Genetic study reports
A genetic study is reported under the guideline for its kind: STREGA for a genetic association study, STREIS for an immunogenomic study and GRIPS for a study that predicts risk from genetic factors. STREGA and STREIS extend the STROBE checklist.
Genetic association studies
STREGA (Strengthening the Reporting of Genetic Association Studies), published in 2009 as an extension of the STROBE statement, recommends the following for a report of a genetic association study.
State whether the study is the first report of a genetic association, a replication effort or both. Where relevant, give the criteria and methods for selecting any subset of participants from a larger study. Define the genetic variants in a widely used nomenclature system, and identify the variables likely to be associated with population stratification (confounding by ethnic origin). Describe the laboratory methods, including the source and storage of DNA, the genotyping methods and platforms, such as the allele-calling algorithm and its version, the error rates and the call rates. State the laboratory or centre where genotyping was done. Where there is more than one group, describe how comparable their laboratory methods were. Specify whether genotypes were assigned from all of the study's data at once or in smaller batches.
For quantitative outcomes, specify whether bias from pharmacotherapy was investigated. If relevant, describe the nature and magnitude of the potential bias and the approach used to deal with it. If applicable, describe how effects of treatment were dealt with. State the software version and the options or settings chosen. State whether Hardy–Weinberg equilibrium was considered and, if so, how. Describe any methods used to infer genotypes or haplotypes, to address multiple comparisons or control the risk of false-positive findings, and to address and correct for relatedness among subjects.
Report the numbers of individuals in whom genotyping was attempted and in whom it was successful. Consider giving the descriptive data on participants by genotype. In a cohort study, report outcomes (phenotypes) for each genotype category over time; in a case-control study, report the numbers in each genotype category; and in a cross-sectional study, report outcomes (phenotypes) for each genotype category. Report the results of any adjustment for multiple comparisons. Where detailed results are available elsewhere, state how they can be reached.
Give the information on data sources and laboratory methods, on the numbers of participants and genotyped individuals, on descriptive data and on outcomes separately for cases and controls in a case-control study and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
Immunogenomic studies
STREIS (Strengthening the Reporting of Immunogenomic Studies), proposed in 2011 as a further extension of STROBE and STREGA, recommends the following for a report of an immunogenomic study. Describe HLA alleles in accordance with the WHO Nomenclature Committee for Factors of the HLA System and KIR alleles in accordance with the IPD-KIR database, and identify the IMGT/HLA and IPD-KIR database release numbers pertinent to the data. Describe the systems used to store, manage and validate genotype and allele data and to prepare them for analysis. Document all methods applied to resolve ambiguity, define any codes used to represent ambiguities, and describe any binning or combining of alleles into common categories. Describe genotyping systems and genotyping results in objective terms that identify the features assessed for each gene, and avoid subjective terms that may change over time, such as low, intermediate, high or allele resolution. Provide access to the primary, ambiguous genotype data for each individual. Discuss any modifications made to the data to fit a method's expectations, and their impact. Document and discuss any caveats associated with each analysis as they pertain to immunogenomic data, and discuss any potential impact of ambiguity resolution on the results.
Genetic risk-prediction studies
GRIPS (Strengthening the Reporting of Genetic Risk Prediction Studies) of 2011 recommends the following for a report of a genetic risk-prediction study. Identify the article as a study of risk prediction using genetic factors, and use the recommended key words in the abstract: genetic or genomic, risk and prediction. Explain the scientific background and rationale for the prediction study. Specify the objectives and the model or models investigated, and state whether the study concerns the development of a model, a validation effort or both.
Specify the key elements of the study design, and describe the setting, locations and relevant dates, including the periods of recruitment, follow-up and data collection. Describe the eligibility criteria and the sources and methods of selecting participants. Define all participant characteristics, risk factors and outcomes, and define the genetic variants in a widely used nomenclature system. Describe the sources of data and the methods of assessment for each variable, and give a detailed description of genotyping and other laboratory methods.
Describe how the genetic variants were handled in the analyses, and explain how the other quantitative variables were handled and, if applicable, which groupings were chosen and why. Specify the procedure and data used to derive the model, the candidate variables initially examined, any variable selection procedure and other model-building issues. Specify the time horizon of the prediction, for example 5-year risk. Specify the procedure and data used to validate the model, and how missing data were handled. Specify all measures used to evaluate the model, including but not limited to measures of model fit and predictive ability. Describe all subgroups, interactions and exploratory analyses examined.
Report the numbers of individuals at each stage of the study with the reasons for nonparticipation at each stage, and the number of participants not genotyped with the reasons. Report the demographic and clinical characteristics of the study population, including the risk factors used in the modelling. Report the unadjusted associations between the model variables and the outcome, and the adjusted estimates with their precision from the full model for each variable. Report the distributions of predicted risks or risk scores, the measures of model fit and predictive ability, and any other performance measures if pertinent. Report any validation of the model and, whenever pertinent, the results of any subgroup, interaction or exploratory analyses.
Discuss the limitations and assumptions of the study, particularly those concerning its design, the selection of participants, and its measurements and analyses, and their impact on the results. Give an overall interpretation of the results that considers the objectives, the limitations, the multiplicity of analyses, the results of similar studies and other relevant evidence. Discuss the generalizability of the findings and, if pertinent, their health care relevance. State whether databases of the analysed data, the risk models or the protocols are or will become publicly available and, if so, how they can be accessed. Give the source of funding and the role of the funders, and state whether there are any conflicts of interest.
The items on study design and setting, the selection of participants, the definition and assessment of variables, the participants at each stage of the study, the population's characteristics and the distributions of predicted risks should be reported for every population in the study.