Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.
In human immune system, V(D)J recombination produces an enormously large repertoire of immunoglobulins (Ig) so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(D)J recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(D)J recombination within a day by personal genome sequencers.
Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, United States of America.
Fan
F
Gao
Edwin
E
Lin
Yaping
Y
Feng
William J
WJ
Mack
Yufeng
Y
Shen
Kai
K
Wang
D005260:Female; D015894:Genome, Human; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000097:blood / Q000235:genetics; D008297:Male; D008577:Meningeal Neoplasms / Q000097:blood / Q000235:genetics; D008579:Meningioma / Q000097:blood / Q000235:genetics; D060885:Multiplex Polymerase Chain Reaction; D060152:V(D)J Recombination / Q000235:genetics*
D007143:Immunoglobulin Heavy Chains