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UNC Lineberger Comprehensive Cancer Center

Genomic Profiling

The Translational Genomics Lab (TGL) performs bulk DNA sequencing using the following technologies and assays.

If submitting DNA, it is our recommendation for us to perform our own quality control of the samples before performing downstream assays to ensure the samples meet the QC requirements for the assays being performed.

Our Laboratory Management System (LIMS) and freezers are designed to accept individually labeled tubes. If possible, please avoid submitting samples in tube strips or plates.

 

Whole Genome Sequencing

  • Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
    Image provided by Twist Bioscience
  • Input Material: Genomic DNA, cell free DNA (cfDNA)
  • Recommended Input:
    • Intact DNA: 100-500 ng in 40 µL of Tris buffer
    • Fragmented DNA: 500 ng in 40 µL of Tris buffer
    • cfDNA: 5-30 ng in 40 µL of Tris buffer
  • Instrument: Hamilton NGS STAR Automated Liquid Handlers
  • Kit: Twist Bioscience Library Preparation EF 2.0 with Enzymatic Fragmentation and Twist UMI Adapter System (Cat 104207)
  • Recommended Sequencing Depth: 30X raw sequencing coverage, 500 million clusters

 

Targeted Sequencing: Whole Exome Panel

  • Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
  • Input Material: Genomic DNA, cell free DNA (cfDNA)
  • Recommended Input:
    • Intact DNA: 100-500 ng in 40 µL of Tris buffer
    • Fragmented DNA: 500 ng in 40 µL of Tris buffer
    • cfDNA: 5-30 ng in 40 µL of Tris buffer
  • Instrument: Hamilton NGS STAR Automated Liquid Handlers
  • Kits:
    • Twist Bioscience Library Preparation EF 2.0 with Enzymatic Fragmentation and Twist UMI Adapter System (Cat 104207)
    • Twist Bioscience Target Enrichment Standard Hybridization v2 (Cat 105561)
  • Panel: Twist Bioscience Exome 2.0 (Cat 104134)
  • Recommended Sequencing Depth: 450X raw sequencing coverage, 110 million clusters, 85-90% of targeted bases with > 100 unique reads

 

Targeted Sequencing: UNCseqTM Panel

  • Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
  • Input Material: Genomic DNA, cell free DNA (cfDNA)
  • Recommended Input:
    • Intact DNA: 100-500 ng in 40 µL of Tris buffer
    • Fragmented DNA: 500 ng in 40 µL of Tris buffer
    • cfDNA: 5-30 ng in 40 µL of Tris buffer
  • Instrument: Hamilton NGS STAR Automated Liquid Handlers
  • Kits:
    • Twist Bioscience Library Preparation EF 2.0 with Enzymatic Fragmentation and Twist UMI Adapter System (Cat 104207)
    • Twist Bioscience Target Enrichment Standard Hybridization v2 (Cat 105561)
  • Panel: UNCseq
  • Recommended Sequencing Depth: 2000X raw sequencing coverage, 65 million clusters, 85-90% of targeted bases with > 250 unique reads

 

Whole Genome Methylation Sequencing

  • Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
  • Input Material: Genomic DNA, cell free DNA (cfDNA)
    NEB EM-seq™ conversion method. Image provided by New England Biolabs.
  • Recommended Input:
    • Intact DNA: 50-200 ng in 40 µL of Tris buffer
    • Fragmented DNA: 200 ng in 40 µL of Tris buffer
    • cfDNA: >5-10 ng in 40 µL of Tris buffer
  • Instrument: Hamilton NGS STAR Automated Liquid Handlers
  • Kits:
    • NEBNext UltraShear (Cat M7634S)
    • NEBNext Enzymatic Methyl-seq Kit (Cat E7120L)
  • Recommended Sequencing Depth: 30X raw sequencing coverage, 500 million clusters

 

Targeted Methylation Sequencing

  • Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
  • Input Material: Genomic DNA, cell free DNA (cfDNA)
  • Recommended Input:
    • Intact DNA: 50-200 ng in 40 µL of Tris buffer
    • Fragmented DNA: 200 ng in 40 µL of Tris buffer
    • cfDNA: >5-10 ng in 40 µL of Tris buffer
  • Instrument: Hamilton NGS STAR Automated Liquid Handlers
  • Kits:
    • NEBNext UltraShear (Cat M7634S)
    • NEBNext Enzymatic Methyl-seq Kit (Cat E7120L)
    • Twist Bioscience Target Enrichment Standard Hybridization v2 (Cat 105561)
  • Panel: Twist Bioscience Human Methylome (Cat 105520)
  • Recommended Sequencing Depth: To be determined