Evidence map›Paper›PMID 29898407›Full record

ArticleCell reports2018

Integrated Molecular Characterization of Testicular Germ Cell Tumors.

Hui Shen, Juliann Shih, Daniel P Hollern, Linghua Wang, Reanne Bowlby, Satish K Tickoo, Vésteinn Thorsson, Andrew J Mungall, Yulia Newton, Apurva M Hegde and 41 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 251 papers, 5 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
251citing papers in PubMed, 5 pooled it
50.0field-weighted citation impact, top 1% 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

251 citing papers in PubMed, 5 syntheses or guidelines pooled it, 452 citations in OpenAlex.

  1. Pooled it
  2. Association Study between Polymorphisms in DNA Methylation-Related Genes and Testicular Germ Cell Tumor Risk.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2022
    Pooled it
  3. Guideline
  4. Meta-Analysis of Gene Expressions in Testicular Germ Cell Tumor Histologies.International journal of molecular sciences · 2020
    Pooled it
  5. Statistical genomics in rare cancer.Seminars in cancer biology · 2020
    Pooled it
  6. Trial
  7. Review
  8. Article
  9. Review
  10. Article
  11. Article
  12. Review
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Review
  20. Article

191 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

51 authors at 20 institutions in 6 countries.

Hui ShenVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Juliann ShihThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA.
Daniel P HollernDepartment of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Linghua WangHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
Reanne BowlbyCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
Satish K TickooDepartment of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Vésteinn ThorssonInstitute for Systems Biology, Seattle, WA 98109, USA.
Andrew J MungallCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
Yulia NewtonDepartment of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Apurva M HegdeDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Joshua ArmeniaCenter for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
Francisco Sánchez-VegaCenter for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
John PlutaDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105, USA.
Louise C PyleDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105, USA; Division of Genetics and Metabolism, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Rohit MehraUniversity of Michigan Hospital and Health Systems, 2G332 UH, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA.
Victor E ReuterDepartment of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Guilherme GodoyScott Department of Urology, Baylor College of Medicine, Houston, TX 77030, USA.
Jeffrey JonesScott Department of Urology, Baylor College of Medicine, Houston, TX 77030, USA.
Carl S ShelleyUniversity of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
Darren R FeldmanGenitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Daniel O VidalMolecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, Sao Paolo-SP, 14784-400, Brazil.
Davor LesselInstitute of Human Genetics, University of Ulm, 89081 Ulm, Germany; Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
Tomislav KulisDepartment of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, 10000 Zagreb, Croatia.
Flavio M CárcanoDepartment of Clinical Oncology, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, Sao Paolo-SP, 14784-400, Brazil.
Kristen M LeraasThe Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
Tara M LichtenbergThe Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
Denise BrooksCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
Andrew D CherniackThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Juok ChoThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
David I HeimanThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Katayoon KasaianCanada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
Minwei LiuComputational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Michael S NobleThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Liu XiHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Hailei ZhangThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Wanding ZhouVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Jean C ZenKlusenNational Cancer Institute, NIH, Bethesda, MD 20892, USA.
Carolyn M HutterNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Ina FelauNational Cancer Institute, NIH, Bethesda, MD 20892, USA.
Jiashan ZhangNational Cancer Institute, NIH, Bethesda, MD 20892, USA.
Nikolaus SchultzCenter for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
Gad GetzThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
Matthew MeyersonThe Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Joshua M StuartDepartment of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Cancer Genome Atlas Research Network
Rehan AkbaniDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
David A WheelerHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Peter W LairdVan Andel Research Institute, Grand Rapids, MI 49503, USA.
Katherine L NathansonDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105, USA; Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Victoria K CortessisDepartments of Preventive Medicine and Obstetrics and Gynecology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA. Electronic address: cortessis_v@med.usc.edu.
Katherine A HoadleyDepartment of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: hoadley@med.unc.edu.
Broad Institute · USMemorial Sloan Kettering Cancer Center · USBaylor College of Medicine · USBC Cancer Agency · CAVan Andel Institute · USThe University of Texas MD Anderson Cancer Center · USUniversity of North Carolina at Chapel Hill · USUniversity of Pennsylvania · USNational Cancer Institute · USNationwide Children's Hospital · USHospital de Câncer de Barretos · BRUniversity of Southern California · USChildren's Hospital of Philadelphia · USUniversity Hospital Centre Zagreb · HRUniversity of California, Santa Cruz · USUniversity of Wisconsin–Madison · USDana-Farber Cancer Institute · USInstitute for Systems Biology · USNational Human Genome Research Institute · USUniversität Hamburg · DE

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7M
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Nicholas D Socci · 1985 to 2026
$347.4M
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
Virology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Deborah F. Tate · 1985 to 2026
$201.5M
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Melissa A. Troester · 2001 to 2026
$36.3M
Translational Research Support CoreP30ES013508 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI Rebecca A Simmons · 2006 to 2026
$35.3M
Gene Expression Patterns in Human Tumors Identified Using Transcript SequencingU24CA143848 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, PEROU, CHARLES M · 2009 to 2016
$20.8M
Genome Characterization Center (GCC)U24CA143867 · NCI · BROAD INSTITUTE, INC. · PI GABRIEL, STACEY, MEYERSON, MATTHEW L. · 2009 to 2016
$17.0M
The Cancer Genome Atlas Data Analysis CenterU24CA143845 · NCI · BROAD INSTITUTE, INC. · PI CHIN, LYNDA, GETZ, GAD A · 2009 to 2016
$16.0M
Harvard Genome Characterization CenterU24CA144025 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI KUCHERLAPATI, RAJU S. · 2009 to 2016
$14.0M
NCATS NIH HHS KL2 TR001879NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA016086NCI NIH HHS P30 CA016672NCI NIH HHS R01 CA180778NCI NIH HHS U24 CA143799NCI NIH HHS U24 CA143835NCI NIH HHS U24 CA143840NCI NIH HHS U24 CA143843NCI NIH HHS U24 CA143845NCI NIH HHS U24 CA143848NCI NIH HHS U24 CA143858NCI NIH HHS U24 CA143866NCI NIH HHS U24 CA143867NCI NIH HHS U24 CA143882NCI NIH HHS U24 CA143883NCI NIH HHS U24 CA144025NCI NIH HHS U24 CA210949NCI NIH HHS U24 CA210969NCI NIH HHS U24 CA210988NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54 HG003273NIEHS NIH HHS P30 ES010126NIEHS NIH HHS P30 ES013508NIGMS NIH HHS T32 GM008638
6 · The paper itself

Abstract

We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These tumors exhibited high aneuploidy and a paucity of somatic mutations. Somatic mutation of only three genes achieved significance-KIT, KRAS, and NRAS-exclusively in samples with seminoma components. Integrated analyses identified distinct molecular patterns that characterized the major recognized histologic subtypes of TGCT: seminoma, embryonal carcinoma, yolk sac tumor, and teratoma. Striking differences in global DNA methylation and microRNA expression between histology subtypes highlight a likely role of epigenomic processes in determining histologic fates in TGCTs. We also identified a subset of pure seminomas defined by KIT mutations, increased immune infiltration, globally demethylated DNA, and decreased KRAS copy number. We report potential biomarkers for risk stratification, such as miRNA specifically expressed in teratoma, and others with molecular diagnostic potential, such as CpH (CpA/CpC/CpT) methylation identifying embryonal carcinomas.

Indexed as

DNA Copy Number VariationsDNA MethylationGene Expression Regulation, NeoplasticHumansMaleMicroRNAsNeoplasms, Germ Cell and EmbryonalProto-Oncogene Proteins c-kitras ProteinsSeminomaTesticular NeoplasmsMicroRNAsProto-Oncogene Proteins c-kitras Proteinscopy numberDNA methylationexome sequencingKITmiR-375nonseminomaseminomatesticular germ cell tumorsThe Cancer Genome Atlas

Identifiers

PMID29898407
PMCPMC6075738
OpenAlexW2807733000

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.