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University of Colorado Cancer Center

University of Colorado Cancer Center, A National Cancer Institute-designated Comprehensive Cancer Center

Preanalytical Evaluation & Molecular Testing Services

The Pre-analytical Evaluation and Molecular Testing (PEMT) Service ensures the use of adequate and accurately classified tumor and ancillary specimens for molecular testing. Sample processing including macro- and micro-dissection followed by nucleic acid extraction is provided. Molecular tests performed include several single-gene assays (Sanger sequencing, allele-specific qPCR, sizing), micro-satellite instability (MSI) testing, and targeted next-generation sequencing (NGS) assays. All services are performed in a CLIA-certified environment and all molecular assays are accompanied with full data analysis (including bioinformatic analysis for NGS) and a complete report.


  • Retrieval of appropriate materials for testing (fluids, blocks or slides) from bio-specimen archives
  • Review of histological slides to confirm diagnosis and ensure adequacy of specimen  
  • Selection of appropriate technique for tumor cell enrichment (macro-dissection, micro-dissection, coring)
  • Nucleic acid extraction  
  • Sanger sequencing, allele-specific qPCR, and sizing assays for select genes 
  • Next-generation sequencing (NGS) library preparation (cancer-gene specific panels), sequencing on Illumina MiSeq instrument, and full bioinformatic analysis
  • Micro-satellite instability (MSI) testing
  • Molecular assay data interpretation  
  • Tissue grossing, processing and embedding 
  • Cutting paraffin  
  • H and E Staining



  • Automated extraction equipment (Qiacube) 
  • Nanodrop and Qubit nucleic acid quantitation systems  
  • Agilent Bioanalyzer and TapeStation nucleic acid analysis systems  
  • Pipetting robot 
  • Thermocyclers  
  • Roche Lightcycler for quantitative PCR and RT-PCR analysis  
  • Qiagen Rotor-Gene Q instrument for qPCR  
  • Olympic microscopes, photomicroscopic equipment and Leica microdissection scopes 
  • ABI 3500xl DNA analyzer 
  • Three Illumina MiSeq NGS sequencers 
  • Illumina NextSeq (for upcoming expanded NGS assays)



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