Evidence map›Paper›PMID 28329770›Full record

ArticleNature2017

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens.

Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund and 16 more

Registry-linked trialAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03373955 (A Prospective Study of Constructing Immune Repertoire Using Next-generation Sequencing), which is not on this map. Cited by 162 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
162citing papers in PubMed, 1 pooled it
28.2field-weighted citation impact, top 1% 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.

NCT03373955 unknown statusnot on this map

A Prospective Study of Constructing Immune Repertoire Using Next-generation Sequencing (NGS) to Monitor the Therapeutic Effect in NSCLC Patients

TypeobservationalSponsorSichuan UniversityRan2017 to 2021Enrolled60ConditionsNon-small Cell Lung CancerArmspembrolizumab
3 · Its place in the literature

Who cites it

162 citing papers in PubMed, 1 synthesis or guideline pooled it, 261 citations in OpenAlex.

  1. Pooled it
  2. Trial
  3. Cancer discovery · 2018
    Trial
  4. Review
  5. Review
  6. Idiotype-specific CD4Nature communications · 2026
    Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Article
  12. Review
  13. Review
  14. Article
  15. Complement C3d enables cell-mediated immunity capable of distinguishing spontaneously transformed from nontransformed cells.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Review

102 more citing papers are in PubMed but not listed here.

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

26 authors at 4 institutions in 1 country.

Michael S KhodadoustDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Niclas OlssonDepartment of Chemical &Systems Biology, Stanford University, Stanford, California 94305, USA.
Lisa E WagarDepartment of Microbiology &Immunology, Stanford University, Stanford, California 94305, USA.
Ole A W HaabethDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Binbin ChenDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Kavya SwaminathanDepartment of Chemical &Systems Biology, Stanford University, Stanford, California 94305, USA.
Keith RawsonDepartment of Chemical &Systems Biology, Stanford University, Stanford, California 94305, USA.
Chih Long LiuDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
David SteinerDepartment of Pathology, Stanford University, Stanford, California 94305, USA.
Peder LundDepartment of Microbiology &Immunology, Stanford University, Stanford, California 94305, USA.
Samhita RaoDepartment of Chemical &Systems Biology, Stanford University, Stanford, California 94305, USA.
Lichao ZhangDepartment of Chemical &Systems Biology, Stanford University, Stanford, California 94305, USA.
Caleb MarceauDepartment of Microbiology &Immunology, Stanford University, Stanford, California 94305, USA.
Henning StehrDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Aaron M NewmanDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Debra K CzerwinskiDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Victoria E H CarltonAdaptive Biotechnologies, South San Francisco, California 94080, USA.
Martin MoorheadAdaptive Biotechnologies, South San Francisco, California 94080, USA.
Malek FahamAdaptive Biotechnologies, South San Francisco, California 94080, USA.
Holbrook E KohrtDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Jan CaretteDepartment of Microbiology &Immunology, Stanford University, Stanford, California 94305, USA.
Michael R GreenDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Mark M DavisDepartment of Microbiology &Immunology, Stanford University, Stanford, California 94305, USA.
Ronald LevyDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Joshua E EliasDepartment of Chemical &Systems Biology, Stanford University, Stanford, California 94305, USA.
Ash A AlizadehDepartment of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA.
Stanford University · USAdaptive Biotechnologies (United States) · USCenter for Systems Biology · USHoward Hughes Medical Institute · US

Funding

Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
TUMOR SPECIFIC CYTOTOXIC T-LYMPHOCYTES IN BONE MARROW TRANSPLANTATIONP01CA049605 · NCI · STANFORD UNIVERSITY · PI David B. Miklos · 1989 to 2026
$73.3M
Modeling the Molecular Determinants of Induced Anti-Tumor Immune Responses in Mantle Cell LymphomaU01CA194389 · NCI · STANFORD UNIVERSITY · PI ALIZADEH, ASH ARASH, DAVIS, MARK MORRIS · 2015 to 2019
$3.1M
NCI NIH HHS P01 CA049605NCI NIH HHS U01 CA194389NIAID NIH HHS U19 AI057229NIH HHS CA194389NIH HHS S10 RR02933801
6 · The paper itself

Abstract

Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4

Indexed as

Antigen PresentationAntigens, NeoplasmCD4-Positive T-LymphocytesCytotoxicity, ImmunologicDNA Mutational AnalysisEpitopes, T-LymphocyteExomeGenomicsHistocompatibility Antigens Class IHLA-D AntigensHumansImmunoglobulin Variable RegionImmunotherapyLymphoma, Mantle-CellMutationProteomicsAntigens, NeoplasmEpitopes, T-LymphocyteHistocompatibility Antigens Class IHLA-D AntigensImmunoglobulin Variable Region

Identifiers

PMID28329770
PMCPMC5808925
OpenAlexW2599601523

What OpenQuestion holds

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Read underepoch 390

Registered trials

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.