Data from: 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 β chain of the αβ 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 TCRβ locus, and we
determined the presence and the proportion of productive rearrangements
for each TCRβ V gene segment in each individual. We then used this
information to annotate the functional status of TCRβ V gene segments in
this cohort. Results: For most TCRβ 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 TCRβ
locus of a large cohort of healthy volunteers to evaluate the use of
functional and non-functional alleles of individual TCRβ V gene segments.
With some modifications, our method has the potential to be extended to
gene segments in the α, γ, and δ TCR loci, as well as the genes encoding
for B-cell receptor chains.