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Establishing a reference dataset for the authentication of spinal muscular atrophy cell lines using STR profiling and digital PCR

  • Deborah L. Stabley
    Affiliations
    Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
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  • Jennifer Holbrook
    Affiliations
    Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
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  • Ashlee W. Harris
    Affiliations
    Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
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  • Kathryn J. Swoboda
    Affiliations
    Neurogenetics Research Program, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA, USA
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  • Thomas O. Crawford
    Affiliations
    Department of Neurology, Johns Hopkins University, Baltimore, MD, USA

    Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
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  • Katia Sol-Church
    Affiliations
    Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA

    Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA

    Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
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  • Matthew E.R. Butchbach
    Correspondence
    Corresponding author. Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, 240 Rockland Center One, 1600 Rockland Road, Wilmington, DE 19803. Fax: +302 651 6539.
    Affiliations
    Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA

    Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA

    Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA

    Department of Biological Sciences, University of Delaware, Newark, DE, USA
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Published:February 06, 2017DOI:https://doi.org/10.1016/j.nmd.2017.02.002

      Highlights

      • SMA cell line authentication is essential for rigor and reproducibility.
      • STR profiling and dPCR can generate molecular identity codes for SMA cell lines.
      • GM03815 is the father of, as opposed to the brother of, GM03813.

      Abstract

      Fibroblasts and lymphoblastoid cell lines (LCLs) derived from individuals with spinal muscular atrophy (SMA) have been and continue to be essential for translational SMA research. Authentication of cell lines helps ensure reproducibility and rigor in biomedical research. This quality control measure identifies mislabeling or cross-contamination of cell lines and prevents misinterpretation of data. Unfortunately, authentication of SMA cell lines used in various studies has not been possible because of a lack of a reference. In this study, we provide said reference so that SMA cell lines can be subsequently authenticated. We use short tandem repeat (STR) profiling and digital PCR (dPCR), which quantifies SMN1 and SMN2 copy numbers, to generate molecular identity codes for fibroblasts and LCLs that are commonly used in SMA research. Using these molecular identity codes, we clarify the familial relationships within a set of fibroblasts commonly used in SMA research. This study presents the first cell line reference set for the SMA research community and demonstrates its usefulness for re-identification and authentication of lines commonly used as in vitro models for future studies.

      Keywords

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