NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE131267 Query DataSets for GSE131267
Status Public on Dec 16, 2019
Title A large peptidome dataset improves HLA class I epitope prediction across most of the human population
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.
 
Overall design RNA transcript expression was quantified for mono-allelic HLA-C cell lines (HLA-C*04:01 and HLA-C*07:01, 4 replicates each) in order to assess its contribution to Class I peptide prediction and compare it against HLA-A and HLA-B.
 
Contributor(s) Wu CJ, Keskin DB
Citation(s) 31844290
Submission date May 15, 2019
Last update date Mar 16, 2020
Contact name Nir Hacohen
Organization name Broad Institute
Lab Nir Hacohen
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (8)
GSM3768244 A01 C0401-transduced B721.221 cells
GSM3768245 B01 C0401-transduced B721.221 cells
GSM3768246 C01 C0401-transduced B721.221 cells
Relations
BioProject PRJNA543098
SRA SRP198497

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE131267_RAW.tar 9.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap