Affymetrix - Genotyping Console 2.0 - Cytogenetics Sample Data



		Cytogenetics sample data set provided for viewing in the Genotyping Console 2.0 Browser

Five cytogenetic samples have been analyzed using the Genotyping Console 2.0 Copy Number and LOH algorithms. As indicated by their names below, these files represent cases from Duchenne's Muscular Dystrophy (MD), DiGeorge Syndrome, and Beckwith-Wiedemann Syndrome.

There are two types of Genotyping Console files available:

cnchp files: These contain the copy number data for each marker on the SNP Array 6.0.
cn_segments files: These contain the predicted copy number changes in each sample as determined by the Segment Reporting Tool.

The available files are:

Trisomy21.71.CN5.cnchp
Trisomy21.71.cn_segments
DiGeorge_15.cnchp
DiGeorge_15.cn_segments
Di George_25.CN5.cnchp
DiGeorge_25.cn_segments
MD_80.cnchp
MD_80.cn_segments
MD_91.cnchp
MD_91.cn_segments

Download the sample data files (zip, 178 MB)

To view these files within the Genotyping Console 2.0:

Open Genotyping Console 2.0.
Select or create a User Profile.
Select or create a workspace (each workspace contains its own data set).

Name the data set
Select GenomeWideSNP_6 as the array

Add data to this workspace (Figure 1) :

The only checkboxes selected should be "Batch Copy Number / LOH Results" folder (CNCHP, LOHCHP, CN_SEMGENTS)

Figure 1	Figure 2
		Figure 1 : Data To Workspace Figure 2 : Genotyping Console Browser

Identify folder that contains the data (Figure 2).
Data will be imported into Genotyping Console Browser:

	Figure 3	Figure 4
Figure 3 : Karyoview Icon Figure 4 : Chromosome Viewer

To view data in the browser, select the karyoview icon (Figure 3).
Select copy number results to view in the browser (select all and click OK).
The Browser will open in a new window.

View the samples at the chromosome level, or zoom in further in the Chromosome Viewer by clicking on any of the chromosomes.
View the copy number changes identified in each sample by clicking on the "View Segment Report" button in the whole karyoview. The Segment Report will appear for the sample that is shown in the karyoview at that time.

See if you can detect the copy number changes from these known syndromes. Enjoy!!

Here are the locations affected by the selected syndromes:

Duchenne's Muscular Dystrophy: DMD gene on chromosome X
Trisomy 21 Syndrome: chromosome 21
DiGeorge Syndrome: chromosome 22q11.2