Welcome to SNPscan_CNAT4. It is modified from the original SNPscan to accommodate chanages Affymetrix made in its Copy Number Analysis Tool (CNAT) 4.0, including both the algorithm and the output format.

Among the various columns exported by CNAT 4.0, only two columns will be used for each sample: ".cn_Log2Ratio", to be used as the copy number; and ".loh_Call", to be used as the genotype call. Based on our observation, adding other columns will further obscure the scan result.

Your input file should be a text output file exported from Affymetrix's Copy Number Analysis Tool (CNAT) 4.0. Do not use any file saved in the ".cnt" file format as your input to SNPscan. In CNAT Viewer, open both the ".cn.cnt" and the ".loh.cnt" files at the same time. Keep the first three columns (Probe Set, Chromosome, Physical Position), plus .cn_Log2Ratio and .loh_Call for each sample. Hide all other columns to reduce the table size. Select "Export", "Table" form CNAT Viewer's menu bar to save you SNP data as a tab-delimited file. Delete the first line ("Copy Number Viewer"). Now, the first line of your file shall be column headers, followed by data lines, one line per SNP. The first field of each Data lines shall be a serial count for that SNP. SNPscan expects the column headers to be in the exact format exported by the Copy Number Analysis Tool 4.0. Visit the sample data page to see examples of the appropriate formats.

The current file size limitation is 100 MB per upload. It's enough for five 500K SNP cases, if you have removed unused column.

The Copy Number of each SNP will be plotted as dots against chromosomal positions, color coded according to each SNP's call: AA, BB, AB, NC. In this version, LOH and p-value will not be plotted.

Step 1 Please choose a file to upload:
(If you want to try a sample file, visit the sample data page, or try a 10K dataset by clicking here and saving as a text file to your hard drive.)
Step 2 The height of plot in inches: 
Step 3 The width of plot in inches:
Step 4 The width ratio of label vs. plot:
Step 5 Plot range for the Y-axis (Copy Number):
(Leave this blank to plot the whole range; for most applications, try the default value 1.5)
Step 6 Specify chromosomes: 
(For most applications, leave this blank to select all chromosomes as a default. You can enter any chromosome numbers separated by spaces [e.g. 1 9 21], or a single chromosome group letter [A-G,X,Y]. Please use capital letters (e.g. X not x). Enter asterisk symbol '*' for all autosomes. New: Cytobands will be ploted when a single chromosome is entered here.)
Step 7 Plot comparison of paired data?
Homoz. unchanged Heteroz. unchanged Homoz. to Heteroz. Heteroz. to Homoz. NoCall in #1 NoCall in #2 NoCall in both Diploid Switch
(If your data file includes multiple SNP data sets, each pair of datasets will be analyzed with an output of two tracks plus a third track showing the differences as specified above. Step 10 is typically used for paired tumor versus normal sample comparisons.)
No Yes
Step 8 Your data is based on which NCBI Build?
(NCBI Build 35 is known as "May 2004" or "hg17" in UCSC Genome Browser. Build 36 is known as "March 2006" or "hg18". CNAT 4.0 uses Build 35.)

Build 35
Build 36

Step 9 Click on the Submit button:
Depending on the size of your file, the work load of the server and the traffic load of the network, it may take SNPscan some time before your results are sent back to you. Also, if you have submitted multiple 100K+ samples, the PS and PDF files could contain a very large number of coordinats for points to be plotted. Please be patient for uploading and downloading!


Sample SNPscan Plot Patterns:

Normal Autosomes Duplication
(Low LOH, high p_value, elevated copy
number dots, many dots above 3)
Normal Female Chromosome X Diploid Deletion
(Very low LOH, high p_value, green dots with
copy number below 1)
Normal Male Chromosome X Hemizygous Deletion
(High LOH, high p_value, dropped blue and
green dots, some dots below 1)
Mosaic Female Chromosome X Mosaic Microdeletion
(Low LOH, medium p_value, dropped copy
number, few dots below 1, some red dots)
Mislabelled 100K Chr X
(50K male mixed with 50K female)
Uniparental Isodisomy
(High LOH, low p_value, normal copy number,
almost no red dots)


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Please send questions or comments to ting@kennedykrieger.org or pevsner@kennedykrieger.org.

Last updated: Auguest 16, 2007.