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Biomarkers in Patients With Rhabdomyosarcoma

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ClinicalTrials.gov Identifier: NCT01466283
Recruitment Status : Completed
First Posted : November 7, 2011
Last Update Posted : May 19, 2016
Information provided by (Responsible Party):

November 2, 2011
November 7, 2011
May 19, 2016
October 2011
May 2016   (Final data collection date for primary outcome measure)
  • Genome-wide alterations in DNA methylation in ARMS and ERMS
  • Genome-wide DNA copy number alterations in ARMS and ERMS
  • Pathogenic genes and pathways by integrative genomic analysis
Same as current
Complete list of historical versions of study NCT01466283 on ClinicalTrials.gov Archive Site
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Biomarkers in Patients With Rhabdomyosarcoma
Integrative Epigenomic Approach to Gene Discovery in Rhabdomyosarcoma (RMS)

RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.

PURPOSE: This research study is studying biomarkers in patients with rhabdomyosarcoma.


  • Determine genome-wide alterations in DNA methylation in ARMS and ERMS.
  • Determine genome-wide DNA copy number alterations in ARMS and ERMS.
  • Determine pathogenic genes and pathways by integrative genomic analysis.

OUTLINE: Genome-wide DNA-methylation analysis on ARMS, ERMS, and normal human skeletal myoblasts will be conducted using the HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR) assay. The methylation status of 1.3 million CpGs at promoters, gene bodies, and intergenic areas will be analyzed. Parallel gene expression analysis will be done and correlated with changes in methylation to uncover genes regulated by epigenetic alterations and altered by genomic losses or gains.

Genes that are altered by both genetic and epigenetic alterations in different sets of patients will be selected by the MIGHT (Multi-dimensional Integration of Genomic data from Human Tissues) algorithm to uncover new genes that are potentially involved in the pathogenesis of ARMS and ERMS. Gene ontology, pathway, and DNA motif analysis algorithms, and other computational approaches will be used to determine the biological consequences of the changes. Prioritized set of epigenetic and genetic alterations will be validated by bisulfite MassArray, FISH, and qRT-PCR in larger numbers of ARMS and ERMS samples.

Observational Model: Case Control
Time Perspective: Retrospective
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Non-Probability Sample
Cooperative Human Tissue Network (CHTN)
  • Genetic: DNA methylation analysis
  • Genetic: fluorescence in situ hybridization
  • Genetic: gene expression analysis
  • Genetic: reverse transcriptase-polymerase chain reaction
  • Other: laboratory biomarker analysis
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*   Includes publications given by the data provider as well as publications identified by ClinicalTrials.gov Identifier (NCT Number) in Medline.
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May 2016   (Final data collection date for primary outcome measure)


  • 10 ARMS and 10 ERMS frozen samples will be collected from the COG bank via the Cooperative Human Tissue Network (CHTN)
  • Human skeletal myoblasts (ZenBio, Research Triangle Park, NC) will serve as controls


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Sexes Eligible for Study: All
Child, Adult, Senior
Contact information is only displayed when the study is recruiting subjects
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COG-ARST12B2 ( Other Identifier: Children's Oncology Group )
ARST12B2 ( Other Identifier: Children's Oncology Group )
NCI-2011-03634 ( Registry Identifier: CTRP (Clinical Trial Reporting Program) )
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Children's Oncology Group
Children's Oncology Group
National Cancer Institute (NCI)
Principal Investigator: Caroline Y. Hu, MD Tomorrows Children's Institute at Hackensack University Medical Center
Children's Oncology Group
May 2016