1. Short description on how to use dChip SNP Please watch in slide show mode Updated 02-24-2004

2. dChip SNP Available upon request from Cheng Li Available upon request from Cheng Li Please send Email to: Please send Email to: – Cheng Li at: cli@hsph.harvard.edu cli@hsph.harvard.edu Parametric linkage analysis Parametric linkage analysis – Dominant – Recessive Genome annotation with Genes, Cytoband, Lod score and SNP information in one window Genome annotation with Genes, Cytoband, Lod score and SNP information in one window No error correction neede No error correction neede Runs up to 17 bites Runs up to 17 bites

3. Step-by-Step Export GDAS files Export GDAS files – Only the Affy SNPID and Genotypes need to be included – Generate the standard pedigree file as discussed – Add an array column in the pedigree file before the affection status – This column needs to have the identical name as the experiment name in GDAS – For individuals without genotypes add “Nofile” in the field – Save as text file (tab delimited)

4. dChip SNP : Data file

5. dChip SNP : Pedigree file

6. dChip SNP: Import data

7. 1. Assign a name for the analysis 2. Select the data file 3. Select SNP analysis 4. Press OK

8. dChip SNP: Import data

9. dChip SNP: Import annotation files (all files are distributed with the software) 1. Select 2. Select 3. Select 4. Select (optional) 5. Select

10. Genotype Information

11. dChip SNP: Linkage analysis Select the pedigree file Define: Disease allele freq. Penetrance Disease model Simulation? Press: OK

12. LOD Graph