Reflection on modern methods: constructing directed acyclic graphs (DAGs) with domain experts for health services research

Instrumental variables in real-world clinical studies of dementia and neurodegenerative disease: Systematic review of the subject-matter argumentation, falsification test, and study design strategies to justify a valid instrument

OBJECTIVES

We systematically reviewed how investigators argued for and justified the validity of their instrumental variables (IV) in clinical studies of dementia and neurodegenerative disease.

METHODS

We included studies using IV analysis with observational data to investigate causal effects in clinical research studies of dementia and neurodegenerative disease. We reported the subject-matter argumentation, falsification test, and study design strategies used to satisfy the three assumptions of a valid IV: relevance, exclusion restriction, and exchangeability.

RESULTS

Justification for the relevance assumption was performed in all 12 included studies, exclusion restriction in seven studies, and exchangeability in nine studies. Two subject-matter argumentation strategies emerged from seven studies on the relevance of their IV. All studies except one provided quantitative evidence for the strength of the association between the IV and exposure variable. Four argumentation strategies emerged for exclusion restriction from six studies. Four falsification tests were performed across three studies. Three argumentation strategies emerged for exchangeability across four studies. Nine falsification tests were performed across nine studies. Two notable study design strategies were reported.

CONCLUSION

Our results reinforce IV analysis as a feasible option for clinical researchers in dementia and neurodegenerative disease by clarifying known strategies used to validate an IV.

Social deprivation and kidney failure due to an undiagnosed nephropathy

BACKGROUND

In France, kidney diseases of undetermined origin account for 5%-20% of all causes of end-stage kidney disease. We investigated the impact of social disadvantage on the lack of aetiological diagnosis of nephropathies.

METHODS

Data from patients who started dialysis in France between 1 January 2017 and 30 June 2018 were extracted from the French Renal Epidemiology and Information Network registry. The social deprivation of each individual was estimated by the European Deprivation Index (EDI) defined by the patient's address. Logistic regression was used to perform mediation analysis to study the potential association between social deprivation and unknown nephropathy.

RESULTS

Of the 7218 patients included, 1263 (17.5%) had unknown kidney disease. A total of 394 (31.4%) patients in the unknown kidney disease belonged to the most deprived quintile of the EDI [fifth quintile (Q5)], vs 1636 (27.5%) patients in the known kidney disease group. In the multivariate analysis, unknown kidney disease was associated with Q5 (odds ratio 1.40, 95% confidence interval 1.12-1.74, P = .003). Mediation analysis did not identify any variables (e.g. obesity, initiation of dialysis in emergency, number of visits to the general practitioner and nephrologist before initiation of dialysis, date of first nephrology consultation) that mediated the association between social deprivation and nephropathy of unknown origin.

CONCLUSIONS

Our results show that, compared with nondeprived subjects, individuals experiencing social deprivation have a higher risk of unknown nephropathy at dialysis initiation. However, mediation analysis did not identify any variables that explained the association between social deprivation and nephropathy of unknown origin.

Software Application Profile: The daggle app-a tool to support learning and teaching the graphical rules of selecting adjustment variables using directed acyclic graphs

MOTIVATION

Directed acyclic graphs (DAGs) are used in epidemiological research to communicate causal assumptions and guide the selection of covariate adjustment sets when estimating causal effects. For any given DAG, a set of graphical rules can be applied to identify minimally sufficient adjustment sets that can be used to adjust for bias due to confounding when estimating the causal effect of an exposure on an outcome. The daggle app is a web-based application that aims to assist in the learning and teaching of adjustment set identification using DAGs.

GENERAL FEATURES

The application offers two modes: tutorial and random. The tutorial mode presents a guided introduction to how common causal structures can be presented using DAGs and how graphical rules can be used to identify minimally sufficient adjustment sets for causal estimation. The random mode tests this understanding by presenting the user with a randomly generated DAG-a daggle. To solve the daggle, users must correctly identify a valid minimally sufficient adjustment set.

IMPLEMENTATION

The daggle app is implemented as an R shiny application using the golem framework. The application builds upon existing R libraries including pcalg to generate reproducible random DAGs, dagitty to identify all valid minimal adjustment sets and ggdag to visualize DAGs.

AVAILABILITY

The daggle app can be accessed online at [http://cbdrh.shinyapps.io/daggle]. The source code is available on GitHub [https://github.com/CBDRH/daggle] and is released under a Creative Commons CC BY-NC-SA 4.0 licence.

Perinatal outcomes in singleton live births after blastocyst transfer: an analysis of 60,926 in vitro fertilization cycles from the United Kingdom

OBJECTIVE

To compare perinatal outcomes between singleton live births after blastocyst-stage and cleavage-stage fresh embryo transfer using data from all United Kingdom licensed fertility clinics.

DESIGN

A cohort study.

SETTING

Not applicable.

PATIENT(S)

A total of 60,926 in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) cycles resulting in a singleton live birth after blastocyst-stage and cleavage-stage fresh embryo transfer between 2012 and 2018.

INTERVENTION(S)

Baseline characteristics between IVF/ICSI blastocyst and cleavage-stage transfer groups were compared using the χ2 test for categorical/dichotomized variables and the Mann-Whitney test for continuous variables. Statistical significance was set at <.05. Association between perinatal outcomes and blastocyst transfer compared with cleavage-stage transfer was assessed using multinomial logistic regression, adjusting for confounders selected using directed acyclic graphs (95% confidence interval [CI], adjusted relative risk ratio [aRRR]). A subgroup analysis included cycles in women undergoing their first IVF/ICSI cycle.

MAIN OUTCOMES MEASURE(S)

Gestational age at birth and birth weight.

RESULT(S)

The blastocyst group comprised 42,677 IVF/ICSI cycles and cleavage-stage group 18,249 cycles. There was likely little to no difference in the risk of preterm (aRRR, 1.07; 95% CI, 1.00-1.15) and very preterm birth (aRRR, 1.05; 95% CI, 0.91-1.21) in singleton live births after fresh blastocyst and cleavage-stage transfer. Risks of low birth weight (aRRR, 1.02; 95% CI, 0.95-1.09), very low birth weight (aRRR 0.96; 95% CI, 0.83-1.11), high birth weight (aRRR, 0.97; 95% CI, 0.90-1.04), and very high birth weight (aRRR, 0.91; 95% CI, 0.77-1.08) were likely similar between the groups. The findings were consistent in the subgroup analysis.

CONCLUSION(S)

Fresh blastocyst transfer does not appear to have a negative impact on gestational age at birth and birth weight in singleton live births compared with fresh cleavage-stage transfer.

Directed acyclic graphs in perioperative observational research-A systematic review and critique against best practice recommendations

The Directed Acyclic Graph (DAG) is a graph representing causal pathways for informing the conduct of an observational study. The use of DAGs allows transparent communication of a causal model between researchers and can prevent over-adjustment biases when conducting causal inference, permitting greater confidence and transparency in reported causal estimates. In the era of 'big data' and increasing number of observational studies, the role of the DAG is becoming more important. Recent best-practice guidance for constructing a DAG with reference to the literature has been published in the 'Evidence synthesis for constructing DAGs' (ESC-DAG) protocol. We aimed to assess adherence to these principles for DAGs constructed within perioperative literature. Following registration on the International Prospective Register of Systematic Reviews (PROSPERO) and with adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting framework for systematic reviews, we searched the Excerpta Medica dataBASE (Embase), the Medical Literature Analysis and Retrieval System Online (MEDLINE) and Cochrane databases for perioperative observational research incorporating a DAG. Nineteen studies were included in the final synthesis. No studies demonstrated any evidence of following the mapping stage of the protocol. Fifteen (79%) fulfilled over half of the translation and integration one stages of the protocol. Adherence with one stage did not guarantee fulfilment of the other. Two studies (11%) undertook the integration two stage. Unmeasured variables were handled inconsistently between studies. Only three (16%) studies included unmeasured variables within their DAG and acknowledged their implication within the main text. Overall, DAGs that were constructed for use in perioperative observational literature did not consistently adhere to best practice, potentially limiting the benefits of subsequent causal inference. Further work should focus on exploring reasons for this deviation and increasing methodological transparency around DAG construction.