B-cell receptor data from intratumoural B cells in melanoma patients

This record contains data used in the Crescioli et al. analysis of B-cell response in melanoma, specifically analysis concerning high-throughput BCR repertoire.

Files:

"Visium_all_Aug22_comboDatBoth.txt": IMGT/HighV-Quest output of the high-throughput intratumoural BCR repertoire from n=5 melanoma tumours. In tab-separated text file format.

"HV_EB_COV_MEL_comb_Oct22.RDS": A R data object (readable into R with "readRDS(...)") containing combined data from the melanoma (MEL) data with analogous high-throughput BCR repertoire data from healthy volunteers (HV), Ebola convalescent patients (EB) and hospitalised COVID-19 patients (COV). HV, EB and COV data are taken from https://dx.doi.org/10.5281/zenodo.5146019. Here the sequences are filtered to contain only unique combinations of isotype and IMGT-numbered V-domain DNA sequence (to remove redundancies due to e.g. capturing BCR transcripts from plasma cells).

"BM_Master_Light_Useasreftrue_140325_withPepStats_8.csv". IMGT/HighV-Quest output of the Bone Marrow light chain repertoire data. Published in Townsend et al. Front Immunol 7:388 (2016). Used here for the comparison of gene conversion frequencies against the melanoma light chain repertoire.

"BM_Master_Light_Useasreftrue_140325_withPepStats_8_Vgapped.fasta". The IMGT-gapped V-gene sequence from the Townsend et al. (see above) Bone Marrow light chain repertoire data. This is the raw input to BrepConvert. Provided here for this dataset; same sequences for the melanoma/healthy data are already in the RDS object ("HV_EB_COV_MEL_comb_Oct22.RDS").

"2_IMGT-gapped-nt-sequences_visa.txt", "2_IMGT-gapped-nt-sequences_visb.txt": Raw output of IMGT/HighV-Quest containing IMGT-gapped nucleotide sequences. These files were parsed to extract the IMGT-gapped V-gene sequence for BrepConvert analysis.

"BrepConvert.zip": BrepConvert gene conversion analysis results for Healthy and Melanoma repertoires.

See code in https://github.com/josef0731/melanoma-ig for ways to use these input files for reproducing the analyses.