DataSHIELD: taking the analysis to the data, not the data to the analysis

Research in modern biomedicine and social science requires sample sizes so large that they can often only be achieved through a pooled co-analysis of data from several studies. But the pooling of information from individuals in a central database that may be queried by researchers raises important ethico-legal questions and can be controversial. In the UK this has been highlighted by recent debate and controversy relating to the UK's proposed 'care.data' initiative, and these issues reflect important societal and professional concerns about privacy, confidentiality and intellectual property. DataSHIELD provides a novel technological solution that can circumvent some of the most basic challenges in facilitating the access of researchers and other healthcare professionals to individual-level data. Commands are sent from a central analysis computer (AC) to several data computers (DCs) storing the data to be co-analysed. The data sets are analysed simultaneously but in parallel. The separate parallelized analyses are linked by non-disclosive summary statistics and commands transmitted back and forth between the DCs and the AC. This paper describes the technical implementation of DataSHIELD using a modified R statistical environment linked to an Opal database deployed behind the computer firewall of each DC. Analysis is controlled through a standard R environment at the AC. Based on this Opal/R implementation, DataSHIELD is currently used by the Healthy Obese Project and the Environmental Core Project (BioSHaRE-EU) for the federated analysis of 10 data sets across eight European countries, and this illustrates the opportunities and challenges presented by the DataSHIELD approach. DataSHIELD facilitates important research in settings where: (i) a co-analysis of individual-level data from several studies is scientifically necessary but governance restrictions prohibit the release or sharing of some of the required data, and/or render data access unacceptably slow; (ii) a research group (e.g. in a developing nation) is particularly vulnerable to loss of intellectual property-the researchers want to fully share the information held in their data with national and international collaborators, but do not wish to hand over the physical data themselves; and (iii) a data set is to be included in an individual-level co-analysis but the physical size of the data precludes direct transfer to a new site for analysis

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

Peer reviewe

Involving students in real-world research: a pilot study for teaching public health and research skills

Abstract Background There is some evidence that medical students consider population health issues less important than other domains in the health sciences and attitudes to this field may become more negative as training progresses. A need to improve research skills among medical students has also been suggested. Therefore we piloted an integrative teaching exercise that combined teaching of research skills and public health, with real-world research. Methods Third year medical students at the University of Otago (Dunedin, New Zealand) filled in a questionnaire on their housing conditions and health. The students were given the results of the survey to discuss in a subsequent class. Student response to this teaching exercise was assessed using a Course Evaluation Questionnaire. Results Of the 210 students in the class, 136 completed the Course Evaluation Questionnaire (65%). A majority of those who responded (77%) greatly supported or supported the use of the survey and seminar discussion for future third year classes. Most (70%) thought that the session had made them more aware and concerned about societal problems, and 72% felt that they now had an improved understanding of the environmental determinants of health. Students liked the relevance and interaction of the session, but thought it could be improved by the inclusion of small group discussion. The findings of the students' housing and health were considered by the tutors to be of sufficient value to submit to a scientific journal and are now contributing to community action to improve student housing in the city. Conclusion In this pilot study it was feasible to integrate medical student teaching with real-world research. A large majority of the students responded favourably to the teaching exercise and this was generally successful in raising the profile of public health and research. This approach to integrated teaching/research should be considered further in health sciences training and continue to be evaluated and refined.</p

Impact of COVID-19 control on lung, breast, and colorectal pathological cancer diagnoses. A comparison between the Netherlands, Aotearoa New Zealand, and Northern Ireland

Abstract Background The COVID-19 pandemic was managed in Aotearoa New Zealand (NZ) by a COVID-19 elimination policy, involving border closure and an initial national lockdown. This was different to most other countries including Northern Ireland (NI) and the Netherlands (NED). We quantify the effect of these policies on the diagnosis of three major cancers, comparing NZ with these two European countries. Method Data from NED, NZ and NI population-based cancer registries were used to assess trends in all pathologically diagnosed (PD) lung, breast, and colorectal cancers from March to December 2020 (pandemic period) and compared to the similar pre-pandemic period (2017–2019). Trend data were also collated on COVID-19 cases and deaths per 100,000 in each population. Results Comparing the pre-pandemic period to the pandemic period there were statistically significant reductions in numbers of lung (↓23%) and colorectal (↓15%) PD cancers in NI and numbers of breast (↓18%) and colorectal cancer (↓18.5%) diagnosed in the NED. In NZ there was no significant change in the number of lung (↑10%) or breast cancers (↑0.2%) but a statistically significant increase in numbers of colorectal cancer diagnosed (↑5%). Conclusion The impact of COVID-19 on cancer services was mitigated in NZ as services continued as usual reflecting minimal healthcare disruption and protected cancer services linked with the elimination approach adopted. The reduction in PD cases diagnosed in NED and NI were linked with higher COVID-19 rates and reflect societal restrictions which resulted in delayed patient presentation to primary and secondary care, disruption to screening and healthcare services as a result of COVID-19 infections on staff and the need to shift intensive care to COVID-19 patients. Reductions in PD cancers in NI and the NED and in particularly lung cancers in NI, highlight the need for targeted public health campaigns to identify and treat ‘missing’ patients. Protecting cancer services should be a priority in any future pandemic or systemic healthcare system disruption

The impact of COVID-19 on lung cancer detection, diagnosis and treatment for Māori in Aotearoa New Zealand.

AIM: The purpose of this article is to examine disparities in the impact of the COVID-19 pandemic on access to lung cancer diagnosis and access to clinical services between Māori and non-Māori. METHODS: Using national-level data, we examined age-standardised lung cancer registrations, diagnostic procedures (bronchoscopy) and lung surgeries separately by ethnic group for the years 2018-2020, as well as patterns of stage of diagnosis. RESULTS: We found a trend toward a reduction in rates of lung cancer registration in Māori (but not non-Māori/non-Pacific) New Zealanders in 2020 compared to 2018 and 2019, but no apparent shift in the distribution of stage at diagnosis. We found a trend toward a reduction in rates of bronchoscopy for both Māori and non-Māori/non-Pacific patients, with the largest reduction observed for Māori. Rates of lung cancer surgery appeared to have reduced for Māori patients, although this was based on a small number of procedures. CONCLUSIONS: We observed disparities between Māori and non-Māori/non-Pacific patients in lung cancer registration and bronchoscopy as a result of the COVID-19 pandemic

Molecular Analysis of Phyllodes Tumors Reveals Distinct Changes in the Epithelial and Stromal Components

Phyllodes tumors are fibroepithelial mammary lesions that tend to behave in a benign fashion but may undergo sarcomatous transformation. A study of clonality in these tumors has suggested that the epithelial component is polyclonal, but the stroma is monoclonal, and thus forms the neoplastic component of the lesion. In this study microsatellites on chromosome 1q and chromosome 3p were assessed for allelic imbalance (AI) in 47 phyllodes tumors; in all cases stroma and epithelium were analyzed separately. Ten of 42 (24%) phyllodes tumors showed AI at one or more markers on 3p, and 14 of 46 (30%) showed AI on chromosome 1. Five tumors had changes in both the epithelium and stroma. Eight tumors had changes only detectable in the stroma and eight, changes in the epithelium only. Three tumors exhibited low-level microsatellite instability in the epithelium but not in the stroma. The results show that AI on 3p and 1q does occur in phyllodes tumors and that it can occur in both the stroma and epithelium, sometimes as independent genetic events. These unexpected findings throw into doubt the classical view that phyllodes tumors are simply stromal neoplasms and raise questions about the nature of stromal and epithelial interactions in these tumors