Evidence map›Paper›PMID 36932241›Full record

ArticleNature medicine2023

Diagnostic classification of childhood cancer using multiscale transcriptomics.

Federico Comitani, Joshua O Nash, Sarah Cohen-Gogo, Astra I Chang, Timmy T Wen, Anant Maheshwari, Bipasha Goyal, Earvin S Tio, Kevin Tabatabaei, Chelsea Mayoh and 20 more

Open access · hybridFull text read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.

0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed
10.0field-weighted citation impact, top 2% 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.

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

30 citing papers in PubMed, 42 citations in OpenAlex.

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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

30 authors at 7 institutions in 3 countries.

Federico ComitaniProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.ORCID http://orcid.org/0000-0003-3226-1179
Joshua O NashProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Sarah Cohen-GogoDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.ORCID http://orcid.org/0000-0002-8852-1104
Astra I ChangProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Timmy T WenProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Anant MaheshwariProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Bipasha GoyalProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Earvin S TioProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.ORCID http://orcid.org/0000-0002-0521-779X
Kevin TabatabaeiProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Chelsea MayohChildren's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0002-6398-3046
Regis ZhaoProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Ben HoLaboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
Ledia BrungaProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
John E G LawrenceWellcome Sanger Institute, Hinxton, UK.
Petra BaloghDepartment of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, UK.
Adrienne M FlanaganDepartment of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, UK.ORCID http://orcid.org/0000-0002-2832-1303
Sarah TeichmannWellcome Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-6294-6366
Annie HuangDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.
Vijay RamaswamyDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.ORCID http://orcid.org/0000-0002-6557-895X
Johann HitzlerDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.ORCID http://orcid.org/0000-0003-1158-186X
Jonathan D WassermanProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.ORCID http://orcid.org/0000-0001-7088-8146
Rebecca A GladdyDepartment of Surgical Oncology, Princess Margaret Cancer Centre/Mount Sinai Hospital, Toronto, ON, Canada.ORCID http://orcid.org/0000-0003-4143-6620
Brendan C DicksonDepartment of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada.ORCID http://orcid.org/0000-0003-2269-6216
Uri TaboriProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.ORCID http://orcid.org/0000-0002-5019-2683
Mark J CowleyChildren's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0002-9519-5714
Sam BehjatiWellcome Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-6600-7665
David MalkinDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.ORCID http://orcid.org/0000-0001-5752-9763
Anita VillaniDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.
Meredith S IrwinDepartment of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.
Adam ShlienProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada. adam.shlien@sickkids.ca.ORCID http://orcid.org/0000-0002-0368-5370
University of Toronto · CAHospital for Sick Children · CACancer Institute of New South Wales · AUMount Sinai Hospital · CARoyal National Orthopaedic Hospital · GBWellcome Sanger Institute · GBUniversity of Cambridge · GB

Funding

CIHR 162267
6 · The paper itself

Abstract

The causes of pediatric cancers' distinctiveness compared to adult-onset tumors of the same type are not completely clear and not fully explained by their genomes. In this study, we used an optimized multilevel RNA clustering approach to derive molecular definitions for most childhood cancers. Applying this method to 13,313 transcriptomes, we constructed a pediatric cancer atlas to explore age-associated changes. Tumor entities were sometimes unexpectedly grouped due to common lineages, drivers or stemness profiles. Some established entities were divided into subgroups that predicted outcome better than current diagnostic approaches. These definitions account for inter-tumoral and intra-tumoral heterogeneity and have the potential of enabling reproducible, quantifiable diagnostics. As a whole, childhood tumors had more transcriptional diversity than adult tumors, maintaining greater expression flexibility. To apply these insights, we designed an ensemble convolutional neural network classifier. We show that this tool was able to match or clarify the diagnosis for 85% of childhood tumors in a prospective cohort. If further validated, this framework could be extended to derive molecular definitions for all cancer types.

Indexed as

NeoplasmsAdultChildGene Expression ProfilingHumansNeural Networks, ComputerProspective StudiesTranscriptome

Identifiers

PMID36932241
PMCPMC10033451
OpenAlexW4327747318

What OpenQuestion holds

Textfull text, public
LicenceCC BY
measurements read60
identifiers read1
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.