Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor
1 Computational Medicine Center, Thomas Jefferson University Jefferson Medical College, Philadelphia, PA, USA
2 National Molecular Laboratory, American Red Cross, Philadelphia, PA, USA
3 The Coriell Institute for Medical Research, Camden, NJ, USA
4 Cancer Genomics Laboratory, Kimmel Cancer Center
5 Department of Cancer Biology, Cardeza Foundation for Hematological Research, Thomas Jefferson University Jefferson Medical College, Philadelphia PA, USA
6 Department of Medicine, Cardeza Foundation for Hematological Research, Thomas Jefferson University Jefferson Medical College, Philadelphia PA, USA
7 Department of Molecular Medicine, Universita' La Sapienza School of Medicine, Rome, Italy
BMC Genomics 2011, 12:464 doi:10.1186/1471-2164-12-464Published: 26 September 2011
The creation of lymphoblastoid cell lines (LCLs) through Epstein-Barr virus (EBV) transformation of B-lymphocytes can result in a valuable biomaterial for cell biology research and a renewable source of DNA. While LCLs have been used extensively in cellular and genetic studies, the process of cell transformation and expansion during culturing may introduce genomic changes that may impact their use and the interpretation of subsequent genetic findings.
We performed whole exome sequencing on a tetrad family using DNA derived from peripheral blood mononuclear cells (PBMCs) and LCLs from each individual. We generated over 4.7 GB of mappable sequence to a 125X read coverage per sample. An average of 19,354 genetic variants were identified. Comparison of the two DNA sources from each individual showed an average concordance rate of 95.69%. By lowering the variant calling parameters, the concordance rate between the paired samples increased to 99.82%. Sanger sequencing of a subset of the remaining discordant variants did confirm the presence of de novo mutations arising in LCLs.
By varying software stringency parameters, we identified 99% concordance between DNA sequences derived from the two different sources from the same donors. These results suggest that LCLs are an appropriate representation of the genetic material of the donor and suggest that EBV transformation can result in low-level generation of de novo mutations. Therefore, use of PBMC or early passage EBV-transformed cells is recommended. These findings have broad-reaching implications, as there are thousands of LCLs in public biorepositories and individual laboratories.