difficulties detecting some colour signs of illness and naming the colours. Because of the use of photographs the extent of the problem in clinical practice is unknown but medical practitioners with CCVD should be aware of the possibility of failing to detect or correctly assess physical signs that are characterised by colour.

Confessions of a colour blind physician.

The author describes his experiences due to his inherited colour vision deficiency, as a child, as student and as a medical practitioner, when he had certain difficulties in clinical work. He quotes from the literature on the clinical skills of physicians with this deficiency and gives an account of his own research that involved meeting and testing other doctors of medicine. This revealed a wide range of difficulties experienced by colour vision defective doctors in their practice of medicine with a potentiality for errors. Although there is a number of publications on this subject, the profession has made little response to them. This suggests that it is facing a dilemma that is inhibiting appropriate action. It is suggested that colour vision scientists and medical practitioners need more understanding of each other's discipline if progress is to be made. The advantages of screening of medical students and advising those found to have a deficiency are discussed and lines of research are proposed.

The Tg.AC (v-Ha-ras) transgenic mouse: nature of the model.

The Tg.AC (v-Ha-ras) transgenic mouse model provides a reporter phenotype of skin papillomas in response to either genotoxic or nongenotoxic carcinogens. In common with the conventional bioassay, the Tg.AC model responds to known human carcinogens and does not respond to noncarcinogens. It also does not respond to most chemicals that are positive in conventional bioassays principally at sites of high spontaneous tumor incidence. The mechanism of response of the Tg.AC model is related to the structure and genomic position of the transgene and the induction of transgene expression through specific mediated interactions between the chemicals and target cells in the skin.

Tg.AC genetically altered mouse: assay working group overview of available data.

In a Government/Industry/Academic partnership to evaluate alternative approaches to carcinogenicity testing, 21 pharmaceutical agents representing a variety of chemical and pharmacological classes and possessing known human and or rodent carcinogenic potential were selected for study in several rodent models. The studies from this partnership project, coordinated by the International Life Sciences Institute, provide additional data to better understand the models' limitations and sensitivity in identifying carcinogens. The results of these alternative model studies were reviewed by members of Assay Working Groups (AWG) composed of scientists from government and industry with expertise in toxicology, genetics, statistics, and pathology. The Tg.AC genetically manipulated mouse was one of the models selected for this project based on previous studies indicating that Tg.AC mice seem to respond to topical application of either mutagenic or nonmutagenic carcinogens with papilloma formation at the site of application. This communication describes the results and AWG interpretations of studies conducted on 14 chemicals administered by the topical and oral (gavage and/or diet) routes to Tg.AC genetically manipulated mice. Cyclosporin A, an immunosuppresant human carcinogen, ethinyl estradiol and diethylstilbestrol (human hormone carcinogens) and clofibrate, an hepatocarcinogenic peroxisome proliferator in rodents, were considered clearly positive in the topical studies. In the oral studies, ethinyl estradiol and diethylstilbestrol were negative, cyclosporin was considered equivocal, and results were not available for the clofibrate study. Of the 3 genotoxic human carcinogens (phenacetin, melphalan, and cyclophosphamide), phenacetin was negative by both the topical and oral routes. Melphalan and cyclophosphamide are, respectively, direct and indirect DNA alkylating agents and topical administration of both caused equivocal responses. With the exception of clofibrate, Tg.AC mice did not exhibit tumor responses to the rodent carcinogens that were putative human noncarcinogens, (di(2-ethylhexyl) phthalate, methapyraline HCl, phenobarbital Na, reserpine, sulfamethoxazole or WY-14643, or the nongenotoxic, noncarcinogen, sulfisoxazole) regardless of route of administration. Based on the observed responses in these studies, it was concluded by the AWG that the Tg.AC model was not overly sensitive and possesses utility as an adjunct to the battery of toxicity studies used to establish human carcinogenic risk.

Topical and oral administration of the natural water-soluble antioxidant from spinach reduces the multiplicity of papillomas in the Tg.AC mouse model.

The Tg.AC mouse carrying the v-Ha-ras structural gene is a useful model for the study of chemical carcinogens, especially those acting via non-genotoxic mechanisms. This study evaluated the efficacy of the non-toxic, water-soluble antioxidant from spinach, natural antioxidant (NAO), in reducing skin papilloma induction in female hemizygous Tg.AC mice treated dermally five times over 2.5 weeks with 2.5 microg 12-O-tetradecanoylphorbol-13-acetate (TPA). The TPA-only group was considered as a control; the other two groups received, additionally, NAO topically (2 mg) or orally (100 mg/kg), 5 days/week for 5 weeks. Papilloma counts made macroscopically during the clinical observations showed a significant decrease in multiplicity (P<0.01) in the NAO topically treated group. According to histological criteria, papilloma multiplicity were lower in both topical-NAO and oral-NAO groups, but significantly so only in the oral-NAO mice (P<0.01). The beneficial effect of NAO in the Tg.AC mouse is reported.

Age-dependent skin tumorigenesis and transgene expression in the Tg.AC (v-Ha-ras) transgenic mouse.

Transgenic Tg.AC (v-Ha-ras ) mice develop skin tumors in response to specific carcinogens and tumor promoters. The Tg.AC mouse carries the coding sequence of v-Ha ras, linked to a zeta-globin promoter and an SV40 polyadenylation signal sequence. The transgene confers on these mice the property of genetically initiated skin. This study examines the age-dependent sensitivity of the incidence of skin papillomas in Tg.AC mice exposed to topically applied 12-O:-tetradecanoylphorbol-13-acetate (TPA) treatment, full thickness skin wounding or UV radiation. Skin tumor incidence and multiplicity were strongly age-dependent, increasing with increasing age of the animal when first treated at 5, 10, 21 or 32 weeks of age. Furthermore, the temporal induction of transgene expression in keratinocytes isolated from TPA-treated mouse skin was also influenced by the age of the mice. Transgene expression was seen as early as 14 days after the start of TPA treatment in mice that were 10-32 weeks of age, but was not detected in similarly treated 5-week old mice. When isolated keratinocytes were fractionated by density gradient centrifugation the highest transgene expression was found in the denser basal keratinocytes. Transgene expression could be detected in the denser keratinocyte fraction as early as 9 days from start of TPA treatment in 32-week old mice. Using flow cytometry, a positive correlation was observed between expression of the v-Ha-ras transgene and enriched expression of the cell surface protein beta1-integrin, a putative marker of epidermal stem cells. This result suggests that, in the Tg.AC mouse, an age-dependent sensitivity to tumor promotion and the correlated induction of transgene expression are related to changes in cellular development in the follicular compartment of the skin.