Genome-wide association studies - A summary for the clinical gastroenterologist

Table 1 Phases in the initiation and analysis of a genome-wide association study

Sample panel building

Cases and healthy controls of same ethnicity (for power estimates see figure 2)

Enrichment with early onset cases and/or familial cases

Keep variability in phenotype at a minimum

Establish replication cohort(s) after the same principles. Other, yet similar, ethnicities may be included, although matched healthy controls should be collected

Genotyping

Sample preparation (DNA extraction, calibration)

Genotyping chip (cost vs number of samples)

Genetic coverage

Initial quality control

Exclude samples failing platform-specific QC measures

Exclude samples with low call-rate

Exclude SNPs with a low genotyping rate

Exclude SNPs with a low minor allele frequency and those grossly out of Hardy-Weinberg equilibrium (e.g. P < 10-4)

Statistical analysis

Imputation of non-genotyped SNPs using HapMap as the reference

Single-point association analysis, if needed include covariates of interest in the present study (e.g. gender, sex, smoking, imputation uncertainties etc.)

Manually inspect cluster plots for highly significant SNPs that should be followed-up

Select 1-2 SNPs from each associated locus to take forward in replication

Replication

Genotype (preferentially independent technology) in a panel of cases and healthy controls that are properly sized to detect effects in the same range as seen in the discovery panel

Follow-up experiments

Highly depends on results, i.e. nature of genetic finding, and normally not part of the GWAS design