Special Collection

At least 10% disease content must be present in the submitted Fresh, Snap-frozen, OCT, or Bone Marrow samples. At least 25% disease content must be present in the submitted FFPE tissue block or FFPE tissue scrolls (based on internal pathology review). Sample acquisition PRIOR to receiving treatment is strongly preferred. This test is NOT intended for residual disease detection.

Outpatient Submit with Specimen

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone Marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrollsAlternate
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM labAlternate

Outpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

Unacceptable Conditions

Delayed or improper handling, Wrong type of specimen, Wrong temperature, Tissue degradation, Inadequate tissue, Insufficient tumor content in tumor sample

Stability

Paraffin embedded tissue: Room temperature 6 months

Tissue (Snap-frozen): Frozen 3 days

OCT-embedded tissue: Frozen 3 days

Tissue (Fresh): Refrigerated 48 hours

Bone Marrow: Room Temperature 24 hours
                     Refrigerated 48 hours

Tissue scrolls (FFPE): Room temperature 6 months

Remarks

If you are an external healthcare provider with no access to Nationwide Children’s Epic system, submission of a completed Oncology Genetic Test Requisition Form is required. If you are an internal ordering provider with access to Nationwide Children’s Epic system, no requisition form is required; please place the lab order electronically in Epic.

Submission of 10-15 unstained slides at 5-10 microns is recommended. If submitting tissue scroll specimen, please use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory.

SPECIMEN INFORMATION:

Fresh and snap-frozen tissue specimens must contain minimum of 10% disease content. Formalin-fixed paraffin embedded (FFPE) tissue block and FFPE tissue scroll specimens must contain minimum of 25% disease content. Please submit the pathology report from the submitted sample. Internal pathology review will also be performed on non-frozen samples to determine the tumor content in specimen.

If sending FFPE tissue scrolls, an H&E slide from a consecutive cut is also required. Please see scroll calculator application above.

All specimens must be labeled with a patient name and one other identifier (DOB, MRN, Specimen ID#, etc). Sample acquisition prior to receiving therapy is strongly preferred.

SPECIMEN SHIPPING:

Specimens must be shipped as soon as possible after collection due to time-sensitive specimen stability. Ship all samples via overnight courier. Whenever possible, send specimen immediately after collection. For fresh tumor tissue, ship the sample refrigerated using cold packs. If specimen cannot be sent on the collection date, then snap-freeze the tumor tissue immediately after collection and ship the sample frozen (bury the entire tissue in dry ice). Lab must receive specimen within 48 hours. FFPE tissue and FFPE tissue scrolls should be sent at room temperature via overnight shipping. Saturday deliveries are accepted; please check Saturday Delivery on shipment labels.

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Lab Area

Institute for Genomic Medicine

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81456

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

Special Collection

At least 10% disease content must be present in the submitted Fresh, Snap-frozen, OCT, or Bone Marrow samples. At least 25% disease content must be present in the submitted FFPE tissue block or FFPE tissue scrolls (based on internal pathology review). Sample acquisition PRIOR to receiving treatment is strongly preferred. This test is NOT intended for residual disease detection.

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone Marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrollsAlternate
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerMinimum Volume
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Paraffin embedded tissueParaffin block1 block
Tissue (Snap-frozen)Tissue cassette50 mg
Tissue (Snap-frozen)Cryogenic tube50 mg
OCT-embedded tissueTissue cassette50 mg
OCT-embedded tissueCryogenic tube50 mg
Tissue (Fresh)Tissue culture transport media50 mg
Tissue (Fresh)Sterile container with saline50 mg
Bone Marrow4 mL Purple tube (EDTA)4 mL
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrolls
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM lab

 

Inpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

Unacceptable Conditions

Delayed or improper handling, Wrong type of specimen, Wrong temperature, Tissue degradation, Inadequate tissue, Insufficient tumor content in tumor sample

Stability

Paraffin embedded tissue: Room temperature 6 months

Tissue (Snap-frozen): Frozen 3 days

OCT-embedded tissue: Frozen 3 days

Tissue (Fresh): Refrigerated 48 hours

Bone Marrow: Room Temperature 24 hours
                     Refrigerated 48 hours

Tissue scrolls (FFPE): Room temperature 6 months

Remarks

If you are an external healthcare provider with no access to Nationwide Children’s Epic system, submission of a completed Oncology Genetic Test Requisition Form is required. If you are an internal ordering provider with access to Nationwide Children’s Epic system, no requisition form is required; please place the lab order electronically in Epic.

Submission of 10-15 unstained slides at 5-10 microns is recommended. If submitting tissue scroll specimen, please use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory.

SPECIMEN INFORMATION:

Fresh and snap-frozen tissue specimens must contain minimum of 10% disease content. Formalin-fixed paraffin embedded (FFPE) tissue block and FFPE tissue scroll specimens must contain minimum of 25% disease content. Please submit the pathology report from the submitted sample. Internal pathology review will also be performed on non-frozen samples to determine the tumor content in specimen.

If sending FFPE tissue scrolls, an H&E slide from a consecutive cut is also required. Please see scroll calculator application above.

All specimens must be labeled with a patient name and one other identifier (DOB, MRN, Specimen ID#, etc). Sample acquisition prior to receiving therapy is strongly preferred.

SPECIMEN SHIPPING:

Specimens must be shipped as soon as possible after collection due to time-sensitive specimen stability. Ship all samples via overnight courier. Whenever possible, send specimen immediately after collection. For fresh tumor tissue, ship the sample refrigerated using cold packs. If specimen cannot be sent on the collection date, then snap-freeze the tumor tissue immediately after collection and ship the sample frozen (bury the entire tissue in dry ice). Lab must receive specimen within 48 hours. FFPE tissue and FFPE tissue scrolls should be sent at room temperature via overnight shipping. Saturday deliveries are accepted; please check Saturday Delivery on shipment labels.

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

CPT Codes

81456

Lab Area

Institute for Genomic Medicine

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

Estimated Patient Price

$2,500 - $5,000

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

CPT Codes

81456

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Methodology

Next Generation Sequencing (NGS)

Special Collection

At least 10% disease content must be present in the submitted Fresh, Snap-frozen, OCT, or Bone Marrow samples. At least 25% disease content must be present in the submitted FFPE tissue block or FFPE tissue scrolls (based on internal pathology review). Sample acquisition PRIOR to receiving treatment is strongly preferred. This test is NOT intended for residual disease detection.

Outpatient Submit with Specimen

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone Marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrollsAlternate
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerMinimum Volume
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Paraffin embedded tissueParaffin block1 block
Tissue (Snap-frozen)Tissue cassette50 mg
Tissue (Snap-frozen)Cryogenic tube50 mg
OCT-embedded tissueTissue cassette50 mg
OCT-embedded tissueCryogenic tube50 mg
Tissue (Fresh)Tissue culture transport media50 mg
Tissue (Fresh)Sterile container with saline50 mg
Bone Marrow4 mL Purple tube (EDTA)4 mL
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrolls
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM lab

 

Inpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

Outpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

InLab Processing

Send to Institute for Genomic Medicine with all submitted paperwork. CPA needs to order GENSP in Sunquest for Non-EPIC lab order.

Stability

Paraffin embedded tissue: Room temperature 6 months

Tissue (Snap-frozen): Frozen 3 days

OCT-embedded tissue: Frozen 3 days

Tissue (Fresh): Refrigerated 48 hours

Bone Marrow: Room Temperature 24 hours
                     Refrigerated 48 hours

Tissue scrolls (FFPE): Room temperature 6 months

Unacceptable Conditions

Delayed or improper handling, Wrong type of specimen, Wrong temperature, Tissue degradation, Inadequate tissue, Insufficient tumor content in tumor sample

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Remarks

If you are an external healthcare provider with no access to Nationwide Children’s Epic system, submission of a completed Oncology Genetic Test Requisition Form is required. If you are an internal ordering provider with access to Nationwide Children’s Epic system, no requisition form is required; please place the lab order electronically in Epic.

Submission of 10-15 unstained slides at 5-10 microns is recommended. If submitting tissue scroll specimen, please use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory.

SPECIMEN INFORMATION:

Fresh and snap-frozen tissue specimens must contain minimum of 10% disease content. Formalin-fixed paraffin embedded (FFPE) tissue block and FFPE tissue scroll specimens must contain minimum of 25% disease content. Please submit the pathology report from the submitted sample. Internal pathology review will also be performed on non-frozen samples to determine the tumor content in specimen.

If sending FFPE tissue scrolls, an H&E slide from a consecutive cut is also required. Please see scroll calculator application above.

All specimens must be labeled with a patient name and one other identifier (DOB, MRN, Specimen ID#, etc). Sample acquisition prior to receiving therapy is strongly preferred.

SPECIMEN SHIPPING:

Specimens must be shipped as soon as possible after collection due to time-sensitive specimen stability. Ship all samples via overnight courier. Whenever possible, send specimen immediately after collection. For fresh tumor tissue, ship the sample refrigerated using cold packs. If specimen cannot be sent on the collection date, then snap-freeze the tumor tissue immediately after collection and ship the sample frozen (bury the entire tissue in dry ice). Lab must receive specimen within 48 hours. FFPE tissue and FFPE tissue scrolls should be sent at room temperature via overnight shipping. Saturday deliveries are accepted; please check Saturday Delivery on shipment labels.

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81456

Estimated Patient Price

$2,500 - $5,000

DC Code

5321

Downtime Availability

4-Not available
Outpatient Requirements

Special Collection

At least 10% disease content must be present in the submitted Fresh, Snap-frozen, OCT, or Bone Marrow samples. At least 25% disease content must be present in the submitted FFPE tissue block or FFPE tissue scrolls (based on internal pathology review). Sample acquisition PRIOR to receiving treatment is strongly preferred. This test is NOT intended for residual disease detection.

Outpatient Submit with Specimen

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone Marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrollsAlternate
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM labAlternate

Outpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

Unacceptable Conditions

Delayed or improper handling, Wrong type of specimen, Wrong temperature, Tissue degradation, Inadequate tissue, Insufficient tumor content in tumor sample

Stability

Paraffin embedded tissue: Room temperature 6 months

Tissue (Snap-frozen): Frozen 3 days

OCT-embedded tissue: Frozen 3 days

Tissue (Fresh): Refrigerated 48 hours

Bone Marrow: Room Temperature 24 hours
                     Refrigerated 48 hours

Tissue scrolls (FFPE): Room temperature 6 months

Remarks

If you are an external healthcare provider with no access to Nationwide Children’s Epic system, submission of a completed Oncology Genetic Test Requisition Form is required. If you are an internal ordering provider with access to Nationwide Children’s Epic system, no requisition form is required; please place the lab order electronically in Epic.

Submission of 10-15 unstained slides at 5-10 microns is recommended. If submitting tissue scroll specimen, please use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory.

SPECIMEN INFORMATION:

Fresh and snap-frozen tissue specimens must contain minimum of 10% disease content. Formalin-fixed paraffin embedded (FFPE) tissue block and FFPE tissue scroll specimens must contain minimum of 25% disease content. Please submit the pathology report from the submitted sample. Internal pathology review will also be performed on non-frozen samples to determine the tumor content in specimen.

If sending FFPE tissue scrolls, an H&E slide from a consecutive cut is also required. Please see scroll calculator application above.

All specimens must be labeled with a patient name and one other identifier (DOB, MRN, Specimen ID#, etc). Sample acquisition prior to receiving therapy is strongly preferred.

SPECIMEN SHIPPING:

Specimens must be shipped as soon as possible after collection due to time-sensitive specimen stability. Ship all samples via overnight courier. Whenever possible, send specimen immediately after collection. For fresh tumor tissue, ship the sample refrigerated using cold packs. If specimen cannot be sent on the collection date, then snap-freeze the tumor tissue immediately after collection and ship the sample frozen (bury the entire tissue in dry ice). Lab must receive specimen within 48 hours. FFPE tissue and FFPE tissue scrolls should be sent at room temperature via overnight shipping. Saturday deliveries are accepted; please check Saturday Delivery on shipment labels.

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Lab Area

Institute for Genomic Medicine

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81456

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test
Inpatient Requirements

Special Collection

At least 10% disease content must be present in the submitted Fresh, Snap-frozen, OCT, or Bone Marrow samples. At least 25% disease content must be present in the submitted FFPE tissue block or FFPE tissue scrolls (based on internal pathology review). Sample acquisition PRIOR to receiving treatment is strongly preferred. This test is NOT intended for residual disease detection.

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone Marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrollsAlternate
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerMinimum Volume
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Paraffin embedded tissueParaffin block1 block
Tissue (Snap-frozen)Tissue cassette50 mg
Tissue (Snap-frozen)Cryogenic tube50 mg
OCT-embedded tissueTissue cassette50 mg
OCT-embedded tissueCryogenic tube50 mg
Tissue (Fresh)Tissue culture transport media50 mg
Tissue (Fresh)Sterile container with saline50 mg
Bone Marrow4 mL Purple tube (EDTA)4 mL
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrolls
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM lab

 

Inpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

Unacceptable Conditions

Delayed or improper handling, Wrong type of specimen, Wrong temperature, Tissue degradation, Inadequate tissue, Insufficient tumor content in tumor sample

Stability

Paraffin embedded tissue: Room temperature 6 months

Tissue (Snap-frozen): Frozen 3 days

OCT-embedded tissue: Frozen 3 days

Tissue (Fresh): Refrigerated 48 hours

Bone Marrow: Room Temperature 24 hours
                     Refrigerated 48 hours

Tissue scrolls (FFPE): Room temperature 6 months

Remarks

If you are an external healthcare provider with no access to Nationwide Children’s Epic system, submission of a completed Oncology Genetic Test Requisition Form is required. If you are an internal ordering provider with access to Nationwide Children’s Epic system, no requisition form is required; please place the lab order electronically in Epic.

Submission of 10-15 unstained slides at 5-10 microns is recommended. If submitting tissue scroll specimen, please use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory.

SPECIMEN INFORMATION:

Fresh and snap-frozen tissue specimens must contain minimum of 10% disease content. Formalin-fixed paraffin embedded (FFPE) tissue block and FFPE tissue scroll specimens must contain minimum of 25% disease content. Please submit the pathology report from the submitted sample. Internal pathology review will also be performed on non-frozen samples to determine the tumor content in specimen.

If sending FFPE tissue scrolls, an H&E slide from a consecutive cut is also required. Please see scroll calculator application above.

All specimens must be labeled with a patient name and one other identifier (DOB, MRN, Specimen ID#, etc). Sample acquisition prior to receiving therapy is strongly preferred.

SPECIMEN SHIPPING:

Specimens must be shipped as soon as possible after collection due to time-sensitive specimen stability. Ship all samples via overnight courier. Whenever possible, send specimen immediately after collection. For fresh tumor tissue, ship the sample refrigerated using cold packs. If specimen cannot be sent on the collection date, then snap-freeze the tumor tissue immediately after collection and ship the sample frozen (bury the entire tissue in dry ice). Lab must receive specimen within 48 hours. FFPE tissue and FFPE tissue scrolls should be sent at room temperature via overnight shipping. Saturday deliveries are accepted; please check Saturday Delivery on shipment labels.

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

CPT Codes

81456

Lab Area

Institute for Genomic Medicine

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

Estimated Patient Price

$2,500 - $5,000
Overview/Billing

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

CPT Codes

81456
Interpretation

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Methodology

Next Generation Sequencing (NGS)
NCH Lab Only

Special Collection

At least 10% disease content must be present in the submitted Fresh, Snap-frozen, OCT, or Bone Marrow samples. At least 25% disease content must be present in the submitted FFPE tissue block or FFPE tissue scrolls (based on internal pathology review). Sample acquisition PRIOR to receiving treatment is strongly preferred. This test is NOT intended for residual disease detection.

Outpatient Submit with Specimen

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone Marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrollsAlternate
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerMinimum Volume
Unstained tissue slides Unstained slides and consecutive cut H&E10 slides,
10 microns thick
Paraffin embedded tissueParaffin block1 block
Tissue (Snap-frozen)Tissue cassette50 mg
Tissue (Snap-frozen)Cryogenic tube50 mg
OCT-embedded tissueTissue cassette50 mg
OCT-embedded tissueCryogenic tube50 mg
Tissue (Fresh)Tissue culture transport media50 mg
Tissue (Fresh)Sterile container with saline50 mg
Bone Marrow4 mL Purple tube (EDTA)4 mL
Tissue scrolls (FFPE) Sterile containerSterile container10-15 scrolls
RNA *Must be extracted in a
CLIA approved lab
Microcentrifuge tubeContact IGM lab

 

Inpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

Outpatient Specimen Preparation

Unstained slides:
Keep at room temperature
Protect from heat
Must be accompanied by H&E slide from adjacent section
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

Paraffin embedded tissue:
Protect from heat
Keep at room temperature

Tissue (Snap-frozen):
Freeze immediately after collection.
Transport to laboratory as soon as possible
Protect from heat
Keep frozen

OCT-embedded tissue:
Keep frozen
Transport to laboratory as soon as possible
Protect from heat
Freeze immediately after collection.

Tissue (Fresh):
Refrigerate after collection. If delay in transport is greater than 24 hours, freeze.
Transport to lab on ice immediately after collection
Protect from heat 
Do not add fixative
Do not formalin fix the sample
Keep refrigerated

Bone marrow: 
If delay in transport is greater than 24 hours, refrigerate
Transport to the lab immediately after collection
Room temperature 24 hours

Tissue scrolls (FFPE):
Protect from heat
Keep at room temperature
Must be accompanied by H&E slide from the same tissue block used to make FFPE scrolls
Samples decalcified with a strong acid are not accepted. EDTA-based decalcification methods                          (such as Formical) are acceptable. 

RNA:
Please contact laboratory before sending
Keep frozen

InLab Processing

Send to Institute for Genomic Medicine with all submitted paperwork. CPA needs to order GENSP in Sunquest for Non-EPIC lab order.

Stability

Paraffin embedded tissue: Room temperature 6 months

Tissue (Snap-frozen): Frozen 3 days

OCT-embedded tissue: Frozen 3 days

Tissue (Fresh): Refrigerated 48 hours

Bone Marrow: Room Temperature 24 hours
                     Refrigerated 48 hours

Tissue scrolls (FFPE): Room temperature 6 months

Unacceptable Conditions

Delayed or improper handling, Wrong type of specimen, Wrong temperature, Tissue degradation, Inadequate tissue, Insufficient tumor content in tumor sample

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Remarks

If you are an external healthcare provider with no access to Nationwide Children’s Epic system, submission of a completed Oncology Genetic Test Requisition Form is required. If you are an internal ordering provider with access to Nationwide Children’s Epic system, no requisition form is required; please place the lab order electronically in Epic.

Submission of 10-15 unstained slides at 5-10 microns is recommended. If submitting tissue scroll specimen, please use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory.

SPECIMEN INFORMATION:

Fresh and snap-frozen tissue specimens must contain minimum of 10% disease content. Formalin-fixed paraffin embedded (FFPE) tissue block and FFPE tissue scroll specimens must contain minimum of 25% disease content. Please submit the pathology report from the submitted sample. Internal pathology review will also be performed on non-frozen samples to determine the tumor content in specimen.

If sending FFPE tissue scrolls, an H&E slide from a consecutive cut is also required. Please see scroll calculator application above.

All specimens must be labeled with a patient name and one other identifier (DOB, MRN, Specimen ID#, etc). Sample acquisition prior to receiving therapy is strongly preferred.

SPECIMEN SHIPPING:

Specimens must be shipped as soon as possible after collection due to time-sensitive specimen stability. Ship all samples via overnight courier. Whenever possible, send specimen immediately after collection. For fresh tumor tissue, ship the sample refrigerated using cold packs. If specimen cannot be sent on the collection date, then snap-freeze the tumor tissue immediately after collection and ship the sample frozen (bury the entire tissue in dry ice). Lab must receive specimen within 48 hours. FFPE tissue and FFPE tissue scrolls should be sent at room temperature via overnight shipping. Saturday deliveries are accepted; please check Saturday Delivery on shipment labels.

Clinical Information

This RNA-based transcriptome sequencing test detects gene fusions in CNS and non-CNS solid tumors. Gene fusions resulting from chromosomal rearrangements are a hallmark of many types of neoplasia. Detection of gene fusions can aid in diagnosis and determination of treatment options, including potential treatment with an inhibitor specific to a fusion in an individual’s neoplasm. This test is not limited to specific gene fusion targets or specific exons within genes. Some regulatory fusions (e.g. those involving immunoglobulin loci such as IGH) may not be detected by this test.

In addition to gene fusions, this test can detect certain types of duplications that occur within genes (internal tandem duplications). ITDs involving the following genes are reported: AKT1, BCOR, BRAF, EGFR, FGFR1, FLT3, KMT2A, PDGFRA, PDGFRB, TP53, and UBTF. This test does not identify deletions.

Synonyms

  • Cancer transcriptome, Fusion analysis, RNA Sequencing, Transcriptome, Cancer, Fusion, RNA, RNA seq, Splicing analysis, Alternative splicing, Gene fusion, IGM test

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81456

Estimated Patient Price

$2,500 - $5,000

DC Code

5321

Downtime Availability

4-Not available

Lab Area

Lab Area
Institute for Genomic Medicine

New York DOH Approval Status

New York DOH Approval Status

Not New York State approved