OncoScan™ CNV Plus Reagent Kit for Research

To convert OSCHP files to VCF format in Chromosome Analysis Suite (ChAS), follow these steps:

- Open Analysis Workflow for ChAS
- Go to the QC results tab in the Analysis Workflow Window. Run the CEL files for the OncoScan data
- Once complete, under Files, open the OSCHP file for your sample (this is created by ChAS when you analyze)



- Under Exports, select Export to VCF, select the output directory and the samples and select OK



By following these steps, you should be able to convert OSCHP files to VCF format using ChAS. The files will be found in the output directory you selected. These steps can be used for any CHP files to be exported in VCF format.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

These data files are produced that are key to the process:

ARR file - This file includes sample information.
AUDIT file - This file is a log of the sample history.
DAT file - This file is the raw data from the scanner.
CEL file - This file is the gridded and processed data.
xxCHP file - This file is the output of ChAS 3.1 and contains all of the analysis data.
CHPCAR file - This file stores user-annotated calls, interpretations, and modifications made to CHP file segment data (ChAS v2.0 and higher).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

OncoScanGeneBoundaries.r1 lists the approximately 900 OncoScan cancer genes and includes greater than 10 kb on each side of the gene. OncoScanCancerGeneOnly.r1 lists the same approximately 900 OncoScan cancer genes using the start and stop positions of the gene (no additional 10 kb on each side of the gene).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

The algorithm identifies normal diploid markers in the cancer samples. This is particularly important in highly aberrant samples. The normal diploid markers are used to calibrate the signals so that a log2 ratio of 0 (e.g., copy number 2) is achieved. In about 2% of samples, the algorithm cannot identify a sufficient number of “normal diploid” markers, and no normal diploid calibration occurs. This event triggers “low diploid flag = YES.” In this case, the user needs to carefully examine the log2 ratios and verify that re-centering is necessary.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Celpaircheckstatus checks if the results from the AT channel are consistent with the results from the GC channel and represent the results of the respective channel. This metric will be “out of bounds,” for example, when the AT and GC channels were mispaired between samples or due to sample contamination. We recommend troubleshooting as described in the OncoScan Console User Manual.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.