Ultra-sensitive detection of rare T cell clones

• Published in: Journal of immunological methods Vol. 375; no. 1-2; pp. 14 - 19
• Main Authors: Robins, Harlan, Desmarais, Cindy, Matthis, Jessica, Livingston, Robert, Andriesen, Jessica, Reijonen, Helena, Carlson, Christopher, Nepom, Gerold, Yee, Cassian, Cerosaletti, Karen
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 31.01.2012; Elsevier
• Subjects: adaptive immunity; Biological and medical sciences; Clone Cells; clones; Fundamental and applied biological sciences. Psychology; Fundamental immunology; high-throughput nucleotide sequencing; High-Throughput Nucleotide Sequencing - methods; Humans; Molecular immunology; MRD; Multiplex Polymerase Chain Reaction - methods; polymerase chain reaction; receptors; Receptors, Antigen, T-Cell - genetics; Repertoire; Reproducibility of Results; Sensitivity and Specificity; T-lymphocytes; TCR; Techniques; Repertoire; TCR; MRD; T cell receptor; T-Lymphocyte; Immunologic repertoire; Detection; Immunological method
• ISSN: 0022-1759; 1872-7905
• DOI: 10.1016/j.jim.2011.09.001

Advances in high-throughput sequencing have enabled technologies that probe the adaptive immune system with unprecedented depth. We have developed a multiplex PCR method to sequence tens of millions of T cell receptors (TCRs) from a single sample in a few days. A method is presented to test the precision, accuracy, and sensitivity of this assay. T cell clones, each with one fixed productive TCR rearrangement, are doped into complex blood cell samples. TCRs from a total of eleven samples are sequenced, with the doped T cell clones ranging from 10% of the total sample to 0.001% (one cell in 100,000). The assay is able to detect even the rarest clones. The precision of the assay is demonstrated across five orders of magnitude. The accuracy for each clone is within an overall factor of three across the 100,000 fold dynamic range. Additionally, the assay is shown to be highly repeatable. ► We sequence T cell receptors from a million T cells isolated from human blood samples. ► Spiking in T cell clones, we show the assay reliably detects 1 cell in 100,000. ► The assay is shown to precisely measure clone quantities from 10 to 100,000 T cells. ► We present a series of experiments to show that the assay is repeatable.