| Analysis task |
Details |
| Extraction of raw data |
Genotyping (auto-clustering/manually clustering)
using beadStudio S/W |
| 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.) |
| CNV detection |
CNV detection (cnvPartition/Nexus/Penncnv/HelixTree
etc.) |
| Define CNVR(copy number variation region) |
| Matching detected aberration regions with
reported normal CNV regions from database of genomic variant(Toronto
DB) |
| CNV association |
CNV association between clinical subgroups
(Fisher’s Exact test) |
annotate gene ontology
(biological process, molecular function, cellular component etc.) |
| Linkage analysis |
Nonparametric linkage analysis(IBD, IBS
sharing methods -- npl) |
| Parametric linkage analysis(LOD score) |
Summarize results
& report |
Write the final result report |
