Evidence map›Paper›PMID 40804524›Full record

Trial reportNature2025

Clone copy number diversity is linked to survival in lung cancer.

Piotr Pawlik, Kristiana Grigoriadis, Abigail Bunkum, Helena Coggan, Alexander M Frankell, Carlos Martinez-Ruiz, Takahiro Karasaki, Ariana Huebner, Andrew Rowan, Jasmin Fisher and 4 more

Abstract readClinical Trial
PubMed Full text at PMC Publisher
In one paragraph

Trial report in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Trial
  2. Review
  3. ClonalLife science alliance · 2026
    Article
  4. Review
  5. Article
  6. Review
  7. Organoids glimpse: the nexus for diverse tumor heterogeneity.Frontiers in cell and developmental biology · 2026
    Review
  8. 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

14 authors.

Piotr Pawlik *Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Kristiana Grigoriadis *Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0002-8435-0176
Abigail BunkumCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Helena CogganCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Alexander M FrankellCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0002-0341-7878
Carlos Martinez-RuizCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0002-4817-0565
Takahiro KarasakiCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0001-6863-2360
Ariana HuebnerCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0001-8009-4999
Andrew RowanCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Jasmin FisherComputational Cancer Biology Research Group, University College London Cancer Institute, London, UK.ORCID 0000-0003-4477-9047
Allan HackshawCancer Research UK & UCL Cancer Trials Centre, London, UK.ORCID 0000-0002-5570-5070
Charles SwantonCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0002-4299-3018
Simone ZaccariaCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. s.zaccaria@ucl.ac.uk.ORCID 0000-0002-5265-7392
Nicholas McGranahanCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK. nicholas.mcgranahan.10@ucl.ac.uk.ORCID 0000-0001-9537-4045

Funding

AstraZeneca, Boehringer-Ingelheim, Bristol Myers Squibb, Pfizer, InvitaeWellcome Trust
6 · The paper itself

Abstract

Both single nucleotide variants (SNVs) and somatic copy number alterations (SCNAs) accumulate in cancer cells during tumour development, fuelling clonal evolution. However, accurate estimation of clone-specific copy numbers from bulk DNA-sequencing data is challenging. Here we present allele-specific phylogenetic analysis of copy number alterations (ALPACA), a method to infer SNV and SCNA coevolution by leveraging phylogenetic trees reconstructed from multi-sample bulk tumour sequencing data using SNV frequencies. ALPACA estimates the SCNA evolution of simulated tumours with a higher accuracy than current state-of-the-art methods

Indexed as

Clonal EvolutionClone CellsDNA Copy Number VariationsLung NeoplasmsAllelesChromosomal InstabilityCyclin D1Disease-Free SurvivalGene AmplificationGenes, Tumor SuppressorHumansLoss of HeterozygosityNeoplasm MetastasisPhylogenyPolymorphism, Single NucleotideCCND1 protein, humanCyclin D1

Identifiers

PMID40804524
PMCPMC12488491

What OpenQuestion holds

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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.