Evaluating STR Data

Cell Line Authentication Training Evaluating STR Data

8.1 Beth Bauer; 8.2 Comparing STR Profiles

8.3 Assignment: Analyzing STR data

  1. Analyze the five provided STR profiles.
    1. You are looking at 5 samples that are labeled NCI H2228, SW1116, PC-9, HCC1187, and Jurkat. The STR profiles for these samples are provided in the first column.
    2. Compare each profile with what is expected (you can find this at the NCB Biosample Database (https://www.ncbi.nlm.nih.gov/biosample/)  using the formula in the ICLAC match criteria worksheet (http://iclac.org/resources/match-criteria-worksheet/).
    3. If profiles don’t match, use the DSMZ online search tool to determine the likely identity of cell line (https://www.dsmz.de/services/services-human-and-animal-cell-lines/online-str-analysis.html).  Note: you will need to register to use this tool.
    4. Repeat matching exercise for the predicted cell line.
    5. Is cell line correctly identified, misidentified, contaminated, or unstable?
  1. Analyze your own data.
    1. Compare profiles received with those expected using ICLAC match criteria worksheet (http://iclac.org/resources/match-criteria-worksheet/).
    2. If profiles don’t match, use DSMZ online search tool to determine identity of cell line (https://www.dsmz.de/services/services-human-and-animal-cell-lines/online-str-analysis.html).
    3. Repeat matching exercise for predicted cell line.
    4. What do you conclude?
    5. Check the cell line name against the database of misidentified cell lines (http://iclac.org/databases/cross-contaminations/).
  1. Consider the limits of STR profiling for your samples. What will it be able to tell you, and what additional tests might you need to really determine whether your cell line is what you think it is? If you need additional tests, how might you design them? Also, does the cell name you use actually refer to a unique cell line, or are there multiple cell lines that are different from each other but have the same name? 

STR data analysis worksheet

For each of the five STR profiles in the worksheet

Download Worksheet

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