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
• 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 (Cat 93774-05)
• 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 (Cat 93774-05)
• 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: 200X raw sequencing coverage, 45 million clusters, 85-90% of targeted bases with > 30 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 (Cat 93774-05)
• 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 (In Development)

• Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
• Input Material: Genomic DNA
• Recommended Input:
  • Intact DNA: To-be-determined
  • Fragmented DNA: To-be-determined
• Instrument: Hamilton NGS STAR Automated Liquid Handlers (Cat 93774-05)
• Kits:
  • NEBNext UltraShear (Cat M7634S)
  • NEBNext Enzymatic Methyl-seq Kit (Cat E7120L)
• Recommended Sequencing Depth: To be determined

Targeted Methylation Sequencing (In Development)

• Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE, Whole Blood, Buffy Coat, Plasma, Saliva, Buccal Swabs
• Input Material: Genomic DNA
• Recommended Input:
  • Intact DNA: To-be-determined
  • Fragmented DNA: To-be-determined
• Instrument: Hamilton NGS STAR Automated Liquid Handlers (Cat 93774-05)
• 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