Evidence map›Paper›PMID 35627168›Full record

ArticleGenes2022

ProGeo-Neo v2.0: A One-Stop Software for Neoantigen Prediction and Filtering Based on the Proteogenomics Strategy.

Chunyu Liu, Yu Zhang, Xingxing Jian, Xiaoxiu Tan, Manman Lu, Jian Ouyang, Zhenhao Liu, Yuyu Li, Linfeng Xu, Lanming Chen and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
1.8field-weighted citation impact, top 15% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 23 citations in OpenAlex.

  1. Review
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  12. Tumor Antigens beyond the Human Exome.International journal of molecular sciences · 2024
    Review
  13. Review
  14. Therapeutic cancer vaccines: advancements, challenges, and prospects.Signal transduction and targeted therapy · 2023
    Review
  15. Review
  16. Review
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  19. Article
  20. Molecular therapy. Nucleic acids · 2022
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 4 institutions in 1 country.

Chunyu LiuCollege of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
Yu ZhangShanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China.
Xingxing JianShanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China.
Xiaoxiu TanShanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China.
Manman LuCollege of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
Jian OuyangShanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China.
Zhenhao LiuShanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China.ORCID 0000-0003-4465-5925
Yuyu LiCollege of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
Linfeng XuShanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China.
Lanming ChenCollege of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
Yong LinSchool of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
Lu XieCollege of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
Shanghai Ocean University · CNUniversity of Shanghai for Science and Technology · CNEast China Normal University · CNShanghai Jiao Tong University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

A proteogenomics-based neoantigen prediction pipeline, namely ProGeo-neo, was previously developed by our team to predict neoantigens, allowing the identification of class-I major histocompatibility complex (MHC) binding peptides based on single-nucleotide variation (SNV) mutations. To improve it, we here present an updated pipeline, i.e., ProGeo-neo v2.0, in which a one-stop software solution was proposed to identify neoantigens based on the paired tumor-normal whole genome sequencing (WGS)/whole exome sequencing (WES) data in FASTQ format. Preferably, in ProGeo-neo v2.0, several new features are provided. In addition to the identification of MHC-I neoantigens, the new version supports the prediction of MHC class II-restricted neoantigens, i.e., peptides up to 30-mer in length. Moreover, the source of neoantigens has been expanded, allowing more candidate neoantigens to be identified, such as in-frame insertion-deletion (indels) mutations, frameshift mutations, and gene fusion analysis. In addition, we propose two more efficient screening approaches, including an in-group authentic neoantigen peptides database and two more stringent thresholds. The range of candidate peptides was effectively narrowed down to those that are more likely to elicit an immune response, providing a more meaningful reference for subsequent experimental validation. Compared to ProGeo-neo, the ProGeo-neo v2.0 performed well based on the same dataset, including updated functionality and improved accuracy.

Indexed as

NeoplasmsProteogenomicsAntigens, NeoplasmHumansPeptidesSoftwareAntigens, NeoplasmPeptidesbioinformaticsneoantigenproteogenomictumor immunotherapy

Identifiers

PMID35627168
PMCPMC9141370
OpenAlexW4224998110

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.