Sohn Precision Medicine Program at Columbia University

Sohn Foundation Testing in the Laboratory for Personalized Genomic Medicine is available as below. For more information regarding this testing, email sohnpgmorders@columbia.edu.

Cancer Whole Exome Sequencing with Transcriptome

Purpose

Detects actionable constitutional changes predisposing to cancer; detects cancer specific missense, indel and copy number changes as well as chimeric RNAs and RNAs with altered expression levels using combination of exome and transcriptome sequencing. 

Sohn-PIPseq Initiative Brochure

CPT Codes

81415, 81416, 81479

Methodology

Next Generation Sequencing of mRNA and DNA

Turnaround Time

60 Days – Turnaround times < 60 days are available for rush cases based on clinical context and prior discussion with the laboratory.

Specimen

• DNA and RNA obtained from frozen tumor tissue (please document tumor content on requisition; at least 40% tumor required) and extracted in a CLIA laboratory.
• 30 blanks from FFPE with at least 3 H&E slides, containing > 40% tumor.
• Fresh or frozen bone marrow containing at least 40% tumor sent on ice packs via overnight delivery.
• Please also include a normal control sample (e.g., blood or buccal swab).

Note: The lab cannot accept FFPE blocks or frozen tissue blocks.

Associated Documents

Cancer Genes (Cosmic):

• COSMIC genes reported on

Coverage Disclaimer:

• WES regions not guaranteed greater than 10 fold
• COSMIC gene exons not guaranteed greater than 30 fold
• Recurrent COSMIC mutations not guaranteed to be covered greater than 30 fold

Secondary Findings

• ACMG Secondary Findings List

Forms

• Sohn Oncology Requisition Form
• Sohn Conference Eligibility Checklist
• Cancer Whole Exome Informed Consent
• Insurance Pre-Authorization Form
• CWES Letter of Medical Necessity Template