Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

Background: The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementarity determining region 3 (CDR3) of the beta chain of the alpha beta TCR, which is generated by somatic recombination of noncontiguous variable (V), diversity (D), and joining (J) gene segments. Deletion and non-templated insertion of nucleotides at the D-J and V-DJ junctions further increases diversity. Many of these gene segments are annotated as non-functional owing to defects in their primary sequence, the absence of motifs necessary for rearrangement, or chromosomal locations outside the TCR locus. Methods: We sought to utilize a novel method, based on high-throughput sequencing of rearranged TCR genes in a large cohort of individuals, to evaluate the use of functional and non-functional alleles. We amplified and sequenced genomic DNA from the peripheral blood of 587 healthy volunteers using a multiplexed polymerase chain reaction assay that targets the variable region of the rearranged TCR beta locus, and we determined the presence and the proportion of productive rearrangements for each TCR beta V gene segment in each individual. We then used this information to annotate the functional status of TCR beta V gene segments in this cohort. Results: For most TCR beta V gene segments, our method agrees with previously reported functional annotations. However, we identified novel non-functional alleles for several gene segments, some of which were used exclusively in our cohort to the detriment of reported functional alleles. We also saw that some gene segments reported to have both functional and non-functional alleles consistently behaved in our cohort as either functional or non-functional, suggesting that some reported alleles were not present in the population studied. Conclusions: In this proof-of-principle study, we used high-throughput sequencing of the TCR beta locus of a large cohort of healthy volunteers to evaluate the use of functional and non-functional alleles of individual TCR beta V gene segments. With some modifications, our method has the potential to be extended to gene segments in the alpha, gamma, and delta TCR loci, as well as the genes encoding for B-cell receptor chains.