Trial Information

Integrative Epigenomic Approach to Gene Discovery in Rhabdomyosarcoma (RMS)

OBJECTIVES:

- 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.