Personalized Genomic Medicine

Oncology Testing

Oncology Testing in the Laboratory for Personalized Genomic Medicine is available.  Click on the links below for a description of tests currently offered.  For more information regarding oncology testing, email pgmoncology@cumc.columbia.edu.

Next Generation Sequencing:
Cancer Whole Exome Sequencing (with Transcriptome)
TruSeq Targeted Cancer Panel
TruSeq Targeted Cancer Subpanels
Columbia Combined Cancer Panel (CCCP)

Solid Tumor Testing:
BRAF V600E Mutation Test by Real-Time PCR
EGFR Exon 18-21 Mutations
EGFR VIII Mutation Test by Real-Time RY-PCR
KRAS Mutation Test by Sanger Sequencing
Methylguanine-DNA Methyltransferase (MGMT) Assay
Microsatellite Instability Determination by PCR

Hematological Testing:
BCR-ABL1 Quantitative Test by PCR
Immunoglobulin Heavy Chain Gene Rearrangement by PCR
JAK2 V617F Mutation
T-Cell Receptor Gene Rearrangement by PCR

Next Generation Sequencing

Reference Guide – Ordering Cancer Panels for CUMC Oncologists

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
Specimen: Frozen tissue. A normal control sample (e.q. blood or buccal swab) is required for this testing.
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
Notes: Insurance preauthorization can be obtained by emailing the preauthorization form below to PGMBilling@cumc.columbia.edu. Please submit requisition and consent form to the laboratory.
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)
3. Cancer Whole Exome Informed Consent
4. Insurance Pre-Authorization Form
5. Medicare Advance Beneficiary Notice Form
6. CWES Letter of Medical Necessity Template

TruSeq Targeted Cancer Panel

Purpose: Detect variants in 48 commonly mutated genes in cancer tissue.
CPT Codes: 81445, 88381
Methodology: Next Generation Sequencing of DNA
Turnaround Time: 30 days
Specimen: Paraffin embedded or frozen tissue containing the cancer in question  
Genes Tested: TruSeq Gene list
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Insurance Pre-Authorization Form
4. Medicare Advance Beneficiary Notice Form
5. TruSeq Cancer Panel Letter of Medical Necessity Template

TruSeq Targeted Cancer Subpanel

Purpose: Detect variants in 48 commonly mutated genes in cancer tissue.
Available Subpanels:
Lung Panel
Colorectal Panel
GIST Panel
Melanoma Panel
Cholangiocarcinoma Panel
Thyroidl Panel
Subpanel Genes CPT Codes: Click Here for list of Panel CPT Codes
Methodology: Next Generation Sequencing of DNA
Turnaround Time: 30 days
Specimen: Paraffin embedded or frozen tissue containing the cancer in question  
Genes Tested: TruSeq Gene list
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Insurance Pre-Authorization Form
4. Medicare Advance Beneficiary Notice Form
5. TruSeq Cancer Panel Letter of Medical Necessity Template

Columbia Combined Cancer Panel (CCCP)

Purpose: This test can be used to screen for actionable/novel mutations in a select panel of tumor-specific genes (see requisition for details).
CPT Codes: 81455, 88381
Methodology: Next Generation Sequencing of DNA
Turnaround Time: 30 days
Sample Tested: Paraffin Embedded Tissue  
Genes Tested: Columbia Combined Cancer Panel (CCCP) Gene List
Additional Gene Information: ROI Cancer Gene Exons Not Covered
Notes: Insurance preauthorization can be obtained by emailing the preauthorization form below to PGMBilling@cumc.columbia.edu. Please submit requisition form to the PGM laboratory. For Medicare patients, please complete and submit to the lab a Medicare advanced beneficiary notice.
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Insurance Pre-Authorization Form
4. Medicare Advance Beneficiary Notice Form
5. CCCP Letter of Medical Necessity Template


Solid Tumor Testing

BRAF V600E Mutation Test by Real-time PCR

Purpose: Detect activating mutations of BRAF in various tumors. Select melanoma patients for vemurafenib therapy; aid in the diagnosis of Hairy Cell Leukemia, Langerhans Cell Histiocytosis, and Erdheim Chester Disease; exclude germline MLH1 mutations in colon cancers with MLH1 loss.
CPT Codes: 81210 (88381 if needed)
Methodology: Real-time PCR on DNA obtained from tumor specimens (microdissected to enrich for tumor, if less than 20% tumor nuclei) 
Turnaround Time: 15 days (5 working days for metastatic melanoma; “r/o Hairy Cell Leukemia” and “r/o Langerhans Cell Histiocytosis").
Sample tested: Paraffin embedded OR frozen tissue containing the carcinoma in question (see solid tumor requisition for detailed specimen requirements). 
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

EGFR Exon 18-21 Mutations

Purpose: Detection of activating mutations of EGFR in non-small cell carcinomas of the lung (NSCLC).
CPT Codes: 81235; 88381
Methodology: PCR-Sanger sequencing of DNA obtained from tumor specimens (microdissected to enrich for tumor, if less than 40% tumor nuclei). 
Turnaround Time: 12 days
Specimen: Paraffin embedded OR frozen tissue containing NSCLC (see solid tumor requisition for detailed specimen requirements).
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

EGFR VIII Mutation Test by Real-time RT-PCR

Purpose: Detection of EGFRviii expression in gliomas
CPT Codes: 81479
Methodology: Real-time PCR following reverse transcription of RNA extracted from fresh samples
Turnaround Time: 12 days
Sample tested: FFPE tissue containing more than 50% tumor cells
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

KRAS Mutation Test by Sanger Sequencing

Purpose: Detection of activating mutations of KRAS in various neoplasms. KRAS mutant colon cancers are resistant to Cetuximab; KRAS and EGFR mutations are mutually exclusive in lung carcinomas.
CPT Codes: 81275;  88381
Methodology: PCR-Sanger sequencing of DNA obtained from tumor specimens (microdissected to enrich for tumor, less than 40% tumor nuclei). 
Turnaround Time: 12 days
Samples tested: Paraffin embedded or frozen tissue containing the carcinoma in question (see solid tumor requisition for detailed specimen requirements). 
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

Methylguanine-DNA Methyltransferase (MGMT) Assay

Purpose: Detects MGMT promoter methylation by real-time PCR to aid in therapeutic decision in individuals with glioblastoma.
CPT Codes: 81287
Methodology: PCR on DNA extracted from tumor and normal (with microdissection if necessary) followed by Capillary Electrophoresis 
Turnaround Time: 14 days
Samples tested: Paraffin embedded tissue 
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

Microsatellite Instability Determination by PCR

Purpose: Screen for mismatch repair deficient carcinomas.
CPT Codes: 81301 x 1 (88381 x 1 if necessary)
Methodology: PCR on DNA extracted from tumor and normal (with microdissection if necessary) followed by Capillary Electrophoresis
Turnaround Time: 12 days
Specimen: Paraffin embedded tissue (see requisition for detailed specimen requirements).
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form


Hematological Testing

BCR-ABL1 Quantitative Test by PCR

Purpose: Detection of BCR-ABL1 p190 and p210 fusion transcripts in patients with CML or ALL.
CPT Codes: 81207
Methodology: Real-time PCR following reverse transcription of RNA extracted from fresh samples.
Turnaround Time: 14 days
Sample Tested: Whole blood or bone marrow aspirate. (Blood recommended; RNA can be used as baseline for quantitative test for follow up).  
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

Immunoglobulin Heavy Chain Gene Rearrangement by PCR

Purpose: Screen for B-cell clonality
CPT Codes: 81261; G0452
Methodology: PCR with Capillary Electrophoresis
Turnaround Time: 15 days
Specimen: Whole blood or bone marrow aspirate in EDTA or Paraffin embedded tissue (see requisition for detailed specimen requirements).
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

JAK2 V617F Mutation

Purpose: Detection of JAK2 V617F mutation characteristic of myeloproliferative neoplasms
CPT Codes: 81270; G0452
Methodology: Real-Time Polymerase Chain Reaction with allele-specific probes
Turnaround Time: 15 days
Samples tested: Bone marrow; peripheral blood. Mononuclear cell suspensions are not recommended. Contact lab for other sample types.
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

T-Cell Receptor Gene Rearrangement by PCR

Purpose: Screen for T-cell clonality
CPT Codes: 81340; G0452
Methodology: Polymerase Chain Reaction with Capillary Electrophoresis
Turnaround Time: 15 days
Specimen: Whole blood or bone marrow aspirate in EDTA or Paraffin embedded tissue (see requisition for detailed specimen requirements).
Forms: 1. PGM Oncology Requisition Form (External Client)
2. PGM Oncology Requisition Form (Internal Pathology)

3. Medicare Advance Beneficiary Notice Form

* Test pending NYDOH approval.

 
Contact the Pathology Webmaster at PathWebMaster@columbia.edu