Short description on how to Short description on how to

use dChip SNPuse dChip SNP

Please watch in slide show modePlease watch in slide show mode

Updated 02-24-2004Updated 02-24-2004

dChip SNPdChip SNP

• Available upon request from Cheng LiAvailable upon request from Cheng Li• Please send Email to:Please send Email to:

– Cheng Li at: Cheng Li at: cli@hsph.harvard.educli@hsph.harvard.edu

• Parametric linkage analysisParametric linkage analysis– DominantDominant– RecessiveRecessive

• Genome annotation with Genes, Genome annotation with Genes, Cytoband, Lod score and SNP information Cytoband, Lod score and SNP information in one windowin one window

• No error correction needeNo error correction neede• Runs up to 17 bitesRuns up to 17 bites

Step-by-StepStep-by-Step

• Export GDAS files Export GDAS files – Only the Affy SNPID and Genotypes need to Only the Affy SNPID and Genotypes need to

be includedbe included

– Generate the standard pedigree file as Generate the standard pedigree file as discusseddiscussed

– Add an array column in the pedigree file Add an array column in the pedigree file before the affection statusbefore the affection status

– This column needs to have the identical name This column needs to have the identical name as the experiment name in GDASas the experiment name in GDAS

– For individuals without genotypes add “Nofile” For individuals without genotypes add “Nofile” in the fieldin the field

– Save as text file (tab delimited)Save as text file (tab delimited)

dChip SNP : dChip SNP : Data fileData file

dChip SNP : dChip SNP : Pedigree filePedigree file

dChip SNP: dChip SNP: Import dataImport data

dChip SNP: dChip SNP: Import dataImport data

1. Assign a name for the analysis

2. Select the data file

3. Select SNP analysis

4. PressOK

dChip SNP: dChip SNP: Import dataImport data

dChip SNP: dChip SNP: Import annotation filesImport annotation files (all files are distributed with the software)(all files are distributed with the software)

1. Select

2. Select

3. Select

4. Select(optional)

5. Select

GenotypeInformation

dChip SNP: dChip SNP: Linkage analysisLinkage analysis

Select the pedigree file

Define:Disease allele freq.PenetranceDisease model

Simulation?

Press: OK

LOD Graph