Calculating Percent Similarity between Your DNA Fingerprint(s) and Those of the NCI-60

Calculating PercentSimilarity between Your DNA Fingerprint(s) and Those of the NCI-60

  1. Download and install R (click here for the R homepage, then navigate to the CRAN/DOWNLOAD section).
  2. Prepare your input data, which will consist of the NCI-60 DNA fingerprints and any additional fingerprints you wish to append.
    1. Click here to download the input (*.txt) file, which contains all of the NCI-60 DNA Fingerprint data except MOLT-4.
    2. Open the input file (using a text editor or Microsoft Excel). Notice that each row represents the fingerprint data for a particular cell line. For each of your samples, append a row containing the corresponding data. When finished, save the input.txt file and close it. Make sure that there are no missing values.
    3. NOTE: if your assay measures STRs at different loci than the 16 used for the NCI-60, make sure that you delete any non-intersecting loci/columns from the input file before proceeding to the next step.
  3. Download the R script here
  4. Start R and open the downloaded *.R script (FILE —> SOURCE R CODE). You will be prompted to select the input file created in STEP 2 above. The output file will be named similarity.csv. The simplest way to analyze your data is to delete columns B through BJ in the similarity.csv file. The remaining columns correspond to your samples, and the rows indicate % similarity to each of the NCI-60 lines.

For more information, please see the manuscript: Lorenzi et al. DNA fingerprinting of the NCI-60 cell line panel. Mol Cancer Ther (2009), 8(4):713-24.