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Laboratory Test Directory

ALK Targeted Sequencing

Components

Name Method Department Units
ALK Targeted Sequencing Polymerase chain reaction (PCR)
Sanger sequencing
Targeted sequence analysis
Molecular Genetics

Specimen Requirements

Whole blood

Container Type Container Size Specimen Volume
Preferred

Purple tube (EDTA)

4 mL 4 mL
Stability

Room temperature - 24 hour(s)
Refrigerated - 72 hour(s)

Specimen Preparation

  • Keep at room temperature or refrigerate
  • Do not freeze
  • Do not centrifuge

Bone marrow

Container Type Container Size Specimen Volume
Preferred

Purple tube (EDTA)

4 mL 4 mL
Stability

Room temperature - 24 hour(s)
Refrigerated - 72 hour(s)

Specimen Preparation

  • Keep at room temperature or refrigerate
  • Do not freeze
  • Do not centrifuge
  • Tumor sample must contain a minimum of 40% tumor

Tissue (Fresh)

Container Type Container Size Specimen Volume
Preferred

Tissue culture transport media

N/A
Alternate

Ringer's lactate solution in sterile container

N/A
Alternate

Sterile container with saline

N/A
Stability

Room temperature - 24 hour(s)
Refrigerated - 72 hour(s)

Specimen Preparation

  • Keep at room temperature or refrigerate
  • Do not add fixative
  • Do not freeze
  • Transport to laboratory as soon as possible
  • Tumor sample must contain a minimum of 40% tumor

Paraffin embedded tissue

Container Type Container Size Specimen Volume
Preferred

Paraffin block

N/A
Stability

Room temperature - 6 month(s)

Specimen Preparation

  • Tumor sample must contain a minimum of 40% tumor
  • Protect from heat
  • Keep at room temperature

Tissue (Snap-frozen)

Container Type Container Size Specimen Volume
Preferred

Tissue cassette

N/A
Alternate

Cryogenic tube

N/A
Stability

Frozen - 36 month(s)

Specimen Preparation

  • Freeze immediately after collection.
  • Immediately place on dry ice and transport frozen
  • Keep frozen
  • Transport to laboratory as soon as possible
  • Tumor sample must contain a minimum of 40% tumor

Tissue scrolls (FFPE)

Container Type Container Size Specimen Volume
Preferred

Sterile container

N/A
Stability

Room temperature - 6 month(s)

Specimen Preparation

  • Must accompany H&E slide from adjacent section
  • Keep at room temperature
  • Protect from heat

OCT-embedded tissue

Container Type Container Size Specimen Volume
Preferred

Tissue cassette

N/A
Alternate

Cryogenic tube

N/A
Stability

Frozen - 36 month(s)

Specimen Preparation

  • Freeze immediately after collection.
  • Keep frozen
  • Tumor sample must contain a minimum of 40% tumor
  • Immediately place on dry ice and transport frozen
  • Protect from heat

Reasons for Rejection

  • Inadequate tissue
  • Tissue degradation
  • Delayed or improper handling
  • Clotted EDTA
  • Insufficient tumor content in tumor sample

Comments

Please click on the Lab Form Link in the Forms Section to print and complete the Oncology Genetic Test Requisition Form. Submission of completed Genetic Test Requisition Form is required, and submission of informed consent form is recommended but not required. Please send all sample via overnight delivery. Saturday deliveries are accepted; please mark Saturday Delivery on shipment label.

This is a targeted sequencing analysis of exons 21-28 of the ALK gene. This test can be ordered either as a somatic testing done on neuroblastoma (NBL) sample or as a germline (constitutional) testing done on blood sample. Primarily, targeted ALK sequencing is offered in the context of pediatric NBL and done on the tumor sample. Children with NBL are assigned a specific risk group (low, intermediate, or high) based on a variety of clinical and biological factors.

Most children with NBL will be enrolled in Children's Oncology Group (COG) protocols. However, our laboratory offers the targeted ALK sequencing and ALK amplification detection by FISH on a clinical basis for those patients who are NOT enrolled in a COG protocol or need testing to be done off-study. Samples submitted under a COG protocol can be used in most cases (some cases may require approval from the study chair); please call the laboratory to confirm sample availability.

The detection rate of somatic ALK mutations in NBL is estimated to be 15-20%. For mutations reported as likely pathogenic or variant of unknown significance, a germline sample (e.g. blood or buccal swab sample) from the patient is required to determine whether the mutatoin is present only in the tumor (somatic) or is present in all cells (germline).

A minimum of 40% tumor must be present in the submitted sample (based on internal pathology review) for accurate reporting of somatic mutations. A testing on sample containing <50% tumor may be reported as unsatisfactory (no results reported).

Germline (constitutional) ALK sequencing of exons 21-28 can also be performed in suspected cases of hereditary NBL. While hereditary NBL is rare (~1-2% of NBL cases), approximately 50% of familial forms are due to germline ALK mutations in the kinase domain. Blood sample can be submitted for germline testing.

Forms

Lab Form

CPT Code

  • 81479