Study

RNA-seq consisting of FASTQ paired-end reads from cancer samples

Study ID Alternative Stable ID Type
EGAS00001003724 Other

Study Description

Efforts to precisely identify tumor human leukocyte antigen presented peptides (HLAp) capable of mediating T cell based tumor rejection still face important challenges. Recent reports suggest that non-canonical cancer HLAp could be immunogenic but their identification requires highly sensitive and accurate mass-spectrometry (MS)-based proteogenomics approaches. Here, we present a MS-based analytical pipeline that can precisely characterize the non-canonical HLAp repertoire, incorporating whole exome sequencing, bulk and single cell transcriptomics, ribosome profiling, and a combination of two MS/MS search tools. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLAp. Albeit often at low levels and in distinct subpopulations of cells, numerous non-canonical HLAp are shared across tumors. This analytical platform holds great promise for the discovery of novel cancer antigens for cancer immunotherapy.

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
EGAD00001005097
Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples
Illumina HiSeq 2500 22

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