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Test Code NGSHM OncoHeme Next-Generation Sequencing (NGS), Hematologic Neoplasms

Useful For

Evaluation of hematologic neoplasms at the time of diagnosis, to assist in appropriate classification and prognosis

 

Determining the presence of new clinically important gene mutation changes at relapse

Testing Algorithm

The following are available in Special Instructions:

-Targeted Genes Interrogated by OncoHeme Next-Generation Sequencing; this is a list of the genes and exons targeted by this test.

-Myelodysplastic Syndrome: Guideline to Diagnosis and Follow-up

Method Name

Somatic Mutation Detection by Next-Generation Sequencing (NGS)

Reporting Name

OncoHeme NGS for Hematologic Cancer

Specimen Type

Varies


Shipping Instructions


Peripheral blood and bone marrow specimens must arrive within 14 days of collection.



Necessary Information


The following information is required:

1. Clinical Diagnosis

2. Pertinent clinical history

3. Clinical or morphologic suspicion

4. Date of collection

5. Specimen source



Specimen Required


Submit only 1 of the following specimens:

 

Specimen Type: Peripheral blood

Container/Tube:

Preferred: EDTA (lavender top) or ACD (yellow top)

Acceptable: Heparin (green top)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

3. Label specimen as blood.

Specimen Stability: Ambient (preferred)/Refrigerate

 

Specimen Type: Bone marrow aspirate

Container/Tube:

Preferred: EDTA (lavender top) or ACD (yellow top)

Acceptable: Heparin (green top)

Specimen Volume: 2 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

2. Send specimen in original tube.

3. Label specimen as bone marrow.

Specimen Stability: Ambient (preferred)/Refrigerate

 

Specimen Type: Extracted DNA

Container/Tube: 1.5- to 2-mL tube with indication of volume and concentration of the DNA.

Specimen Volume: Entire specimen

Collection Instructions: Label specimen as extracted DNA and source of specimen.

Specimen Stability: Frozen (preferred)/Refrigerate/Ambient


Specimen Minimum Volume

Blood, Bone Marrow: 1 mL
Extracted DNA: 100 mcL at 20 ng/mcL concentration

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies 14 days

Reject Due To

Hemolysis

Mild OK; Gross reject

Lipemia

Mild OK; Gross OK

Icterus

NA

Other

Bone marrow biopsies, slides, paraffin shavings or frozen tissues and paraffin-embedded tissues, paraffin-embedded bone marrow aspirates, moderately to severely clotted, or lithium heparin anticoagulant

Clinical Information

Next-generation sequencing (NGS) is a rapidly evolving and complex methodology that can interrogate multiple regions of genomic tumor DNA in a single assay. Many hematologic neoplasms are characterized by morphologic or phenotypic similarities, but can have characteristic somatic mutations in many genes. In addition, many myeloid neoplasms lack a clonal cytogenetic finding at diagnosis (normal karyotype) but can be diagnosed and classified according to the gene mutation profile. The presence and pattern of gene mutations can provide critical diagnostic, prognostic, and sometimes therapeutic information for the managing physicians.

Reference Values

An interpretive report will be provided.

Interpretation

Mutations (gene alterations) identified, if present. An interpretive report will be provided.

Cautions

This test is a targeted next-generation sequencing (NGS) (panel) assay that encompasses 35 genes with variable full exon, partial region, or hot spot coverage (depending on specific 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), as well as small insertion or deletion type events, but it does not detect gene rearrangements (ie, translocations), gene fusions, copy number alterations, or large scale (segmental chromosome region) deletions and complex changes.

 

This assay does not distinguish between somatic and germ line alterations in analyzed gene regions, particularly with variant allele frequencies (VAF) near 50% or 100%. If nucleotide alterations in genes associated with germ line mutation syndromes are present and there is also a strong clinical suspicion or family history of malignant disease predisposition, additional genetic testing and appropriate counseling may be indicated. Mutation cells detected between 5% and 10% VAF may indicate low-level (ie, subclonal) tumor populations, although the clinical significance of these findings may not be clear. A low incidence of gene mutations associated with myeloid neoplasms can be detected in nonmalignant hematopoietic cells in individuals with advancing age and these may not be clearly distinguishable from tumor-associated mutations. Some apparent mutations classified as variants of undetermined significance (VUS) may represent rare or low frequency polymorphisms.

 

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

 

Correlation with clinical, histopathologic and additional laboratory findings is required for final interpretation of these results. The final interpretation of results for clinical management of the patient is the responsibility of the managing physician.

 

If this test is ordered in the setting of erythrocytosis and suspicion of polycythemia vera, interpretation requires correlation with a concurrent or recent prior bone marrow evaluation.

Method Description

Next-generation sequencing is performed for the presence of a mutation in targeted regions of the following 35 genes: ASXL1, BCOR, BRAF, CALR, CBL, CEBPA, CSF3R, DNMT3A, ETV6, EZH2, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PHF6, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, TERT, TET2, TP53, U2AF1, WT1, and ZRSR2. See Targeted Gene Regions Interrogated by OncoHeme Next-Generation Sequencing in Special Instructions for details regarding the targeted gene regions identified in this test. This is a laboratory-developed test using Research Use Only reagents. Extracted DNA from the clinical specimen is fragmented, adapter ligated, and a sequence library of fragments is prepared using a custom capture hybridization method. Individual patient samples are indexed ("bar-coded") for identification and the library is sequenced on an Illumina platform. Sequence data are processed through the Mayo Clinic Clinical Genome Sequencing Lab bioinformatics pipeline and a variant call file is generated for final analysis and reporting.(Unpublished Mayo method)

Day(s) and Time(s) Performed

Tuesday, Friday

Analytic Time

14 days

Specimen Retention Time

1 year

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

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

CPT Code Information

81450-Targeted genomic sequence analysis panel, hematolymphoid neoplasm or disorder, DNA and RNA when performed, 5-50 genes (eg, BRAF, CEBPA, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KRAS, KIT, MLL, NRAS, NPM1, NOTCH1), interrogation for sequence variants and copy number variants or rearrangements, or isoform expression of mRNA expression levels, if performed.

LOINC Code Information

Test ID Test Order Name Order LOINC Value
NGSHM OncoHeme NGS for Hematologic Cancer In Process

 

Result ID Test Result Name Result LOINC Value
MP024 Specimen Type 31208-2
NGSD Indication for Test 42349-1
37276 Pathogenic Mutations Detected 41103-3
37283 Interpretation 69047-9
37282 Clinical Trials 82786-5
37277 Variants of Unknown Significance 82939-0
37278 Additional Notes 48767-8
37279 Method Summary 49549-9
37420 Disclaimer 62364-5
37280 OncoHeme Panel Gene list 36908-2
37287 Reviewed By: 19139-5

Forms

1. Hematopathology Patient Information (T676) in Special Instructions

2. If not ordering electronically, complete, print, and send a Hematopathology/Cytogenetics Test Request Form (T726) with the specimen (http://www.mayomedicallaboratories.com/it-mmfiles/hematopathology-request-form.pdf)

Genetics Test Information

This test includes next-generation sequencing to evaluate for the following 35 genes and intronic regions: ASXL1, BCOR, BRAF, CALR, CBL, CEBPA, CSF3R, DNMT3A, ETV6, EZH2, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PHF6, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, TERT, TET2, TP53, U2AF1, WT1, and ZRSR2.