First-in-human clinical trial of personalized neoantigen vaccines as early intervention in untreated patients with lymphoplasmacytic lymphoma

We performed single cell RNA-seq gene expression analysis on bone marrow of 9 lymphoplasmacytic lymphoma patients before and after vaccination with personalized idiotype DNA vaccine to study changes in tumor microenvironment Bone marrow samples before and after vaccination of 8 patients and one sample of pre vaccination sample for one patient were processed for single cell RNA seq using 10x genomics 5' chromium kit. For all except one patient samples of pre and post for a given patient were processed together on the same day and loaded separately into a well of 10x Genomics chip. For one patient (LPL008) samples of pre and post were first stained with two hashing antibodies, and then samples were mixed together at 1:1 ratio and loaded into a single well of 10x Genomics chip (additional data files are included for that patient for cell surface barcode sequencing). Bone marrow samples before and after vaccination of 9 patients were processed for single cell RNA seq paired with single cell TCR and single cell BCR seq using 10x genomics 5' chromium kit.