MUSC Hollings Cancer Center

Genomics Shared Resource

Scientific Director
Stephen P. Ethier, PhD
Professor, Pathology & Laboratory Medicine

Contact Information
Operations Director

Name: Robert C. Wilson, PhD
Research Associate Professor, Pathology & Laboratory Medicine
Phone: 843-876-2217

Name: Jennifer Schulte
Phone: 843-876-2243
Location: 433 Bioengineering Building


The Hollings Cancer Center Genomics­­ Core Facility at MUSC offers state of the art next generation sequencing (NGS) including DNA-Seq, RNA-Seq, ChIP-Seq, Methyl-Seq, Targeted sequencing utilizing Illumina HiScanSQ and Ion Torrent instrumentation. See below for other types of applications. In addition to NGS, Bead-Array analyses for GWAS, RNA expression and other analyses are available.

Illumina HiScanSQ

ApplicationsSequencing ApplicationsBead Array Applications
Whole-Genome AnalysisWhole-Genome DiscoveryWhole-Genome Genotyping, FFPE Sample Analysis
Copy Number Variation (CNV)CNV AnalysisCNV Discovery
Targeted Genome AnalysisExome Sequencing, Targeted Resequencing (Custom Panels)Custom and Focused Genotyping
Gene Regulation and Epigenetic AnalysisChIP-Seq, Small RNA Analysis, Methylation (Methyl-Seq) Discover and AnalysisWhole-Genome DNA Methylation Profiling
Gene ExpressionTranscriptome (RNA-Seq) Discovery, ProfilingWhole-Genome Expression Profiling, FFPE Sample
CytogeneticsDigital KaryotypingCytogenetic Analysis







ApplicationsDNA SequencingRNA Sequencing
Agricultural ResearchSmall Genome SequencingGene Expression by Sequencing
Cancer ResearchGene Sequencing (Cancer Panels)Small-RNA Sequencing
Forensic ScienceExome SequencingWhole-Transcriptome Sequencing for Low Complexity Genomes
Stem Cell ResearchMitochondrial Sequencing
EpigenomicsHLA Sequencing
MetagenomicsSNP Confirmation
Ancient DNA GenomicsLibrary Assessment
16S Metagenomic Sequencing
ChIP Sequencing
Methylation Analysis
De novo Sequencing









  • Illumina HiSeq 2500 sequencer, Illimina HiScanSQ sequencer and micro-array scanner, Illumina cBot Cluster generation system
  • Ion Torrent PGM sequencer
  • Ion One Touch System
  • Agilent ® 2200 TapeStation
  • Sage Science Pippin Prep
  • Diagenode Bioruptor UCD-600 TS 
  • QuBit Fluorometer
  • IBM compute analysis, storage cluster

DATA Analysis

  • Using CASAVA the sequencing data will be generated in either the SAM format or FASTq format for the downstream analysis.
  • Bead array image files will be analyzed by Illumina Genome Studio.  Files will be available for 3rd party software analysis.

Publication Acknowledgement

If you publish a manuscript including research supported by the Genomics Core Facility, the HCC recommends the following text to be placed in the acknowledgement section: "Supported in part by the Genomics Shared Resource, Hollings Cancer Center, Medical University of South Carolina."


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