TY - JOUR
T1 - Genetic ancestry analysis reveals misclassification of commonly used cancer cell lines
AU - Hooker, Stanley E.
AU - Woods-Burnham, Leanne
AU - Bathina, Madhavi
AU - Lloyd, Stacy
AU - Gorjala, Priyatham
AU - Mitra, Ranjana
AU - Nonn, Larisa
AU - Kimbro, K. Sean
AU - Kittles, Rick A.
N1 - Funding Information:
This study is supported by NIH grant numbers 1R01MD007105 (R.A. Kittles), 1T32CA186895 (L. Woods-Burnham), U01CA167234 (S. Lloyd), U54MD012392-02, and P20MD000175-15 (K.S. Kimbro).
Funding Information:
35. National Institutes of Health. Implementing rigor and transparency in NIH and AHRQ research grant applications. October 9, 2015;NOT-OD-16-011.
Publisher Copyright:
© 2019 American Association for Cancer Research.
PY - 2019/6/1
Y1 - 2019/6/1
N2 - Background: Given the scarcity of cell lines from underrepresented populations, it is imperative that genetic ancestry for these cell lines is characterized. Consequences of cell line mischaracterization include squandered resources and publication retractions. Methods: We calculated genetic ancestry proportions for 15 cell lines to assess the accuracy of previous race/ethnicity classification and determine previously unknown estimates. DNA was extracted from cell lines and genotyped for ancestry informative markers representing West African (WA), Native American (NA), and European (EUR) ancestry. Results: Of the cell lines tested, all previously classified as White/Caucasian were accurately described with mean EUR ancestry proportions of 97%. Cell lines previously classified as Black/African American were not always accurately described. For instance, the 22Rv1 prostate cancer cell line was recently found to carry mixed genetic ancestry using a much smaller panel of markers. However, our more comprehensive analysis determined the 22Rv1 cell line carries 99% EUR ancestry. Most notably, the E006AA-hT prostate cancer cell line, classified as African American, was found to carry 92% EUR ancestry. We also determined the MDA-MB-468 breast cancer cell line carries 23% NA ancestry, suggesting possible Afro-Hispanic/ Latina ancestry. Conclusions: Our results suggest predominantly EUR ancestry for the White/Caucasian-designated cell lines, yet high variance in ancestry for the Black/African American- designated cell lines. In addition, we revealed an extreme misclassification of the E006AA-hT cell line. Impact: Genetic ancestry estimates offer more sophisticated characterization leading to better contextualization of findings. Ancestry estimates should be provided for all cell lines to avoid erroneous conclusions in disparities literature.
AB - Background: Given the scarcity of cell lines from underrepresented populations, it is imperative that genetic ancestry for these cell lines is characterized. Consequences of cell line mischaracterization include squandered resources and publication retractions. Methods: We calculated genetic ancestry proportions for 15 cell lines to assess the accuracy of previous race/ethnicity classification and determine previously unknown estimates. DNA was extracted from cell lines and genotyped for ancestry informative markers representing West African (WA), Native American (NA), and European (EUR) ancestry. Results: Of the cell lines tested, all previously classified as White/Caucasian were accurately described with mean EUR ancestry proportions of 97%. Cell lines previously classified as Black/African American were not always accurately described. For instance, the 22Rv1 prostate cancer cell line was recently found to carry mixed genetic ancestry using a much smaller panel of markers. However, our more comprehensive analysis determined the 22Rv1 cell line carries 99% EUR ancestry. Most notably, the E006AA-hT prostate cancer cell line, classified as African American, was found to carry 92% EUR ancestry. We also determined the MDA-MB-468 breast cancer cell line carries 23% NA ancestry, suggesting possible Afro-Hispanic/ Latina ancestry. Conclusions: Our results suggest predominantly EUR ancestry for the White/Caucasian-designated cell lines, yet high variance in ancestry for the Black/African American- designated cell lines. In addition, we revealed an extreme misclassification of the E006AA-hT cell line. Impact: Genetic ancestry estimates offer more sophisticated characterization leading to better contextualization of findings. Ancestry estimates should be provided for all cell lines to avoid erroneous conclusions in disparities literature.
UR - http://www.scopus.com/inward/record.url?scp=85067219266&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85067219266&partnerID=8YFLogxK
U2 - 10.1158/1055-9965.EPI-18-1132
DO - 10.1158/1055-9965.EPI-18-1132
M3 - Article
C2 - 30787054
AN - SCOPUS:85067219266
SN - 1055-9965
VL - 28
SP - 1003
EP - 1009
JO - Cancer Epidemiology Biomarkers and Prevention
JF - Cancer Epidemiology Biomarkers and Prevention
IS - 6
ER -