SNPscan at the Pevsnerlab

Welcome to SNPscan. This version of SNPscan support data exported from CNAT 2 and CNAT 3. If you used CNAT 4.0 to export your data, please go to SNPscan_CNAT4 to process your data.
Your input file should be a text output file exported from Affymetrix's Copy Number Analysis Tool (CNAT) v2.0 or later, with the first line ("Copy Number Analysis Tool" form CNAT 2.0/2.1 or "Copy Number Viewer" from CNAT 3.0) been deleted. If you use CNAT 3.0 or GTYPE 4.0, do not use any file saved in the ".cnt" file format as your input to SNPscan. Select "Export", "Table" form GTYPE's CNAT Viewer menu bar to save you SNP data as a tab-delimited file. The first line of your input file shall be ColumnNanes (column headers), followed by Data lines, one line per SNP. The first field of each Data lines shall be a serial number for that SNP. SNPscan expects the ColumnNames to be in the exact format exported by the Copy Number Analysis Tool (XXX_Call, XXX_SPA_CN, etc.) Visit the sample data page to see examples of the appropriate formats.

The current file size limitation is 40 MB per upload. It's enough for 10 100K SNP cases. You can increase this limitation by installing SNPscan locally (instructions).

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, NoCall. In addition, LOH and p-value can also be plotted, as gray bars and yellow lines, respectively.

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

Upper limit for the Y-axis (Copy Number):
(Leave this blank to plot the whole range; for most applications, try the default value 8)

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 LOH? (For most applications, select Yes.)

No Yes

Step 8

Plot p value?
(Choose SPA to use single point p_values in your plot. The regional smoothed p_value is called CPA for 10K data, and GSA for 50K and 100K data. Reginal smoothed p_value is recommended. If your dataset is noisy [high variance], turn this off so that you can see your results more easily. Your plot will not be completed if you selected a wrong type here.)

No
SPA_pValue (10K, 50K, 100K)
CPA_pValue (10K only)
GSA_pValue (50K & 100K)

Step 9

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 10

Your data is based on which NCBI Build?
(Build 34 is also known as "July 2003", or "hg16" in UCSC Genome Browser. Build 35 is known as "May 2004" or "hg17", and Build 36 is known as "March 2006" or "hg18", respectively. Affy's CNAT 3.0 uses Build 35.)

Build 34
Build 35
Build 36

Step 11

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: August 16, 2007.