Computer-Assisted Cohort Identification in Practice

The standard approach to expert-in-the-loop machine learning is active learning, where, repeatedly, an expert is asked to annotate one or more records and the machine finds a classifier that respects all annotations made until that point. We propose an alternative approach, IQRef , in which the expert iteratively designs a classifier and the machine helps him or her to determine how well it is performing and, importantly, when to stop, by reporting statistics on a fixed, hold-out sample of annotated records. We justify our approach based on prior work giving a theoretical model of how to re-use hold-out data. We compare the two approaches in the context of identifying a cohort of EHRs and examine their strengths and weaknesses through a case study arising from an optometric research problem. We conclude that both approaches are complementary, and we recommend that they both be employed in conjunction to address the problem of cohort identification in health research.

Harmonising the human biobanking consent process: an Irish experience

Biobanks are repositories of human biological samples and data. They are an important component of clinical research in many disease areas and often represent the first step toward innovative treatments. For biobanks to operate, researchers need human participants to give their samples and associated health data. In Ireland, research participants must provide their freely given informed consent for their samples and data to be taken and used for research purposes. Biobank staff are responsible for communicating the relevant information to participants prior to obtaining their consent, and this communication process is supported by the Participant Information Leaflets and Informed Consent Form (PI/ICFs). PILs/ICFs should be concise, intelligible, and contain relevant information. While not a substitute for layperson and research staff discussions, PILs and ICFs ensure that a layperson has enough information to make an informed choice to participate or not. However, PILs/ICFs are often lengthy, contain technical language and can be complicated and onerous for a layperson to read. The introduction of the General Data Protection Regulation and the related Irish Health Research Regulation presented additional challenges to the Irish biobank community. In May 2019, the National Biobanking Working Group (NBWG) was established in Ireland. It consists of members from diverse research backgrounds located in universities, hospitals and research centres across Ireland and a public/patient partner. The NBWG aimed to develop a suite of resources for health research biobanks via robust and meaningful patient engagement, which are accessible, General Data Protection Regulation/Health Research Regulation-compliant and could be used nationally, including a PIL/ICF template. This open letter describes the process whereby this national biobank PIL/ICF template was produced. The development of this template included review by the Patient Voice in Cancer Research, led by Professor Amanda McCann at University College Dublin and the Health Research Data Protection Network.

GWAS and ExWAS of blood Mitochondrial DNA copy number identifies 71 loci and highlights a potential causal role in dementia

Background: Mitochondrial DNA copy number (mtDNA-CN) is an accessible blood-based measurement believed to capture underlying mitochondrial function. The specific biological processes underpinning its regulation, and whether those processes are causative for disease, is an area of active investigation.Methods: We developed a novel method for array-based mtDNA-CN estimation suitable for biobank-scale studies, called 'AutoMitoC'. We applied AutoMitoC to 395,781 UKBiobank study participants and performed genome and exome-wide association studies, identifying novel common and rare genetic determinants. Finally, we performed two-sample Mendelian Randomization to assess whether genetically low mtDNA-CN influenced select mitochondrial phenotypes.Results: Overall, genetic analyses identified 71 loci for mtDNA-CN, which implicated several genes involved in rare mtDNA depletion disorders, dNTP metabolism, and the mitochondrial central dogma. Rare variant analysis identified SAMHD1 mutation carriers as having higher mtDNA-CN (beta=0.23 SDs; 95% CI, 0.18- 0.29; P=2.6x10-19), a potential therapeutic target for patients with mtDNA depletion disorders, but at increased risk of breast cancer (OR=1.91; 95% CI, 1.52-2.40; P=2.7x10-8). Finally, Mendelian randomization analyses suggest a causal effect of low mtDNA-CN on dementia risk (OR=1.94 per 1 SD decrease in mtDNA-CN; 95% CI, 1.55-2.32; P=7.5x10-4).Conclusions: Altogether, our genetic findings indicate that mtDNA-CN is a complex biomarker reflecting specific mitochondrial processes related to mtDNA regulation, and that these processes are causally related to human diseases.Funding: No funds supported this specific investigation. Awards and positions supporting authors include: Canadian Institutes of Health Research (CIHR) Frederick Banting and Charles Best Canada Graduate Scholarships Doctoral Award (MC, PM); CIHR Post-Doctoral Fellowship Award (RM); Wellcome Trust Grant number: 099313/B/12/A; Crasnow Travel Scholarship; Bongani Mayosi UCT-PHRI Scholarship 2019/2020 (TM); Wellcome Trust Health Research Board Irish Clinical Academic Training (ICAT) Programme Grant Number: 203930/B/16/Z (CJ); European Research Council COSIP Grant Number: 640580 (MO); E.J. Moran Campbell Internal Career Research Award (MP); CISCO Professorship in Integrated Health Systems and Canada Research Chair in Genetic and Molecular Epidemiology (GP).

Who published what on Somali health issues?

In this editorial we attempt to define additional rationales for SHAJ, the Somali Health Action Journal, further to those presented in our inaugural editorial. We recognize the health information divide as one of the three health gaps characterizing the global health inequality landscape. The SHAJ venture emerged from a joint Somali-Swedish initiative to revive a former collaborative research programme also recognizing the need for a Somali-based platform for research communication. The members of the SHAJ Editorial team decided to join forces in designing and carrying out an empirical bibliometric study to assess the state of the art of the published literature on Somali health issues over a 75-year period covering major societal development eras in Somali academic history. This editorial is basically presented in the form of a report from this study, concluding with a statement on the policy implications for SHAJ and Somali based research for health. The study raises concerns about the scarcity of research publications on Somali public health issues. This points to the need for research capacity strengthening in general and with special attention to the important role of the newly established Somali universities. We note a lack of balance regarding the topics and public health relevance of published papers in relation to the burden of prevailing health problems which calls for efforts to set research priorities in tune with the broad needs of the communities. Another observation is that the papers reviewed indicate a heavy dependence of the research agenda on external organisations and funders, which calls for active attention to research ownership issues in terms of Somali leadership and authorship. There is a lack of dissemination channels for Somali based health research and limited possibilities for young Somali scientists to publish their studies. As a Somali-owned journal, we envisage that SHAJ can play a catalytic role in the promotion and dissemination of "Essential Somali Health Research".

‘Working relationships’ across difference - a realist review of community engagement with malaria research

Background: Community engagement (CE) is increasingly accepted as a critical aspect of health research, because of its potential to make research more ethical, relevant and well implemented. While CE activities linked to health research have proliferated in Low and Middle Income Countries (LMICs), and are increasingly described in published literature, there is a lack of conceptual clarity around how engagement is understood to ‘work’, and the aims and purposes of engagement are varied and often not made explicit. Ultimately, the evidence base for engagement remains underdeveloped. Methods: To develop explanations for how and why CE with health research contributes to the pattern of outcomes observed in published literature, we conducted a realist review of CE with malaria research – a theory driven approach to evidence synthesis. Results: We found that community engagement relies on the development of provisional ‘working relationships’ across differences, primarily of wealth, power and culture. These relationships are rooted in interactions that are experienced as relatively responsive and respectful, and that bring tangible research related benefits. Contextual factors affecting development of working relationships include the facilitating influence of research organisation commitment to and resources for engagement, and constraining factors linked to the prevailing ‘dominant health research paradigm context’, such as: differences of wealth and power between research centres and local populations and health systems; histories of colonialism and vertical health interventions; and external funding and control of health research. Conclusions: The development of working relationships contributes to greater acceptance and participation in research by local stakeholders, who are particularly interested in research related access to health care and other benefits. At the same time, such relationships may involve an accommodation of some ethically problematic characteristics of the dominant health research paradigm, and thereby reproduce this paradigm rather than challenge it with a different logic of collaborative partnership.

Using Facebook Advertisements for Women’s Health Research: Methodology and Outcomes of an Observational Study

Background Recruitment of diverse populations for health research studies remains a challenge. The COVID-19 pandemic has exacerbated these challenges by limiting in-person recruitment efforts and placing additional demands on potential participants. Social media, through the use of Facebook advertisements, has the potential to address recruitment challenges. However, existing reports are inconsistent with regard to the success of this strategy. Additionally, limited information is available about processes that can be used to increase the diversity of study participants. Objective A Qualtrics survey was fielded to ascertain women’s knowledge of and health care experiences related to breast density. This paper describes the process of using Facebook advertisements for recruitment and the effectiveness of various advertisement strategies. Methods Facebook advertisements were placed in 2 rounds between June and July 2020. During round 1, multiple combinations of headlines and interest terms were tested to determine the most cost-effective advertisement. The best performing advertisement was used in round 2 in combination with various strategies to enhance the diversity of the survey sample. Advertisement performance, cost, and survey respondent data were collected and examined. Results In round 1, a total of 45 advertisements with 5 different headlines were placed, and the average cost per link click for each headline ranged from US $0.12 to US $0.79. Of the 164 women recruited in round 1, in total 91.62% were eligible to complete the survey. Advertisements used during recruitment in round 2 resulted in an average cost per link click of US $0.11. During the second round, 478 women attempted the survey, and 87.44% were eligible to participate. The majority of survey respondents were White (80.41%), over the age of 55 years (63.94%), and highly educated (63.71%). Conclusions Facebook advertisements can be used to recruit respondents for health research quickly, but this strategy may yield participants who are less racially diverse, more educated, and older than the general population. Researchers should consider recruiting participants through other methods in addition to creating Facebook advertisements targeting underrepresented populations.