Short description on how to use dChip SNP

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

3. Step-by-Step • 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. dChip SNP: Import data 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