Evidence map›Paper›PMID 37576901›Full record

ArticleFrontiers in oncology2023

Linked-read based analysis of the medulloblastoma genome.

Melissa Zwaig, Michael J Johnston, John J Y Lee, Hamza Farooq, Marco Gallo, Nada Jabado, Michael D Taylor, Jiannis Ragoussis

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Long-read sequencing for brain tumors.Frontiers in oncology · 2024
    Review
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

8 authors.

Melissa ZwaigVictor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada.
Michael J JohnstonAlberta Children's Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
John J Y LeeDepartment of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
Hamza FarooqBioBox Analytics Inc., Toronto, ON, Canada.
Marco GalloAlberta Children's Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
Nada JabadoDepartment of Human Genetics, McGill University, Montreal, QC, Canada.
Michael D TaylorDivision of Neurosurgery, The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
Jiannis RagoussisVictor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada.

Funding

Mouse models to discover new drivers of medulloblastomaR01CA159859 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Michael D. Taylor, WILLIAM A WEISS · 2011 to 2026
$10.4M
CCL2 and CCR2 as metastatic drivers and therapeutic targets in medulloblastomaR01CA255369 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GARZIA, LIVIA, TAYLOR, MICHAEL D. · 2021 to 2025
$3.9M
Prevention and treatment of lethal metastases in group 3 medulloblastomaR01NS106155 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TAYLOR, MICHAEL D., WEISS, WILLIAM A · 2018 to 2022
$2.8M
NCI NIH HHS R01 CA159859NCI NIH HHS R01 CA255369NINDS NIH HHS R01 NS106155
6 · The paper itself

Abstract

Introduction: Medulloblastoma is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases. However, the molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants in recurrently affected genes typically requires the application of long-read technologies. Methods: Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements. Results: We demonstrate the detection of complex structural variants and point mutations in these tumors, and, for the first time, the detection of extrachromosomal DNA (ecDNA) with linked-reads. We provide further evidence for the high heterogeneity of somatic mutations in G4 MBs and add new complex events associated with it. Discussion: We detected several enhancer-hijacking events, an ecDNA containing the

Indexed as

enhancer hijackingextrachromosomal DNAlinked-readsmedulloblastomaRNA sequencingwhole-genome sequencing

Identifiers

PMID37576901
PMCPMC10419201

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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.