Evidence map›Paper›PMID 42124572›Full record

ArticlebioRxiv : the preprint server for biology2026

A Pan-Cancer Single-Cell Atlas to Evaluate Tumor Identity, Cell Line Concordance, and Dependency Mapping.

Rosyli F Reveron-Thornton, James P Agolia, Chuner Guo, Maria Korah, Chia-Hsin Hsu, Peter Y Xie, Renceh Ab Flojo, Andrea E Delitto, Amanda Gonçalves, Angela D Tabora and 15 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

25 authors.

Rosyli F Reveron-ThorntonDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
James P AgoliaDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.ORCID 0000-0001-5357-3871
Chuner GuoDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Maria KorahDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Chia-Hsin HsuDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Peter Y XieDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Renceh Ab FlojoDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Andrea E DelittoDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Amanda GonçalvesDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Angela D TaboraDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Michael JanuszykHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Victoria E SanchezDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Kevin NeeDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Biren ReddyDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Wesley BobstHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Byrne LeeDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
George A PoultsidesDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Amanda R KiraneDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Derrick C WanDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Jeffrey A NortonDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Edgar G EnglemanDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Aaron M NewmanStanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.ORCID 0000-0002-1857-8172
Michael T LongakerDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Deshka S FosterDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Daniel DelittoDepartment of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Bulk RNA sequencing enables pan-cancer transcriptional analyses, but obscures cancer cell-specific programs due to admixture with nonmalignant cells, thereby limiting direct comparison between experimental models and primary tumors. Single-cell RNA sequencing (scRNA-seq) overcomes these limitations; however, the biological interpretability of public datasets is often compromised by variable data quality, inconsistent annotation, and atlas-scale aggregation strategies that prioritize data volume over biological coherence. We therefore developed a stringent integration framework that prioritizes representative malignant transcriptional states. Using Mahalanobis distance-based selection within batch-corrected latent space, we constructed a pan-cancer atlas comprising 135,424 high-quality malignant cells from 499 samples across 36 adult and pediatric cancers. Atlas-derived cancer signatures were used to determine tumor-cell line concordance and project ElasticNet models trained on DepMap CRISPR screens to infer cancer-specific gene dependencies. The scTumor Atlas establishes a scalable framework for tumor identity inference, cancer cell line benchmarking, and systematic identification of genetic vulnerabilities.

Indexed as

Cancer cell linesCRISPR screeningDepMapGene dependency predictionModel fidelityPan-cancer analysisscRNA-seqSingle-cell RNA sequencingTumor atlas

Identifiers

PMID42124572
PMCPMC13160036

What OpenQuestion holds

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LicenceCC BY-NC
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.