Resources
Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease
Part II:
Methods and Approaches 1: Assessing Disease Associations and Interactions
Chapter 10 Tables
Reporting and Review of Human Genome Epidemiology Studies
Julian Little
Table 10-1
Proposed checklist for reporting and appraising studies of (i) genotype prevalence, (ii) gene-disease associations, and (iii) gene-environment interactions
| Genotype prevalence | Gene-disease associations | Genotype- environment interaction | |
|---|---|---|---|
1. Purpose of study |
√ |
Detect associations or estimate magnitude of association |
Describe joint effects; test specific hypotheses about interaction |
2. Analytical validity of genotyping |
|||
Types of samples used |
√ |
For cases and for controls |
For cases and for controls |
Timing of sample collection and analysis, by study group* |
e.g. ethnic group |
e.g. cases vs. controls |
e.g. cases vs. controls |
Success rate in extracting DNA, by study group* |
e.g. ethnic group |
e.g. cases vs. controls |
e.g. cases vs. controls |
Definition of the genotype(s) investigated; when there are multiple alleles, those tested for should be specified |
√ |
√ |
√ |
Genotyping method used (reference; for PCR methods – primer sequences*, thermocyle profile*, number of cycles*) |
√ |
√ |
√ |
Percentage of potentially eligible subjects for whom valid genotypic data were obtained, by study group |
e.g. ethnic group |
e.g. cases vs. controls |
e.g. cases vs. controls |
If pooling was used, strategy for pooling of specimens from cases and controls |
√ |
||
Quality control measures* |
√ |
Including blinding of laboratory staff |
Including blinding of laboratory staff |
Samples from each group of subjects compared (e.g cases and controls)included in each batch analyzed* |
√ |
||
3. Assessment of exposures |
|||
Reproducibility and validity of exposure documented |
√ |
||
Categories or exposure scale justified |
√ |
||
4. Selection of study subjects |
|||
Geographical area from which subjects were recruited |
√ |
√ |
√ |
The recruitment period |
√ |
√ |
√ |
Recruitment methods for subjects whose genotypes were determined, such as random population-based sampling, blood donors, hospitalized subjects with reasons for hospitalization |
√ |
||
Definition of cases and method of ascertainment |
√ |
√ |
|
Number of cases recruited from families and methods used to account for related subjects |
√ |
√ |
|
Recruitment rates |
Where possible by sex, age and ethnic group | For cases and controls | For cases and controls |
Mean age (±SD) or age-range of study subjects, and the distribution by sex |
√ |
For cases and controls | For cases and controls |
If the subject were controls from a case-control study, information of the disease under investigation and any matching criteria such as age, gender, and/or risk factor levels
|
√ |
||
Ethnic group of study subjects |
√ |
||
Similarity of socio-demographic (or other) characteristics of subjects for whom valid genotypic data were obtained with characteristics of subjects for whom such data were not obtained* |
√ |
√ |
|
Steps taken to ensure that controls are non-cases* |
√ |
||
5. Confounding, including population stratification |
|||
Design |
√ |
√ |
|
If other than a case-family control design, matching for ethnicity, or adjustment for ethnicity in analysis |
√ |
√ |
|
6. Statistical issues |
|||
Distinguish clearly a priori hypotheses and hypotheses generated |
√ |
√ |
|
If haplotypes used, specify how these were constructed |
√ |
√ |
v |
Number of subjects included in the analysis, by cell numbers where possible |
√ |
√ |
√ |
Method of analysis, with reference, and software used to do this |
√ |
√ |
|
Confidence intervals |
Of genotype frequency | Of measures of association with the genotype | |
For interaction analysis, 2xK presentation nused, or choice of stratified analysis justified |
√ |
||
For interaction analysis, P value for interaction calculated and choice of Wald test or likelihood ratio test specified and justified |
√ |
||
For interaction analysis, null interactions listed |
√ |
||
Assessment of goodness-of-fit of the model used* |
√ |
√ |
*Additional information recorded (ideally in web-based methods register)
[back to chapter]
Box 10-1
| Guidelines for causal inference (modified from Hill [120] and Surgeon General [119]) |
|---|
aAdditional considerations specified by Hill (120) |
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