Last Updated: December 12, 2024
SECTION 1: GENERAL PRINCIPLES
1. Study Design Requirements
□ Essential elements:
- Clear hypothesis statement
- Power calculation justification
- Sample size determination
- Population stratification consideration
- Control selection criteria
- Replication strategy
2. Ethical Considerations
□ Mandatory requirements:
- IRB/Ethics committee approval
- Informed consent documentation
- Data privacy protection
- Genetic counseling provisions
- Return of results policy
- Biobank compliance (if applicable)
SECTION 2: PHENOTYPE CHARACTERIZATION
1. Phenotype Definition
□ Required documentation:
- Detailed phenotype description
- Standardized terminology use
- Assessment methods
- Quality control measures
- Phenotype validation
- Environmental factors consideration
2. Data Collection Standards
□ Requirements for:
- Standardized collection methods
- Validated instruments
- Inter-rater reliability
- Missing data handling
- Outlier identification
- Longitudinal tracking (if applicable)
SECTION 3: GENOTYPE ANALYSIS
1. Sample Collection and Processing
□ Standards for:
- DNA/RNA extraction methods
- Sample quality control
- Storage conditions
- Chain of custody
- Batch effects monitoring
- Technical replication
2. Genotyping Methods
□ Requirements:
- Platform description
- Quality metrics
- Call rate thresholds
- Hardy-Weinberg equilibrium testing
- Minor allele frequency reporting
- Variant annotation standards
SECTION 4: STATISTICAL ANALYSIS
1. Primary Analysis
□ Required elements:
- Association test methods
- Multiple testing correction
- Population stratification control
- Effect size estimation
- Confidence interval calculation
- Power analysis results
2. Secondary Analyses
□ Guidelines for:
- Subgroup analyses
- Interaction testing
- Pathway analysis
- Functional prediction
- Meta-analysis
- Replication studies
SECTION 5: DATA SHARING AND REPORTING
1. Data Deposition
□ Requirements for:
- Raw data submission
- Metadata documentation
- Approved repositories
- Access controls
- Version control
- Data retention period
2. Results Reporting
□ Standards for:
- Effect size reporting
- P-value presentation
- Forest plots
- Manhattan plots
- Q-Q plots
- Regional association plots
SECTION 6: QUALITY CONTROL
1. Laboratory QC
□ Requirements:
- Sample tracking
- Contamination prevention
- Batch effect monitoring
- Control sample inclusion
- Technical replication
- Standard operating procedures
2. Data QC
□ Standards for:
- Genotype calling
- Missing data handling
- Relatedness testing
- Sex verification
- Ancestry estimation
- Batch effect correction
SECTION 7: REPRODUCIBILITY
1. Documentation Requirements
□ Must include:
- Analysis scripts
- Software versions
- Parameter settings
- Reference genome version
- Annotation databases
- Pipeline documentation
2. Validation Studies
□ Guidelines for:
- Independent replication
- Cross-population validation
- Functional validation
- Clinical correlation
- Meta-analysis inclusion
SECTION 8: SPECIAL CONSIDERATIONS
1. Rare Variants
□ Guidelines for:
- Variant calling
- Frequency estimation
- Functional prediction
- Segregation analysis
- Family studies
- Population-specific considerations
2. Complex Traits
□ Requirements for:
- Heritability estimation
- Genetic architecture
- Pleiotropy analysis
- Gene-environment interactions
- Phenotype decomposition
APPENDIX A: SUBMISSION CHECKLIST
Required Documentation
□ Must include:
- Study protocol
- Ethics approval
- Data sharing statement
- STROBE-G checklist
- Quality metrics report
- Analysis scripts
Note: These guidelines align with COPE standards, NIH Genomic Data Sharing Policy,
and International Committee of Medical Journal Editors (ICMJE) requirements.