Evidence map›Paper›PMID 33242424›Full record

ArticleCell2020

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.

Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury, Dmitry Rykunov, Azra Krek, Weiping Ma, Yuankun Zhu, Jiayi Ji and 79 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 213 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
213citing papers in PubMed, 2 pooled it
–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

213 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Molecular features in gangliogliomas: a systematic review.Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2026
    Pooled it
  2. Pooled it
  3. Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2024
    Trial
  4. Article
  5. Article
  6. Time to adjuvant treatment for newly diagnosed pediatric brain tumors in the molecular era: a single center retrospective study.Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2026
    Article
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153 more citing papers are in PubMed but not listed here.

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

89 authors.

Francesca PetraliaDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Nicole TignorDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Boris RevaDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Mateusz KoptyraCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Shrabanti ChowdhuryDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Dmitry RykunovDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Azra KrekDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Weiping MaDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Yuankun ZhuCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Jiayi JiDepartment of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Anna CalinawanDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jeffrey R WhiteakerFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Antonio ColapricoDepartment of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Vasileios StathiasDepartment of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA.
Tatiana OmelchenkoCell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Xiaoyu SongDepartment of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Pichai RamanCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Yiran GuoCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Miguel A BrownCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Richard G IveyFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
John SzpytThermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Sanjukta Guha ThakurtaThermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Marina A GritsenkoBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Karl K WeitzBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Gonzalo LopezDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Selim KalayciDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Zeynep H GümüşDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Seungyeul YooDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Felipe da Veiga LeprevostDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Hui-Yin ChangDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Karsten KrugBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA.
Lizabeth KatsnelsonInstitute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Ying WangInstitute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Jacob J KennedyFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Uliana J VoytovichFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Lei ZhaoFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Krutika S GaonkarCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Brian M EnnisCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Bo ZhangCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Valerie BaubetCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Lamiya TauhidCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Jena V LillyCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Jennifer L MasonCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Bailey FarrowCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Nathan YoungCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Sarah LearyFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Jamie MoonBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Vladislav A PetyukBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Javad NazarianChildren's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland.
Nithin D AdappaDepartment of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA.
James N PalmerDepartment of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Robert M LoberDepartment of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA.
Samuel Rivero-HinojosaChildren's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
Liang-Bo WangDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Joshua M WangInstitute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Matilda BrobergInstitute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Rosalie K ChuBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Ronald J MooreBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Matthew E MonroeBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Rui ZhaoBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Richard D SmithBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Jun ZhuDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Mehdi MesriOffice of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Emily BojaOffice of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Tara HiltkeOffice of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Henry RodriguezOffice of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Bing ZhangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Eric E SchadtDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
D R ManiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA.
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Antonio IavaroneInstitute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.
Maciej WiznerowiczPoznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland.
Stephan SchürerDepartment of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA.
Xi S ChenDepartment of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Allison P HeathCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Jo Lynne RokitaCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Alexey I NesvizhskiiDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
David FenyöInstitute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Karin D RodlandBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
Tao LiuBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Steven P GygiThermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Amanda G PaulovichFred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Adam C ResnickCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Electronic address: resnick@email.chop.edu.
Phillip B StormCenter for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Electronic address: storm@email.chop.edu.
Brian R RoodChildren's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA. Electronic address: brood@childrensnational.org.
Pei WangDepartment of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: pei.wang@mssm.edu.
Children’s Brain Tumor Network
Clinical Proteomic Tumor Analysis Consortium

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4M
Utilizing FHIR to expand the availability of interoperable clinical and phenotypic data to the pediatric research communityU2CHD109731 · NICHD · CHILDREN'S HOSP OF PHILADELPHIA · PI Adam Cain Resnick · 2022 to 2026
$31.6M
U2C Kids First Admin Supplement - data transferU2CHL138346 · NHLBI · CHILDREN'S HOSP OF PHILADELPHIA · PI RESNICK, ADAM CAIN · 2017 to 2022
$21.5M
New Sample Multiplexing Technologies to Identify Chemical Probes and Illuminate Ubiquitin BiologyR01GM067945 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI GYGI, STEVEN P · 2003 to 2024
$10.5M
Proteogenomic Studies aimed at understanding ovarian tumor responses to agents targeting the DNA damage response and translating this knowledge into clinical benefitU01CA214114 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BIRRER, MICHAEL, PAULOVICH, AMANDA G · 2017 to 2021
$8.4M
Research Training in Childhood CancerT32CA128583 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Eric Alejandro Sweet-Cordero · 2007 to 2026
$6.0M
The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic TargetsU24CA210985 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2016 to 2020
$5.3M
PNNL Proteome Characterization CenterU24CA210955 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI LIU, TAO, SMITH, RICHARD D · 2016 to 2020
$5.3M
iPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTACU24CA210954 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ZHANG, BING · 2016 to 2020
$4.9M
Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision MedicineU24CA210993 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SCHADT, ERIC E, WANG, PEI · 2016 to 2020
$4.6M
Integrated high throughput proteogenomic data analysis center for CPTACU24CA210979 · NCI · BROAD INSTITUTE, INC. · PI BIRGER, CHET, GETZ, GAD A · 2016 to 2020
$4.4M
University of Michigan Proteogenomics Data Analysis CenterU24CA210967 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M, DHANASEKARAN, SARAVANA M · 2016 to 2020
$4.1M
NCI NIH HHS P30 CA008748NCI NIH HHS R50 CA211499NCI NIH HHS T32 CA128583NCI NIH HHS U01 CA214114NCI NIH HHS U24 CA210954NCI NIH HHS U24 CA210955NCI NIH HHS U24 CA210967NCI NIH HHS U24 CA210972NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210985NCI NIH HHS U24 CA210993NHLBI NIH HHS U2C HL138346NICHD NIH HHS U2C HD109731NIGMS NIH HHS R01 GM067945NINDS NIH HHS R01 NS085336NINDS NIH HHS R01 NS091620
6 · The paper itself

Abstract

We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.

Indexed as

ProteogenomicsBrain NeoplasmsChildDNA Copy Number VariationsGene Expression Regulation, NeoplasticGene Regulatory NetworksGenome, HumanGliomaHumansLymphocytes, Tumor-InfiltratingMutationNeoplasm GradingNeoplasm Recurrence, LocalPhosphoproteinsPhosphorylationRNA, MessengerPhosphoproteinsRNA, MessengerBRAF alterationCPTACCTNNB1 mutationkinase activity scorekinase substrate regulationpediatric brain tumorpost-translational modificationproteomic clusterrecurrent versus primary tumorstumor microenvironment

Identifiers

PMID33242424
PMCPMC8143193

What OpenQuestion holds

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Registered trials

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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.