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

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: Cell line authentication; Digital PCR; SMN1; SMN2; Short tandem repeat profiling; Spinal muscular atrophy.

Conflict of interest statement

AUTHORS CONFLICTS OF INTEREST

None declared.

Copyright © 2017 Elsevier B.V. All rights reserved.

Figures

Figure 1. Identification of familial relationships within family #3042 of the NIGMS Cell Collection using the D8S1179 microsatellite marker

(A) Pedigree analysis of family #3042. GM23686 was diagnosed with type I SMA. (B) Electrophoretograms showing the D8S1179 alleles for GM23686, GM23687 and GM23688.

Figure 2. Identification of familial relationships within family #553 of the NIGMS Cell Collection using the D21S11 microsatellite marker

(A) Pedigree analysis of family #553. GM03813 was diagnosed with type II SMA and had a brother with the same SMA phenotype. (B) Electrophoretograms showing the D21S11 alleles for GM03813, GM03814 and GM03815.