Human influenza TCR dataset from VDJdb

A dataset of 2271 paired alpha-beta human T-cell receptors specific to 4 influenza epitopes, compiled from the VDJdb database (September 2020 release). This dataset covers both MHC class I and class II restricted responses from 63 subjects and is useful for benchmarking human TCR distance calculations.

Usage

flu

Format

A data.frame with 2271 rows and 13 columns:

subject: Subject identifier from the original study (may be NA if not annotated).
epitope: Epitope peptide sequence (e.g., "GILGFVFTL").
epitope_gene: Source gene of the epitope (e.g., "M1").
mhc_a: MHC alpha chain allele (e.g., "HLA-A*02").
mhc_b: MHC beta chain allele (e.g., "B2M").
mhc_class: MHC class: "MHCI" or "MHCII".
count: Clone count (set to 1 for all entries).
va: V-alpha gene with allele (e.g., "TRAV12-2*01").
ja: J-alpha gene with allele (e.g., "TRAJ33*01").
cdr3a: CDR3-alpha amino acid sequence.
vb: V-beta gene with allele (e.g., "TRBV19*01").
jb: J-beta gene with allele (e.g., "TRBJ2-7*01").
cdr3b: CDR3-beta amino acid sequence.

Source

VDJdb: https://vdjdb.cdr3.net/

Bagaev et al. (2020). VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. Nucleic Acids Research, 48(D1), D1057–D1062. doi:10.1093/nar/gkz874

Examples

data(flu)
dim(flu)         # 2271 x 13
#> [1] 2271   13
table(flu$epitope)
#> 
#>     CVNGSCFTV  DATYQRTRALVR     GILGFVFTL PKYVKQNTLKLAT 
#>            14           109          2078            70