Ordering Recommendations

A completed test request form must be included with the specimen. Ensure that the following information is included on the test request form:
  • Clinical Indication
  • ICD-10 Diagnosis Code
  • If Surgical Pathology needs to perform lymphoma protocol, this must be notated on the requisition

Performed

Monday - Friday

Methodology

Polymerase Chain Reaction / Sanger Sequencing

Reported

Routine: 10 days

Synonyms

  • Tumor
  • Tissue
  • FFPE Tissue
  • Cancer
  • Hairy Cell Leukemia
  • Colorectal Carcinoma
  • Colorectal Cancer
  • Papillary Thyroid Cancer
  • Malignant Melanoma
  • Metastatic Melanoma
  • V600E
  • p.V600E
  • c.1799T>A
  • BRAF Gene
  • Anti-Epidermal Growth Factor Receptor Therapy
  • Epidermal Growth Factor Receptor
  • EFGR
  • Clinical Genomics

Performing Lab

Surgical Pathology: Specimen Preparation and Storage of FFPE ONLY
Clinical Genomics: Testing Laboratory

Turnaround Time

After specimen receipt in the Clinical Genomics Lab, results are generally available within 10 days.

Add-on Eligibility

Yes
*If DNA has been extracted previously for other Clinical Genomics tests, this is stored for 6 weeks and may qualify for add-on

Specimen Type

Tumor Tissue

Specimen Preparation

  1. Formalin Fix the specimen by submerging the Tissue in 10% Neutral Buffered Formalin
  2. Send the Formalin-Fixed Tissue to the Surgical Pathology Lab
  3. The Surgical Pathology Lab will paraffin-embed the tissue and prepare a Tissue Block
  4. The Tissue block will be sent to the Clinical Genomics Laboratory for testing

Specimen Volume

Fresh Tissue Size: 1 cm3 (Minimum: 0.5 cm3)
  • Specimen must contain a region with at least 20% tumor
Fixative Volume: 15 times the volume of the tissue

*This refers to specimen volume at collection prior to any processing

Collection Container

*Tissue specimens need to be sent to Surgical Pathology after collection so that the specimen can be processed prior to transport to the Clinical Genomics Laboratory. Do NOT send directly to Clinical Genomics.
 
  1. Formalin Container
  • EXCEPT for cases of suspected lymphoma
 
OR
 
  1. Non-Sterile Liquid-Proof Container
  • Medium to large specimens for routine processing that do not fit in prefilled formalin containers can be can be sent in specimen containers without formalin
  • Surgical Pathology staff will add formalin when the specimen is recieved in the lab

Unacceptable Conditions

  1. Specimens containing < 20% or no tumor tissue
  2. The provider will be contacted regarding receipt of non-validated specimen types
  3. Specimens that have been improperly collected, stored, or transported
  • Specimens that have been preserved in fixatives other than formalin
  • Specimens that have been preserved in heavy metal fixatives (B-4 or B-5)
  • Specimens that have been frozen
  1. Specimens with insufficient volume for testing
  2. Unlabeled or mislabeled specimens

Storage/Transport Temperature

*Specimens should be collected and transported to the Surgical Pathology Lab for FFPE Tissue Block preparation
 
Transport Instructions
Collection Location Specimen Type Transport Temperature Timeframe
ED/
Inpatient		 Fresh Specimen Room Temperature Specimen must be received by the lab within 1 hour of collection
Refrigerated (Ice Packs) Specimen must be received by the lab within 24 hours of collection
Formalin Fixed Specimen Room Temperature Specimen must be received by the lab within 24 hours of collection
Laboratory/
Outpatient/
Off-Site 		 Fresh Specimen Room Temperature Specimen must be received by the lab within 1 hour of collection
Refrigerated (Ice Packs) Specimen must be received by the lab within 24 hours of collection
Formalin Fixed Specimen Room Temperature Specimen must be received by the lab within 24 hours of collection
 
Storage:
  • Fixed Specimens: Room Temperature
  • Fresh Specimens: Refrigerated

Stability (from collection to initiation)

Stability:

Formalin-Fixed Specimens
  • Room Temperature: 1 week
  • Refrigerated: Not recommended
  • Frozen: Unacceptable

Sterile Container
  • Room Temperature: 3 hours
  • Refrigerated: 24 hours
  • Frozen: Unacceptable

FFPE Tissue Block
  • Room Temperature: Indefinitely
  • Refrigerated: Indefinitely
  • Frozen: Unacceptable

Extracted DNA:
  • Room Temperature: Unacceptable
  • Refrigerated: Unacceptable
  • Frozen: Indefinitely

Laboratory Storage:
  • Tumor Tissue:
    • All tissue specimens are stored at the Surgical Pathology Lab
      • Fixed Specimens: Room Temperature
      • Fresh Specimens: Refrigerated
      • FFPE Tissue Blocks: Room Temperature
  • Extracted DNA: Frozen

Laboratory Retention:
  • FFPE Tissue Blocks: Returned to Surgical Pathology Lab after testing is completed
  • Extracted DNA: 6 weeks

Collection Instructions

Collection Instructions:

Routine Small and Medium Sized Specimens
  1. Collect Tissue specimen and place into a Sterile Container with enough 10% formalin to cover the tissue by at least 2 - 3 inches.
  • Specimens must contain a region with at least 20% tumor
  • Breast Specimens: Immerse in fixative within 1 hour of biopsy or resection procedure for optimum tissue processing. Document the time that the tissue was placed into formalin.
  • Suspicion of Lymphoma: Send FRESH. Do NOT place specimen into formalin.
*Must state that lymphoma protocol is needed on requisition
 
  1. Specimens should be delivered to the Surgical Pathology Lab as soon as possible.  If delivery of a resection specimen to the Surgical Pathology department is delayed (e.g. specimens from remote sites), the tumor should be bisected prior to immersion in fixative.
  • It is important that the surgeon ensure that the identity of the resection margins is retained in the bisected specimen
  • Alternatively, the margins may be separately submitted
  1. Ensure that the cap is tightly secured on the Collection Container
  2. The time of removal of the tissue and the time of immersion of the tissue in fixative should be recorded and submitted to the laboratory

Routine Large Sized Specimens
  1. Collect tissue specimen and place in large leak-proof container
  2. Bring specimen to the Surgical Pathology laboratory immediately, or refrigerate

Specimen Container Labeling Instructions:
  1. Specimen Containers submitted to Surgical Pathology must be labeled with the following patient information:
  • First and Last Name
  • Date of Birth
  • Medical Record Number
  • CSN Number
  • Name of Specimen Site/Source
*If more than one site is sampled, a separate collection container must be submitted for each site
 
  1. Check all labeling of containers prior to leaving the collection site
 
  1. Place the following in a biohazard bag for transport to the Surgical Pathology Lab:
*If more than one site is sampled, all specimen material collected must be packaged and separated according to specimen site
 
  • Specimen Containers
  • Specimen Requisitions

Processing Instructions:
  1. Formalin Fix fresh tissues in 10% Neutral Buffered Formalin
  2. Paraffin-embed the fixed tissue and prepare FFPE Tissue Block
  • Specimens must contain a region with at least 20% tumor
 
  1. Protect specimen from excessive heat and transport one of the following to the Clinical Genomics Laboratory for testing:
  • Tissue Block
    • Tissue block will be returned to the Surgical Pathology Lab after testing
  • Two to four 20 micron sections
  • Two to four unstained tissue sections on slides
    • Place slides into a protective container
     
 
  1. Include the Surgical Pathology report with the specimen

Reference Interval

Not Detected

Interpretive Data

Refer to report for result specific interpretation details.

This assay is specific for mutations within codon 600 of the BRAF gene. Mutations occurring at other sites within the BRAF gene or within other genes will not be detected by this assay. A negative test does not exclude the presence of a variant as the limit of detection of this assay is approximately 20% variant BRAF sequence in a background of wild-type sequence.

BRAF has been shown to be mutated in a variety of cancers, including nearly 100% of cases of hairy cell leukemia, up to 70% of malignant melanomas, 40 to 50% of papillary thyroid cancers, 10% of colorectal cancers, and approximately 4% of gliomas overall.
 
BRAF Mutation Interpretation
Result Interpretation
Not Detected No BRAF codon 600 mutation was detected.

In patients with colorectal cancer, current evidence suggests that only tumors lacking activating mutations in the BRAF gene are responsive to anti-EGFR therapies. The absence of BRAF exon 15 mutations in this tumor specimen suggests that this patient may respond to such therapies.
Detected
(Codon 600)		 BRAF codon 600 mutation was detected.

In patients with colorectal cancer, the presence of a BRAF codon 600 mutation in this tumor specimen predicts a lack of response to such therapies.

This mutation has been shown to produce constitutive BRAF activation. FDA has approved encorafenib in combination with cetuximab for metastatic colorectal cancer with a BRAF V600E mutation.
Detected
(Exon 15, other than codon 600)		 BRAF exon 15 mutation was detected.

In patients with colorectal cancer, current evidence suggests that only tumors lacking activating mutations in the BRAF gene are responsive to anti-EGFR therapies. The significance of the BRAF exon 15 mutation in this tumor specimen is uncertain and may predict a lack of response to such therapies.
Ordering

Ordering Recommendations

A completed test request form must be included with the specimen. Ensure that the following information is included on the test request form:
  • Clinical Indication
  • ICD-10 Diagnosis Code
  • If Surgical Pathology needs to perform lymphoma protocol, this must be notated on the requisition

Performed

Monday - Friday

Methodology

Polymerase Chain Reaction / Sanger Sequencing

Reported

Routine: 10 days

Synonyms

  • Tumor
  • Tissue
  • FFPE Tissue
  • Cancer
  • Hairy Cell Leukemia
  • Colorectal Carcinoma
  • Colorectal Cancer
  • Papillary Thyroid Cancer
  • Malignant Melanoma
  • Metastatic Melanoma
  • V600E
  • p.V600E
  • c.1799T>A
  • BRAF Gene
  • Anti-Epidermal Growth Factor Receptor Therapy
  • Epidermal Growth Factor Receptor
  • EFGR
  • Clinical Genomics

Performing Lab

Surgical Pathology: Specimen Preparation and Storage of FFPE ONLY
Clinical Genomics: Testing Laboratory

Turnaround Time

After specimen receipt in the Clinical Genomics Lab, results are generally available within 10 days.

Add-on Eligibility

Yes
*If DNA has been extracted previously for other Clinical Genomics tests, this is stored for 6 weeks and may qualify for add-on
Collection

Specimen Type

Tumor Tissue

Specimen Preparation

  1. Formalin Fix the specimen by submerging the Tissue in 10% Neutral Buffered Formalin
  2. Send the Formalin-Fixed Tissue to the Surgical Pathology Lab
  3. The Surgical Pathology Lab will paraffin-embed the tissue and prepare a Tissue Block
  4. The Tissue block will be sent to the Clinical Genomics Laboratory for testing

Specimen Volume

Fresh Tissue Size: 1 cm3 (Minimum: 0.5 cm3)
  • Specimen must contain a region with at least 20% tumor
Fixative Volume: 15 times the volume of the tissue

*This refers to specimen volume at collection prior to any processing

Collection Container

*Tissue specimens need to be sent to Surgical Pathology after collection so that the specimen can be processed prior to transport to the Clinical Genomics Laboratory. Do NOT send directly to Clinical Genomics.
 
  1. Formalin Container
  • EXCEPT for cases of suspected lymphoma
 
OR
 
  1. Non-Sterile Liquid-Proof Container
  • Medium to large specimens for routine processing that do not fit in prefilled formalin containers can be can be sent in specimen containers without formalin
  • Surgical Pathology staff will add formalin when the specimen is recieved in the lab

Unacceptable Conditions

  1. Specimens containing < 20% or no tumor tissue
  2. The provider will be contacted regarding receipt of non-validated specimen types
  3. Specimens that have been improperly collected, stored, or transported
  • Specimens that have been preserved in fixatives other than formalin
  • Specimens that have been preserved in heavy metal fixatives (B-4 or B-5)
  • Specimens that have been frozen
  1. Specimens with insufficient volume for testing
  2. Unlabeled or mislabeled specimens

Storage/Transport Temperature

*Specimens should be collected and transported to the Surgical Pathology Lab for FFPE Tissue Block preparation
 
Transport Instructions
Collection Location Specimen Type Transport Temperature Timeframe
ED/
Inpatient		 Fresh Specimen Room Temperature Specimen must be received by the lab within 1 hour of collection
Refrigerated (Ice Packs) Specimen must be received by the lab within 24 hours of collection
Formalin Fixed Specimen Room Temperature Specimen must be received by the lab within 24 hours of collection
Laboratory/
Outpatient/
Off-Site 		 Fresh Specimen Room Temperature Specimen must be received by the lab within 1 hour of collection
Refrigerated (Ice Packs) Specimen must be received by the lab within 24 hours of collection
Formalin Fixed Specimen Room Temperature Specimen must be received by the lab within 24 hours of collection
 
Storage:
  • Fixed Specimens: Room Temperature
  • Fresh Specimens: Refrigerated

Stability (from collection to initiation)

Stability:

Formalin-Fixed Specimens
  • Room Temperature: 1 week
  • Refrigerated: Not recommended
  • Frozen: Unacceptable

Sterile Container
  • Room Temperature: 3 hours
  • Refrigerated: 24 hours
  • Frozen: Unacceptable

FFPE Tissue Block
  • Room Temperature: Indefinitely
  • Refrigerated: Indefinitely
  • Frozen: Unacceptable

Extracted DNA:
  • Room Temperature: Unacceptable
  • Refrigerated: Unacceptable
  • Frozen: Indefinitely

Laboratory Storage:
  • Tumor Tissue:
    • All tissue specimens are stored at the Surgical Pathology Lab
      • Fixed Specimens: Room Temperature
      • Fresh Specimens: Refrigerated
      • FFPE Tissue Blocks: Room Temperature
  • Extracted DNA: Frozen

Laboratory Retention:
  • FFPE Tissue Blocks: Returned to Surgical Pathology Lab after testing is completed
  • Extracted DNA: 6 weeks

Collection Instructions

Collection Instructions:

Routine Small and Medium Sized Specimens
  1. Collect Tissue specimen and place into a Sterile Container with enough 10% formalin to cover the tissue by at least 2 - 3 inches.
  • Specimens must contain a region with at least 20% tumor
  • Breast Specimens: Immerse in fixative within 1 hour of biopsy or resection procedure for optimum tissue processing. Document the time that the tissue was placed into formalin.
  • Suspicion of Lymphoma: Send FRESH. Do NOT place specimen into formalin.
*Must state that lymphoma protocol is needed on requisition
 
  1. Specimens should be delivered to the Surgical Pathology Lab as soon as possible.  If delivery of a resection specimen to the Surgical Pathology department is delayed (e.g. specimens from remote sites), the tumor should be bisected prior to immersion in fixative.
  • It is important that the surgeon ensure that the identity of the resection margins is retained in the bisected specimen
  • Alternatively, the margins may be separately submitted
  1. Ensure that the cap is tightly secured on the Collection Container
  2. The time of removal of the tissue and the time of immersion of the tissue in fixative should be recorded and submitted to the laboratory

Routine Large Sized Specimens
  1. Collect tissue specimen and place in large leak-proof container
  2. Bring specimen to the Surgical Pathology laboratory immediately, or refrigerate

Specimen Container Labeling Instructions:
  1. Specimen Containers submitted to Surgical Pathology must be labeled with the following patient information:
  • First and Last Name
  • Date of Birth
  • Medical Record Number
  • CSN Number
  • Name of Specimen Site/Source
*If more than one site is sampled, a separate collection container must be submitted for each site
 
  1. Check all labeling of containers prior to leaving the collection site
 
  1. Place the following in a biohazard bag for transport to the Surgical Pathology Lab:
*If more than one site is sampled, all specimen material collected must be packaged and separated according to specimen site
 
  • Specimen Containers
  • Specimen Requisitions

Processing Instructions:
  1. Formalin Fix fresh tissues in 10% Neutral Buffered Formalin
  2. Paraffin-embed the fixed tissue and prepare FFPE Tissue Block
  • Specimens must contain a region with at least 20% tumor
 
  1. Protect specimen from excessive heat and transport one of the following to the Clinical Genomics Laboratory for testing:
  • Tissue Block
    • Tissue block will be returned to the Surgical Pathology Lab after testing
  • Two to four 20 micron sections
  • Two to four unstained tissue sections on slides
    • Place slides into a protective container
     
 
  1. Include the Surgical Pathology report with the specimen
Result Interpretation

Reference Interval

Not Detected

Interpretive Data

Refer to report for result specific interpretation details.

This assay is specific for mutations within codon 600 of the BRAF gene. Mutations occurring at other sites within the BRAF gene or within other genes will not be detected by this assay. A negative test does not exclude the presence of a variant as the limit of detection of this assay is approximately 20% variant BRAF sequence in a background of wild-type sequence.

BRAF has been shown to be mutated in a variety of cancers, including nearly 100% of cases of hairy cell leukemia, up to 70% of malignant melanomas, 40 to 50% of papillary thyroid cancers, 10% of colorectal cancers, and approximately 4% of gliomas overall.
 
BRAF Mutation Interpretation
Result Interpretation
Not Detected No BRAF codon 600 mutation was detected.

In patients with colorectal cancer, current evidence suggests that only tumors lacking activating mutations in the BRAF gene are responsive to anti-EGFR therapies. The absence of BRAF exon 15 mutations in this tumor specimen suggests that this patient may respond to such therapies.
Detected
(Codon 600)		 BRAF codon 600 mutation was detected.

In patients with colorectal cancer, the presence of a BRAF codon 600 mutation in this tumor specimen predicts a lack of response to such therapies.

This mutation has been shown to produce constitutive BRAF activation. FDA has approved encorafenib in combination with cetuximab for metastatic colorectal cancer with a BRAF V600E mutation.
Detected
(Exon 15, other than codon 600)		 BRAF exon 15 mutation was detected.

In patients with colorectal cancer, current evidence suggests that only tumors lacking activating mutations in the BRAF gene are responsive to anti-EGFR therapies. The significance of the BRAF exon 15 mutation in this tumor specimen is uncertain and may predict a lack of response to such therapies.

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