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Reporting, Appraising, and Integrating Data On Genotype Prevalence and Gene-Disease Associations Table

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TABLE 1: Proposed checklist for reporting and appraising studies of genotype prevalence and gene-disease associations
Item to be specified Details by type of study
Genotype prevalence Gene-disease associations
Purpose of study
Yes
Detect associations or estimate magnitude of association
Analytic validity of genotyping
 
 
  Types of samples used
Yes
For cases and for controls
  Timing of sample collection and analysis, by study group*
Ethnic group†
Cases vs. controls†
  Success rate in extracting DNA, by study group*
Ethnic group†
Cases vs. controls†
  Definition of the genotype(s) investigated; when there are multiple alleles, those tested for should be specified
Yes
Yes
  Genotyping method used (reference; for polymerase chain reaction methods—primer sequences,* thermocyle profile,* no. of cycles*)
Yes
Yes
  Percentage of potentially eligible subjects for whom valid genotypic data were obtained, by study group
Ethnic group†
Cases vs. controls†
  If pooling was used, strategy for pooling of specimens from cases and controls
 
Yes
  Quality control measures*
Yes
Including blinding of
laboratory staff
  Degree of reproducibility between quality control replicates
Yes
Yes
  Samples from each group of subjects compared (e.g., cases and controls) included in each batch analyzed*
 
Yes
Selection of study subjects
 
 
  Geographic area from which subjects were recruited
Yes
Yes
  The recruitment period
Yes
Yes
  Recruitment methods for subjects whose genotypes were determined, such as random population-based sampling, blood donors, and hospitalized subjects with reasons for hospitalization
Yes
Controls†
  Definition of cases and method of ascertainment
 
Yes
  No. of cases recruited from families and methods used to account for related subjects
 
Yes
  Exclusion criteria for cases and controls
 
Yes
  Recruitment rates
Where possible by sex, age, and ethnic group
For cases and controls
  Mean age and standard deviation or age range of study subjects, and the distribution by sex
Yes
For cases and controls
  If the subjects were controls from a case-control study, information on the disease under investigation and any matching criteria such as age, gender, and/or risk factor levels
Yes
 
  Ethnic group of study subjects

Yes

 
  Similarity of sociodemographic (or other) characteristics of subjects for whom valid genotypic data were obtained with characteristics of subjects for whom such data were not obtained*
 
Yes
  Steps taken to ensure that controls are noncases*
 
Yes
Confounding, including population stratification
 
 
  Design
 
Yes
  If other than a case-family control design, matching for ethnicity or adjustment for ethnicity in analysis
 
Yes
  Potential correlates of the genotype identified and taken into consideration in design or analysis
 
Yes
Statistical issues
 
 
  Distinguish clearly a priori hypotheses and hypotheses generated
 
Yes
  If haplotypes used, specify how these were constructed
Yes
Yes
  No. of subjects included in the analysis
Yes
Yes
  Method of analysis, with reference, and software used to do this
 
Yes
  Confidence intervals
Of genotype frequency
Of measures of association with the genotype
  Assessment of goodness-of-fit of the model used*
 
Yes

* Additional information recorded (ideally in Web-based methods register) but not necessarily presented in journal article.
† For example.

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