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Cancer Epidemiology, Biomarkers & Prevention
Cancer Epidemiology, Biomarkers & Prevention
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Genetic Ancestry Analysis Reveals Misclassification of Commonly Used Cancer Cell Lines

Stanley E. Hooker Jr., Leanne Woods-Burnham, Madhavi Bathina, Stacy Lloyd, Priyatham Gorjala, Ranjana Mitra, Larisa Nonn, K. Sean Kimbro and Rick A. Kittles
Stanley E. Hooker Jr.
1Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California.
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Leanne Woods-Burnham
1Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California.
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  • ORCID record for Leanne Woods-Burnham
Madhavi Bathina
1Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California.
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Stacy Lloyd
2Department of Molecular and Cellular Biology and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, Texas.
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  • ORCID record for Stacy Lloyd
Priyatham Gorjala
3College of Medicine, Roseman University of Health Sciences, Las Vegas, Nevada.
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Ranjana Mitra
3College of Medicine, Roseman University of Health Sciences, Las Vegas, Nevada.
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Larisa Nonn
4The Department of Pathology, University of Illinois, Chicago, Illinois.
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K. Sean Kimbro
5Biomedical/Biotechnology Research Institute (BBRI), North Carolina Central University, Durham, North Carolina.
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Rick A. Kittles
1Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California.
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  • For correspondence: rkittles@coh.org
DOI: 10.1158/1055-9965.EPI-18-1132 Published June 2019
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Abstract

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.

Footnotes

  • Cancer Epidemiol Biomarkers Prev 2019;28:1003–9

  • Received October 18, 2018.
  • Revision received December 20, 2018.
  • Accepted February 14, 2019.
  • Published first February 20, 2019.
  • ©2019 American Association for Cancer Research.
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Cancer Epidemiology Biomarkers & Prevention: 28 (6)
June 2019
Volume 28, Issue 6
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Genetic Ancestry Analysis Reveals Misclassification of Commonly Used Cancer Cell Lines
Stanley E. Hooker Jr., Leanne Woods-Burnham, Madhavi Bathina, Stacy Lloyd, Priyatham Gorjala, Ranjana Mitra, Larisa Nonn, K. Sean Kimbro and Rick A. Kittles
Cancer Epidemiol Biomarkers Prev June 1 2019 (28) (6) 1003-1009; DOI: 10.1158/1055-9965.EPI-18-1132

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Genetic Ancestry Analysis Reveals Misclassification of Commonly Used Cancer Cell Lines
Stanley E. Hooker Jr., Leanne Woods-Burnham, Madhavi Bathina, Stacy Lloyd, Priyatham Gorjala, Ranjana Mitra, Larisa Nonn, K. Sean Kimbro and Rick A. Kittles
Cancer Epidemiol Biomarkers Prev June 1 2019 (28) (6) 1003-1009; DOI: 10.1158/1055-9965.EPI-18-1132
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