Single-Cell Analysis study with AMPLICON, RNA-Seq data on dbGaP (7 participants)

phs003425 — Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined with Nivolumab    and Ipilimumab for Patients with Resected MMR-p Colorectal and    Pancreatic Cancer

<p>We developed INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach to combine molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility. Data available through dbGaP include scRNA-seq with matched TCR-seq.</p>

Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined with Nivolumab    and Ipilimumab for Patients with Resected MMR-p Colorectal and    Pancreatic Cancer