Evidence map›Paper›PMID 39966644›Full record

ArticleNature genetics2025

ImmuneLENS characterizes systemic immune dysregulation in aging and cancer.

Robert Bentham, Thomas P Jones, James R M Black, Carlos Martinez-Ruiz, Michelle Dietzen, Maria Litovchenko, Kerstin Thol, Thomas B K Watkins, Chris Bailey, Oriol Pich and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. 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

16 authors.

Robert BenthamCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Thomas P JonesCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID http://orcid.org/0000-0003-2748-0780
James R M BlackCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID http://orcid.org/0000-0001-5598-7752
Carlos Martinez-RuizCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID http://orcid.org/0000-0002-4817-0565
Michelle DietzenCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID http://orcid.org/0000-0002-6853-7563
Maria LitovchenkoCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Kerstin TholCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID http://orcid.org/0000-0002-4624-118X
Thomas B K WatkinsDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Chris BaileyCancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
Oriol PichCancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.ORCID http://orcid.org/0000-0002-1956-1882
Zhihui ZhangDepartment of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Peter Van LooDepartment of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0003-0292-1949
TRACERx Consortium
Genomics England Consortium
Charles SwantonCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID http://orcid.org/0000-0002-4299-3018
Nicholas McGranahanCancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. nicholas.mcgranahan.10@ucl.ac.uk.ORCID http://orcid.org/0000-0001-9537-4045

Funding

Wellcome Trust CC2041
6 · The paper itself

Abstract

Recognition and elimination of pathogens and cancer cells depend on the adaptive immune system. Thus, accurate quantification of immune subsets is vital for precision medicine. We present immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS), which estimates T cell and B cell fractions, class switching and clonotype diversity from whole-genome sequencing data at depths as low as 5× coverage. By applying ImmuneLENS to the 100,000 Genomes Project, we identify genes enriched with somatic mutations in T cell-rich tumors, significant sex-based differences in circulating T cell fraction and demonstrated that the circulating T cell fraction in patients with cancer is significantly lower than in healthy individuals. Low circulating B cell fraction was linked to increased cancer incidence. Finally, circulating T cell abundance was more prognostic of 5-year cancer survival than infiltrating T cells.

Indexed as

AgingNeoplasmsAgedB-LymphocytesFemaleHumansMaleMutationPrognosisT-Lymphocytes

Identifiers

PMID39966644
PMCPMC11906351

What OpenQuestion holds

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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.