Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prediction of HLA genotypes using NGS data

ABSTRACT: High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate.

PROVIDER: EGAS00001005274 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Crosslinking MS of Antibody-HLA-A*11:01

Project description:Cross-linking mass spectrometry data of cross-linked antibody to human leukocyte antigen (HLA-A*11:01). For antibodies 2E3, 1E3 and 3H10.

2023-11-23 | PXD038059 | JPOST Repository

a4ff8fb9-13fb-404d-9cd6-480521f07f5b - samples

Project description:High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate. We compared the availability and accuracy of eight HLA genotyping tools (OptiType, HLA-HD, PHLAT, seq2HLA, arcasHLA, HLAscan, HLA*LA, and Kourami) using 1,275 cases from the 1000 Genomes Project data and created a new HLA-genotyping algorithm combining tools. Then, we assessed the new algorithmÃ¢Â€Â™s performance in 39 in-house samples with normal whole-exome sequencing (WES) data and polymerase chain reactionÃ¢Â€Â“sequencing-based typing (PCR-SBT) results.

| EGAD00001007733 | EGA

Study of RO7515629 in Participants With HLA-G Positive Solid Tumors

Project description:The main purpose of this study is to evaluate the safety, tolerability, pharmacokinetics, immune response and preliminary anti-tumor activity of RO7515629 alone in participants with advanced or metastatic solid tumors expressing human leukocyte antigen G (HLA-G).

| 11560 | ecrin-mdr-crc

Single cell RNA-seq of HLA-E restricted UL40-specific T cells

Project description:Human cytomegalovirus infection (CMV) can stimulate robust human leukocyte antigen (HLA)-E restricted CD8 T cell responses. These T cells recognize a peptide from UL40, which differs by as little as a single methyl group from self-peptides that also bind HLA-E, challenging their capacity to avoid self-reactivity. We showed in one donor 2 distinct populations of UL40/HLA-E T cells, with vastly different T cell receptor (TCR) affinities for the UL40/HLA-E complex. However, paradoxically, lower cytokine responses were observed from UL40/HLA-E T cells bearing TCRs with high affinity for HLA-E. To identify why these T cells bearing high affinity T cell receptors were less responsive to antigens, we performed single cell RNAseq analysis. These 2 distinct populations of T cells were single-cell sorted into 96-well plates prior to single cell RNA-seq analysis.

2021-05-21 | E-MTAB-10305 | biostudies-arrayexpress

γδ T cells are effectors of immunotherapy in cancers with HLA class I defects

Project description:DNA mismatch repair deficient (MMR-d) cancers present an abundance of neoantigens that likely underlies their exceptional responsiveness to immune checkpoint blockade (ICB). However, MMR-d colon cancers that evade CD8+ T cells through loss of Human Leukocyte Antigen (HLA) class I-mediated antigen presentation frequently remain responsive to ICB, suggesting the involvement of other immune effector cells.

2022-11-01 | GSE216534 | GEO

Improved prediction of endogenous HLA-associated epitopes based on mono-allelic mass spectrometry profiling

Project description:LC-MS/MS-based identification of HLA-peptides is poised to provide a deep understanding of the rules underlying antigen presentation. However, a key obstacle limiting the utility of MS data is the ambiguity arising from the co-expression of multiple HLA alleles. Here, we introduce a strategy for profiling the HLA ligandome one allele at a time. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing a novel spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of novel binding motifs, and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a scalable strategy for systematically learning the rules of endogenous antigen presentation.

2017-02-21 | GSE93315 | GEO

Influenza-derived peptide presentation by HLA-A*24:02

Project description:Identification of influenza virus-derived peptides presented by Human Leukocyte Antigen (HLA) molecules of the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the HLA class I allele HLA-A*24:02, after influenza infection.

2021-04-08 | PXD020292 | Pride

Influenza-derived peptide presentation by HLA-A*11:01

Project description:Analysis of the immunopeptidome of Human Leukocyte Antigen (HLA)-A*11:01 during influenza infection. Analyses were performed using the Class I reduced C1R cell line transfected with the HLA class I allele HLA-A*11:01.

2022-02-15 | PXD028985 | Pride

HLA-I peptidomes and phosphopeptidomes (B*40, B*27, B*07, B*39)

Project description:As aberrant phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify phosphorylated ligands associated with HLA-B*40, -B*27, -B*39 and -B*07. Remarkably, these phosphopeptides showed similar molecular features. Besides the specific anchor motifs imposed by the binding groove of each allotype, the predominance of phosphorylation at peptide position 4 (P4) became strikingly evident, as was the enrichment of basic residues at P1. This molecular understanding of the presentation of phosphopeptides by HLA-B molecules can help in predicting tumor-specific neo-antigens that arise from aberrant phosphorylation in cancer cells.

2016-12-12 | PXD005084 | Pride

The role of chorionic PGRMC2 and HLA-G in maintaining immune homeostasis at the chorio-decidual interface

Project description:The chorio-decidual interface (CDi) is formed by chorion trophoblasts (CTCs) and immune cell-rich decidua (DECs) cells. The roles of human leukocyte antigen (HLA)-G and progesterone receptor membrane component 2 (PGRMC2) in mediating innate immune homeostasis at this maternal-fetal interface interface were investigated.

2024-01-02 | GSE251809 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data