High-Throughput Sequencing for Diagnosis, Prognosis and Monitoring of Lymphoid Malignancies

Abstract

New high-throughput DNA sequencing methods have many advantages for the analysis of rearranged immunoglobulin (Ig) and T cell receptor (TCR) loci in suspected lymphoid malignancies. Instead of primarily analyzing the size distribution of rearranged immune receptors using gel or capillary electrophoresis, sequencing complex nucleic acid pools provides much more complete characterization of the receptor sequences present. Currently, separate assays are used to evaluate Ig and TCR clonality, Ig hypermutation status, and to test for residual malignant cells after treatment. We used multiplexed PCR amplification of immunoglobulin heavy chain loci for high-throughput pyrosequencing with the Roche 454 platform to evaluate the detection of clonal IgH sequences, determination of hypermutation status, and sensitivity of detection of low levels of a known clonal receptor. Our method also evaluated the feasibility of physical “bar-coding” of DNA molecules derived from different samples to enable cost-effective sequencing of sample pools. 23 pooled specimens were sequenced including: known lymphoma specimens (4); peripheral blood leukocytes from normal individuals (4); specimens with indeterminate or discordant results by conventional clonality assays (7); and a dilution series of a clonal CLL/SLL specimen into normal peripheral blood leukocytes. Our initial experiment characterized 522,099 IgH sequences from these specimens, with a mean read length of 242 base pairs. We have employed IgBlast (NCBI) for initial alignment of rearranged IgH sequences to germline V, D and J gene segments. Our data demonstrate that clonal IgH populations can be readily detected and characterized as to their germline or hypermutated status and unique V-D and D-J junctions with this approach. In our dilution series experiment, the clonal receptor sequence could be reliably observed after 1000-fold dilution. Normal patient specimens show expected extensive sequence diversity, and we are exploring methods for optimally summarizing and representing these data. Some PCR artifacts, as well as non-immunoglobulin sequences commonly amplified by current IgH primer sets were also detected, and suggest avenues for further improvement of the methods used for detection and characterization of clonal immune receptors. More broadly, these methods also offer a novel approach to monitoring normal immune responses such as the response of patients to vaccination, and of characterizing the immune system in patients with autoimmune diseases.