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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses
Vincent Plagnol1, Elif Uz, Chris Wallace
1JDRF/WT Diabetes and Inflammation Laboratory, University of Cambridge, Cambridge, United Kingdom. vincent.plagnol@cimr.cam.ac.uk
Plos One
|August 14, 2008
Summary
Lymphoblastoid cell lines (LCLs) can show clonal properties, affecting gene expression studies. For accurate allele-specific expression assays, researchers recommend using diverse, non-clonal ex vivo cells instead of cell lines.
Area of Science:
- Genetics
- Molecular Biology
- Epigenetics
Background:
- Lymphoblastoid cell lines (LCLs) are widely used for gene expression analysis, including allele-specific expression (ASE) studies.
- Recent findings indicate that a significant portion of human genes (~10%) display monoallelic expression in LCL clones, potentially confounding results.
- Clonal or near-clonal populations within LCLs can compromise the reliability of allelic imbalance studies.
Purpose of the Study:
- To investigate and quantify the extent of monoclonality in established lymphoblastoid cell lines.
- To assess the impact of cellular monoclonality on the accuracy of allele-specific expression assays.
- To provide recommendations for optimizing experimental designs for gene expression studies.
Main Methods:
- Utilized X chromosome inactivation patterns as a sensitive indicator of cellular monoclonality.
- Analyzed two independent sets of lymphoblastoid cell lines to confirm findings.
- Quantified the degree of near-monoclonality within the tested cell line populations.
Main Results:
- Confirmed widespread near-monoclonality in both sets of lymphoblastoid cell lines examined.
- Demonstrated that clonal expansion within LCLs can significantly skew allele-specific expression data.
- Highlighted the potential for compromised results in allelic imbalance studies using bulk LCL populations.
Conclusions:
- Lymphoblastoid cell lines frequently exhibit near-monoclonal characteristics, impacting gene expression analyses.
- The use of bulk, non-clonal, ex vivo cells is recommended for allele-specific expression assays to ensure data integrity.
- Researchers should carefully consider cell population homogeneity when designing gene expression studies.
