| Analysis task |
Details |
Extraction of
Raw data |
Genotyping (auto-clustering/manually clustering) using
SDS program |
| Data Quality Check |
Data quality check
(call rate, HWE test, Mendelian inheritance error, reproducibility
etc.) |
| Pedigree information matching |
| Data filtering (HWE p < 0.0001, low call rates) |
| Data transform |
| Clinical information analysis |
| LD & Haplotype |
LD & Haplotype (control group) : Haploview input
formats |
| Excluding of markers existing in strong LD (linkage
analysis only) |
| SNP Association |
Define genetic models
(allelic, additive, genotypic, dominant, recessive models) :
odds, 95%C.I for odds, P-value-Chi-square test, multiple logistic
regression, Linear regression etc
|
| Multiple testing: P-value correction (Bonferroni,
FDR etc.) |
| Significant SNP plot according to chromosome, MAF
distribution, functional location distribution etc. |
| Annotate gene information and gene ontology (biological
process, molecular function, cellular component etc.) |
Summarize results
& report
|
Write the final result report |
