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Biomarkers in Patients With Rhabdomyosarcoma

This study has been completed.
National Cancer Institute (NCI)
Information provided by (Responsible Party):
Children's Oncology Group Identifier:
First received: November 2, 2011
Last updated: May 17, 2016
Last verified: May 2016

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.

Condition Intervention
Genetic: DNA methylation analysis
Genetic: fluorescence in situ hybridization
Genetic: gene expression analysis
Genetic: reverse transcriptase-polymerase chain reaction
Other: laboratory biomarker analysis

Study Type: Observational
Study Design: Observational Model: Case Control
Time Perspective: Retrospective
Official Title: Integrative Epigenomic Approach to Gene Discovery in Rhabdomyosarcoma (RMS)

Resource links provided by NLM:

Further study details as provided by Children's Oncology Group:

Primary Outcome Measures:
  • 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

Estimated Enrollment: 20
Study Start Date: October 2011
Primary Completion Date: May 2016 (Final data collection date for primary outcome measure)
Detailed Description:


  • 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.


Ages Eligible for Study:   Child, Adult, Senior
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Non-Probability Sample
Study Population
Cooperative Human Tissue Network (CHTN)


  • 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


  • Not specified


  • Not specified
  Contacts and Locations
Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study. To learn more about this study, you or your doctor may contact the study research staff using the Contacts provided below. For general information, see Learn About Clinical Studies.

Please refer to this study by its identifier: NCT01466283

Sponsors and Collaborators
Children's Oncology Group
National Cancer Institute (NCI)
Principal Investigator: Caroline Y. Hu, MD Tomorrows Children's Institute at Hackensack University Medical Center
  More Information

Responsible Party: Children's Oncology Group Identifier: NCT01466283     History of Changes
Other Study ID Numbers: ARST12B2
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) )
Study First Received: November 2, 2011
Last Updated: May 17, 2016

Keywords provided by Children's Oncology Group:
childhood rhabdomyosarcoma

Additional relevant MeSH terms:
Neoplasms, Muscle Tissue
Neoplasms, Connective and Soft Tissue
Neoplasms by Histologic Type
Sarcoma processed this record on April 21, 2017