Evidence map›Paper›PMID 40328759›Full record

ArticleNature communications2025

Genomic, transcriptomic, and immunogenomic landscape of over 1300 sarcomas of diverse histology subtypes.

Alex Soupir, Oscar E Ospina, Oliver Hampton, Michelle Churchman, Michael Radmacher, Dale Hedges, David McKean, Phaedra Agius, Saman Zeeshan, Nathan D Seligson and 28 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Article
  12. 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

38 authors.

Alex Soupir *Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0003-1251-9179
Oscar E Ospina *Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA.
Oliver HamptonAster Insights, Hudson, FL, USA.ORCID http://orcid.org/0000-0001-9164-1070
Michelle ChurchmanAster Insights, Hudson, FL, USA.ORCID http://orcid.org/0000-0002-6560-1056
Michael RadmacherAster Insights, Hudson, FL, USA.
Dale HedgesAster Insights, Hudson, FL, USA.
David McKeanAster Insights, Hudson, FL, USA.
Phaedra AgiusAster Insights, Hudson, FL, USA.
Saman ZeeshanDepartment of Biomedical and Health Informatics, School of Medicine, University of Missouri, Kansas City, MO, USA.
Nathan D SeligsonDepartment of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Jacksonville, FL, USA.ORCID http://orcid.org/0000-0002-9670-3792
Raphael PollockDivision of Surgical Oncology, The Ohio State University Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.ORCID http://orcid.org/0000-0002-0443-1583
David LiebnerDivision of Medical Oncology, The Ohio State University Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
James L ChenDivision of Medical Oncology, The Ohio State University Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
Gabriel TinocoDivision of Medical Oncology, The Ohio State University Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
Bodour SalhiaDepartment of Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Martin McCarterUniversity of Colorado School of Medicine, Aurora, CO, USA.ORCID http://orcid.org/0000-0001-8174-1713
Breelyn A WilkyUniversity of Colorado School of Medicine, Aurora, CO, USA.
Benjamin J MillerDepartment of Orthopaedics and Rehabilitation, University of Iowa, Iowa City, IO, USA.
Michael J CavnarDepartment of Surgery, University of Kentucky, Lexington, KY, USA.
John S GroundlandUniversity of Utah, Huntsman Cancer Institute, Salt Lake City, UT, USA.
Bryan P SchneiderIndiana University Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA.ORCID http://orcid.org/0000-0003-1868-7739
Gregory RiedlingerRutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
Stephen B EdgeRoswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
Christopher A MoskalukDepartment of Pathology, University of Virginia, Charlottesville, VA, USA.
Kenneth CardonaDivision of Surgical Oncology, Emory University, Atlanta, GA, USA.
Abdul Rafeh NaqashMedical Oncology/Phase 1 program, Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK, USA.
Ricardo J GonzalezSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA.
John E MullinaxSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA.
David M JoyceSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0003-0042-4367
Odion BinitieSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0002-2674-9939
G Douglas LetsonSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0001-5344-4316
Arash O NaghaviDepartment of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA.
Mihaela DrutaSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA.
Damon R ReedDepartment of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0002-8238-2465
Erin M SiegelDepartment of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0003-1779-2510
Jamie K TeerDepartment of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0003-4513-0282
Brooke L FridleyDepartment of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA.ORCID http://orcid.org/0000-0001-7739-7956
Andrew S BrohlSarcoma Department, Moffitt Cancer Center, Tampa, FL, USA. andrew.brohl@moffitt.org.ORCID http://orcid.org/0000-0002-0071-0534

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Given their rarity and diversity, a fundamental understanding of the genomic underpinnings for many sarcoma subtypes is still lacking. To better define the molecular landscape of this group of diseases, we perform matched whole exome sequencing and RNA sequencing on a cohort of 1340 sarcoma tumor specimens. We identify recurrent somatic mutations and observe an increased mutational burden in metastatic vs. primary samples (p < 0.001). We observe frequent copy number alterations including whole genome doubling, with this feature being more common in metastatic tumors (p = 0.026). Estimation of immune cell abundances followed by hierarchical clustering identifies five immune subtypes ranging from low to high and we observe inferior overall survival in immune deplete clusters compared to immune enriched (p < 0.01). Interestingly, GIST predominantly form a distinct "immune intermediate" cluster that is marked by a specific enrichment for NK cells (FDR < 0.01).

Indexed as

SarcomaTranscriptomeDNA Copy Number VariationsExome SequencingFemaleGene Expression ProfilingGenomicsHumansKiller Cells, NaturalMaleMutation

Identifiers

PMID40328759
PMCPMC12055966

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.