Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade

This study investigates the role of B cells in ICB clinical trials. Our initial observations are done in cohort b1 (discovery) and we validate our findings in cohorts b2 (validation), as well as multiple additional cohorts, as described in figure 1a and the methods section.

The data attached includes 3 assays:
(1) Bulk RNAseq+BCRseq, (2) scRNAseq+scBCRseq and (3) Seromics.

bulk data includes:

discovery cohort b1:

bulk:
bulk_discovery_cohort_BCR_table.csv, BCRseq data.
bulk_discovery_cohort_metadata.csv, relevant metadata for analysis.
bulk_discovery_cohort_voomjDream.RDS, normalized count data.

scRNAseq:
discovery_cohort_b_cells_clean.h5ad, single cell data and self explanatory relevant metadata.
discovery_cohort_BCRseq_table.csv, BCRseq data.

Seromics:
seromics_raw_data.xlsx, processed raw data from seromics.

validation cohort b2:

bulk:
bulk_validation_cohort_BCR_table.csv, BCRseq data.
bulk_validation_cohort_metadata.csv, relevant metadata for analysis.
bulk_validation_cohort_voomjDream.RDS, normalized count data.

scRNAseq:
validation_cohort_b_cells_clean.h5ad, single cell data and self explanatory relevant metadata.
validation_cohort_BCRseq_table.csv, BCRseq data.

Detailed description on the methods applied can be found in the methods section from the article. We also provide the code used for analysis, however, it is important to note that no new methods were developed for analysis. The code consistently applies existing tools and algorithms to investigate single cell and bulk sequencing data. There are multiple code sniplets for discovery cohort and fewer more condensed sniplets for the additional cohorts. Cohorts not provided here are described in the methods section because they are already existing public data.