Evidence map›Paper›PMID 29996110›Full record

ArticleCell reports2018

A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases.

Yiqun Zhang, Lixing Yang, Melanie Kucherlapati, Fengju Chen, Angela Hadjipanayis, Angeliki Pantazi, Christopher A Bristow, Eunjung A Lee, Harshad S Mahadeshwar, Jiabin Tang and 15 more

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

Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.

0numbers the graph read from it
0cells of the map it votes in
57citing papers in PubMed
4.2field-weighted citation impact, top 4% 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

57 citing papers in PubMed, 83 citations in OpenAlex.

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  18. Function and Evolution of the Loop Extrusion Machinery in Animals.International journal of molecular sciences · 2023
    Review
  19. A nine-month-old boy with regression of milestones and severe constipation: an unusual case of a large spinal NTRK1 fusion pilocytic astrocytoma.Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2023
    Article
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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

25 authors at 6 institutions in 1 country.

Yiqun ZhangDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Lixing YangBen May Department for Cancer Research, Department of Human Genetics, Institute for Genomics and Systems Biology, and Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA.
Melanie KucherlapatiDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
Fengju ChenDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Angela HadjipanayisDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
Angeliki PantaziDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; KEW Inc, Cambridge, MA 02139, USA.
Christopher A BristowDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Eunjung A LeeDivision of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Harshad S MahadeshwarDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Jiabin TangDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Jianhua ZhangDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Sahil SethDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Semin LeeCenter for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Xiaojia RenDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; KEW Inc, Cambridge, MA 02139, USA.
Xingzhi SongDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Huandong SunDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Jonathan SeidmanDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Lovelace J LuquetteCenter for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Ruibin XiCenter for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Lynda ChinDepartment of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Alexei ProtopopovKEW Inc, Cambridge, MA 02139, USA; Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Wei LiDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Peter J ParkDivision of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Raju KucherlapatiDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
Chad J CreightonDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: creighto@bcm.edu.
Harvard University · USThe University of Texas MD Anderson Cancer Center · USBaylor College of Medicine · USCenter for Systems Biology · USBrigham and Women's Hospital · USUniversity of Chicago · US

Funding

Tumor BiologyP30CA125123 · NCI · BAYLOR COLLEGE OF MEDICINE · PI DAVID R ROWLEY · 2007 to 2026
$73.9M
The role of somatic mutation in neurodegenerative diseaseK01AG051791 · NIA · BRIGHAM AND WOMEN'S HOSPITAL · PI LEE, EUNJUNG ALICE · 2016 to 2020
$655k
Structural variations and their impact in human cancerK22CA193848 · NCI · UNIVERSITY OF CHICAGO · PI YANG, LIXING · 2017 to 2019
$508k
NCI NIH HHS K22 CA193848NCI NIH HHS P30 CA125123NIA NIH HHS K01 AG051791
6 · The paper itself

Abstract

A systematic cataloging of genes affected by genomic rearrangement, using multiple patient cohorts and cancer types, can provide insight into cancer-relevant alterations outside of exomes. By integrative analysis of whole-genome sequencing (predominantly low pass) and gene expression data from 1,448 cancers involving 18 histopathological types in The Cancer Genome Atlas, we identified hundreds of genes for which the nearby presence (within 100 kb) of a somatic structural variant (SV) breakpoint is associated with altered expression. While genomic rearrangements are associated with widespread copy-number alteration (CNA) patterns, approximately 1,100 genes-including overexpressed cancer driver genes (e.g., TERT, ERBB2, CDK12, CDK4) and underexpressed tumor suppressors (e.g., TP53, RB1, PTEN, STK11)-show SV-associated deregulation independent of CNA. SVs associated with the disruption of topologically associated domains, enhancer hijacking, or fusion transcripts are implicated in gene upregulation. For cancer-relevant pathways, SVs considerably expand our understanding of how genes are affected beyond point mutation or CNA.

Indexed as

Gene Expression Regulation, NeoplasticGenes, NeoplasmGenome, HumanBase SequenceCarcinogenesisDNA Copy Number VariationsEnhancer Elements, GeneticGene RearrangementHumansNeoplasmscancergenomic rearrangementpan-cancerstructural variationTCGAwhole genome sequencing

Identifiers

PMID29996110
PMCPMC6092947
OpenAlexW2811522864

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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.