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Test Code NGTCL MayoComplete T-Cell Lymphoma, Next-Generation Sequencing, Varies


Shipping Instructions


Whole blood, bone marrow aspirate, and body fluid specimens must arrive within 14 days of collection.



Specimen Required


Submit only 1 of the following specimens:

 

Specimen Type: Bone marrow aspirate

Container/Tube:

Preferred: Lavender or pink top (EDTA) or yellow top (ACD)

Acceptable: Green top (sodium heparin)

Specimen Volume: 2 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

2. Send bone marrow specimen in original tube. Do not aliquot.

3. Label specimen as bone marrow.

Specimen Stability Information: Ambient (preferred) 14 days/Refrigerate

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender or pink top (EDTA) or yellow top (ACD)

Acceptable: Green top (sodium heparin)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimen in original tube. Do not aliquot.

3. Label specimen as blood.

Specimen Stability Information: Ambient (preferred) 14 days/Refrigerate

 

Specimen Type: Paraffin-embedded tissue

Container/Tube: Paraffin block

Collection Instructions:

1. Send 1 representative slide stained with hematoxylin and eosin.

2. Minimum amount of tumor nuclei is 20%

3. Required amount of tissue area is at least 25 mm(2)

4. Tissue should be fixed in 10% neutral-buffered formalin. Other fixatives are not acceptable.

5. Decalcified specimens (eg, bone marrow core biopsies) are not acceptable.

Specimen Stability Information: Ambient

 

Specimen Type: Tissue slide

Slides: 10 unstained slides

Container/Tube: Transport in plastic slide holders.

Collection Instructions:

1. Send 10 unstained, nonbaked slides with 5-micron thick sections of tissue and 1 representative slide stained with hematoxylin and eosin.

2. Minimum amount of tumor nuclei is 20%

3. Required amount of tissue area is at least 25 mm(2).

4. Tissue should be fixed in 10% neutral-buffered formalin. Other fixatives are not acceptable.

5. Decalcified specimens (eg, bone marrow core biopsies) are not acceptable.

Specimen Stability Information: Ambient

 

Specimen Type: Frozen tissue

Container/Tube: Plastic container

Specimen Volume: 100 mg

Collection Instructions: Freeze tissue within 1 hour of collection

Specimen Stability Information: Frozen

 

Specimen Type: Body fluid

Container/Tube: Sterile container

Specimen Volume: 5 mL

Specimen Stability Information: Refrigerated 14 days/Frozen

 

Specimen Type: Extracted DNA

Container/Tube: 1.5- to 2-mL tube

Specimen Volume: Entire specimen

Collection Instructions:

1. Label specimen as extracted DNA and source of specimen

2. Indicate volume and concentration of DNA on label

Specimen Stability Information: Frozen (preferred)/Refrigerated/Ambient


Useful For

Aiding in establishing diagnosis, refining prognosis, and potentially identifying targeted therapies for the optimal management of patients with T-cell lymphomas

Method Name

Next-Generation Sequencing (NGS)

Reporting Name

T-cell Lymphoma, NGS, V

Specimen Type

Varies

Specimen Minimum Volume

Whole blood, bone marrow aspirate, body fluid: 1 mL; Frozen tissue: 50 mg; Extracted DNA: 100 microliters (mcL) at 20 ng/mcL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies 14 days

Reject Due To

Gross hemolysis Reject
Gross lipemia OK
Specimens that have been decalcified (all methods)
Bone marrow core biopsies
Paraffin shavings
Fixatives other than 10% neutral-buffered formalin for paraffin-embedded tissue
Moderately to severely clotted bone marrow aspirate		 Reject

Clinical Information

T-cell lymphomas are a heterogenous group of hematological disorders characterized by a range of morphological, immunophenotypic, and clinical features. Many entities share overlapping morphologic and immunophenotypic features resulting in challenges for accurate diagnosis and classification. Genomic profiling by next-generation sequencing has revealed genetic markers that aid in the classification and characterization of mature T-cell neoplasms. This test is intended to interrogate a set of genes with diagnostic, prognostic, and possible therapeutic value in a diverse group of T-cell lymphomas, which includes peripheral T-cell lymphomas and its major subtypes (eg, angioimmunoblastic T-cell lymphomas).

Reference Values

An interpretive report will be provided.

Interpretation

Genomic variants detected by this test will be documented in a detailed laboratory-issued report. This report will contain information regarding the detected alterations and their associations with prognosis or possible therapeutic implications in T-cell lymphomas. The information in the clinical report may be used by the patient’s clinician to help guide decisions concerning management. Final interpretation of next-generation sequencing results requires correlation with all relevant clinical, pathologic, and laboratory findings and is the responsibility of the managing clinician.

Cautions

This test is a targeted next-generation sequencing (NGS) panel assay that encompasses 22 genes with variable full exon, partial region (including select intronic or noncoding regions), or hot spot coverage (depending on specific genetic locus). Therefore, this test will not detect other genetic abnormalities in genes or regions outside the specified target areas. The test detects single-base substitutions (ie, point mutations) and small insertion or deletion type events. This test is not configured to detect structural genomic rearrangements (ie, translocations), gene fusions, copy number alterations, or large-scale (segmental chromosome region) deletions and other complex genomic changes.

 

This assay does not distinguish between somatic and germline alterations in analyzed gene regions, particularly with variant allele frequencies near approximately 50% or 100%. If nucleotide alterations in genes associated with germline mutation syndromes are present and there is a strong clinical suspicion or family history of malignant disease predisposition, additional genetic testing and appropriate counseling may be indicated. Some apparent mutations classified as variants of undetermined significance may represent rare or low population frequency polymorphisms.

 

Prior treatment for hematologic malignancy could affect the results obtained in this assay. Particularly, a prior allogeneic hematopoietic stem cell transplant may cause difficulties in either resolving somatic or polymorphic alterations or assigning variant calls correctly to donor and recipient fractions, if pertinent clinical or laboratory information (eg, chimerism engraftment status) is not provided.

 

Inadequate samples (eg, insufficient DNA quantity or quality) will preclude further testing and will be noted in the interpretive report. For formalin-fixed paraffin-embedded tissue specimens, NGS testing should not be pursued if the quality of the biopsy specimen is poor (eg, limited sample size, presence of extensive necrosis or fibrosis) or the target tumor cell population is low (<20%).

Method Description

This is a target-enriched next-generation sequencing (NGS) panel. DNA is extracted from validated specimen sources, including but not limited to, peripheral blood, bone marrow aspirate, and formalin-fixed paraffin-embedded tissues. Library preparation for NGS is performed, followed by probe hybridization and capture. Sequencing of the final sample library is performed on a NGS instrument. Following bioinformatic processing of the sequencing data, the sequencing results are interpreted to provide a final clinical report. Genomic alterations are called according to human genome reference build GRCh37 (hg19).(Unpublished Mayo method)

Day(s) Performed

Monday through Friday

Report Available

16 to 21 days

Specimen Retention Time

Bone marrow aspirate/whole blood: 2 weeks; DNA: 3 months; Tissue: 1 month; FFPE tissue: Unused portions of blocks will be returned to the client; Unstained slides/body fluid: Not retained

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

81450

LOINC Code Information

Test ID Test Order Name Order LOINC Value
NGTCL T-cell Lymphoma, NGS, V 104242-3

 

Result ID Test Result Name Result LOINC Value
MP071 Specimen Type 31208-2
MP072 Indication for Test 42349-1
618505 NGTCL Result No LOINC Needed
618506 Pathogenic Mutations Detected 82939-0
618507 Interpretation 69047-9
618509 Variants of Unknown Significance 93367-1
618510 Additional Information 48767-8
618508 Clinical Trials 82786-5
618511 Method Summary 85069-3
618512 Disclaimer 62364-5
618513 Panel Gene List 36908-2
618514 Reviewed By 18771-6