Personalized Genomic Medicine

Sohn Foundation Testing

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

Sohn-PIPseq Consent Brochure
Sohn-PIPseq Consent Brochure

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
CPT Codes: 81201, 81216, 81292, 81295, 81298, 81321, 81275, 81235, 81210, 81245, 81310, 81403, 81404, 81405, 81406, 81407, 81408
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).
  • 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: 1. Sohn Oncology Requisition Form
    2. Sohn Conference Eligibility Checklist
    3. Cancer Whole Exome Informed Consent
    4. Insurance Pre-Authorization Form
    5. CWES Letter of Medical Necessity Template
     
    Contact the Pathology Webmaster at PathWebMaster@columbia.edu