Our objectives and eligibility criteria remained the same between the protocol and the review. After the protocol stage, two new outcomes were added to our secondary outcomes: safety of abacavir and cost‐effectiveness. However, these were not in any way conditional to our eligibility criteria, nor were they influenced by the availability of the data from included studies.

We were unable to implement several methodologies from the protocol, due to there only being one included study. The following methods are not applicable with one study: addressing unit of analysis issues; dealing with missing data (contact was made but we did not receive a response); assessment of heterogeneity; assessment of reporting bias; data synthesis; subgroup analysis and investigation of heterogeneity (not applicable with one study, and outcomes not addressed); and sensitivity analysis.

Types of participants: we clarified how we would handle a study with only a subset of relevant participants; however, we did not encounter such studies.

Types of interventions: in the review, we additionally stated that we excluded any participants who had previously been administered the study drugs because of accurate causality assessment. Furthermore, we clarified the comparator in the review and included the following statement "and compared to standard clinical practice which does not include a genetic test".

Types of outcome measures: we added a definition of ‘severe drug‐induced skin rash’ to our primary outcome because phenotype definitions vary widely in the literature and some study authors report hypersensitivity reactions and SJS/TEN as severe or serious drug‐induced skin rash. We also added 'death' as a secondary outcome.

Searching other resources: although not planned in the protocol, we additionally checked the bibliographies of published reviews for relevant references and we requested relevant information from the authors of the included study.

Data extraction and management: we had planned to consult MP if consensus was not reached, but instead discussed disagreements with TC because authorship changed due to availability.

Assessment of risk of bias in included studies: we had planned in the protocol for all authors to assess the risk of bias of three studies as a pilot but did not do this because only one study fulfilled our inclusion criteria.

Unit of analysis issues: we did not encounter cluster‐randomised trials, so did not have to deal with the issues we had planned for in the protocol.

Dealing with missing data: we planned to report the limited results from studies with missing summary data in narrative form in the results section and consider whether they are consistent with the results of the meta‐analysis for that outcome. Also, where appropriate, we had planned to make assumptions about the missing data (e.g. assuming all missing values to have a particular value, e.g. an adverse event) and conduct sensitivity analyses to test how sensitive the analyses are to our assumptions. We had planned to address the potential implications of the missing data in the Discussion section. These plans were not implemented because only one study was included in this review which only reported data on two of our secondary outcomes.

Assessment of heterogeneity, Assessment of reporting biases, Subgroup analysis and investigation of heterogeneity, and Sensitivity analysis: we could not implement our planned methods because only one studies was included in this review.