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Test Code GATA2 GATA-Binding Protein 2 (GATA2), Full Gene, Next-Generation Sequencing, Varies


Advisory Information


Targeted testing for familial variants (also called site-specific or known mutation testing) is available for this gene. See:

-KVAR1 / Known Variant Analysis-1 Variant, Varies

-KVAR2 / Known Variant Analysis-2 Variants, Varies

-KVAR3 / Known Variant Analysis-3+ Variants, Varies

 

Call 800-533-1710 to confirm the appropriate test for targeted testing.



Necessary Information


1. GATA2 Gene Sequencing Patient Information is required. See Special Instructions Testing may proceed without the Patient Information however it aids in providing a more thorough interpretation. Ordering physicians are strongly encouraged to fill out the form.

2. Include physician name and phone number with the specimen.



Specimen Required


Submit only 1 of the following specimens:

 

Preferred:

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 14 days

 

Specimen Type: Peripheral blood mononuclear cells (PBMCs)

Container/Tube: Cell pellet

Collection Instructions: Send as a suspension in freezing medium or cell pellet frozen on dry ice.

Specimen Stability Information: Frozen

 

Specimen Type: Cultured fibroblasts

Container/Tube: T-75 or T-25 flask

Specimen Volume: 1 Full T-75 or 2 full T-25 flasks

Additional Information: Indicate the tests to be performed on the fibroblast culture cells.

Specimen Stability Information: Ambient (preferred)/Refrigerated <24 hours

 

Specimen Type: Skin biopsy

Supplies: Fibroblast Biopsy Transport Media (T115)

Container/Tube: Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin. Tubes of culture media can be supplied upon request (Eagle's minimum essential medium with 1% penicillin and streptomycin).

Specimen Volume: 4-mm punch

Additional Information: A separate culture charge will be assessed under FIBR / Fibroblast Culture. An additional 4 weeks is required to culture fibroblasts before genetic testing can occur.

Specimen Stability Information: Refrigerated (preferred)/Ambient

 

Specimen Type: DNA

Container/Tube: 2 mL screw top tube

Specimen Volume: 100 mcL (microliters)

Collection Instructions:

1. The preferred volume is 100 mcL at a concentration of 250 ng/mcL

2. Include concentration and volume on tube.

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


Forms

New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

Secondary ID

65481

Useful For

A comprehensive evaluation of the GATA2 gene in patients with clinical or immunological symptoms suggestive of GATA-binding protein 2 (GATA2) deficiency

 

Screening family members of patients with confirmed GATA2 deficiency

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
FIBR Fibroblast Culture Yes No
CRYOB Cryopreserve for Biochem Studies No No

Testing Algorithm

For skin biopsy or cultured fibroblast specimens, fibroblast culture and cryopreservation testing will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

Method Name

Custom Sequence Capture and Targeted Next-Generation Sequencing

Reporting Name

GATA2 Comprehensive Gene Sequencing

Specimen Type

Varies

Specimen Minimum Volume

Whole blood: 1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Reject Due To

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Clinical Information

GATA-binding protein 2 (GATA2) deficiency is emerging as the second most common primary immunodeficiency disorder (PIDD) or inborn error of immunity in adults, after common variable immunodeficiency (CVID). There is a spectrum of clinical presentations associated with GATA2 deficiency, including severe viral infections (eg, human papillomavirus [HPV]), warts, fungal infections, bacterial infections (eg, atypical mycobacterial infections such as nontuberculous mycobacterial infections [NTM] or mycobacterium avium complex [MAC]), myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and Emberger syndrome (primary lymphedema with MDS). Other clinical phenotypes of GATA2 deficiency may include aplastic anemia, pulmonary alveolar proteinosis (PAP), sensorineural hearing loss, neutropenia, and congenital lymphedema without MDS at diagnosis. Immunological phenotypes include dendritic cell, monocyte, CD4+ T cell, B and natural killer (NK) cell deficiencies. Also, the loss of a specific NK-cell subset, CD56 bright NK cells, has been reported in these patients. GATA2 deficiency was first described in 2011 as being associated with either MonoMAC (monocytopenia and mycobacterial infection) syndrome or DCML deficiency (dendritic cell, monocyte, B and NK cell lymphocyte deficiency).

 

GATA2 is a zinc finger transcription factor, involved in the generation and function of hematopoietic stem cell progenitors and, therefore, affects several of the subsequent cell lineages.

 

GATA2 deficiency is a disease of haploinsufficiency, and most germline variants appear to arise de novo (spontaneously) but are then transmitted in an autosomal dominant manner. Standard genotype-phenotype correlations are difficult to make, as there is considerable clinical heterogeneity and the age of presentation varies from early childhood to late in adult life. Additionally, there may be a role for environmental factors triggering certain infectious manifestations. There has been incomplete penetrance (not every individual with a variant has a clinical phenotype) observed with GATA2 deficiency as well as variable expressivity (different clinical presentations for the same genetic variant).The genetic alterations observed in GATA2 are heterogeneous, and include missense variants, nonsense variants, and variants in the regulatory region of intron 5, in-frame deletions involving the C-terminal zinc finger domain, frameshift variants, and large deletions. The latter are associated with null alleles, while regulatory variants have been observed in the enhancer region of intron 5.

 

Somatic variants in ASXL1 have been reported in GATA2 deficiency patients and have been postulated to be associated with transformation to myeloid leukemia. The definitive treatment for GATA2 deficiency is hematopoietic cell transplantation (HCT). Additionally, systemic use of interferon-alpha may be helpful in patients with NK cell deficiency who have recurrent or severe HPV or herpes virus infections. Also, prophylactic antibiotics may be needed or mandated in the nontransplanted patient. The pulmonary alveolar proteinosis observed in GATA2 deficiency is in the context of negative results for anti-GM-CSF autoantibodies has been shown to improve after HCT and suggests correction of alveolar macrophage function.

 

Early genetic diagnosis of GATA2 deficiency is critical in determining strategies for managing the disease considering the broad clinical spectrum. Genetic diagnosis by confirmation of a pathogenic GATA2 variant may also aid in family counseling and screening.

Reference Values

An interpretive report will be provided.

Interpretation

Evaluation and categorization of variants is performed using the most recent published American College of Medical Genetics and Genomics (ACMG) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

 

Unless reported or predicted to cause disease, alterations found deep in the intron or alterations that do not result in an amino acid substitution are not reported.

Clinical Reference

1. Spinner MA, Sanchez LA, Hsu AP, et al: GATA2 deficiency: a protean disorder of hematopoiesis, lymphatics and immunity. Blood 2014;123:809-821

2. Dickinson RE, Griffin H, Bigley V, et al: Exome sequencing identifies GATA-2 mutation as the cause of dendritic cells, monocyte, B and NK lymphoid deficiency. Blood 2011;118:2656-2658

3. Hsu AP, Sampaio EP, Khan J, et al: Mutations in GATA2 are associated with the autosomal dominant and sporadic monocytopenia and mycobacterial infection (MonoMAC) syndrome. Blood 2011;118:2653-2655

4. Mace EM, Hsu AP, Monaco-Shawver L, et al: Mutations in GATA2 cause human NK cell deficiency with specific loss of the CD56bright subset. Blood 2013;121:2669-2677

5. Ostergaard P, Simpson MA, Connell FC, et al: Mutations in GATA2 cause primary lymphedema associated with a predisposition to acute myeloid leukemia (Emberger syndrome). Nature Genetics 2011;43:929-931

6. West RR, Hsu AP, Holland SM, et al: Acquired ASXL1 mutations are common in patients with inherited GATA2 mutations and correlate with myeloid transformation. Haematologica 2014;99:276-281

7. Cuellar-Rodriguez J, Gea-Banacloche J, Freeman AF, et al: Successful allogeneic hematopoietic stem cell transplantation for GATA2 deficiency. Blood 2011;118:3715-3720

8. Hsu AP, McReynolds LJ, Holland SM: GATA2 deficiency. Curr Opin Allergy Clin Immunol 2015;15:104-109

Day(s) and Time(s) Performed

Varies

Analytic Time

2 weeks

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. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
GATA2 GATA2 Comprehensive Gene Sequencing In Process

 

Result ID Test Result Name Result LOINC Value
92332 Result Summary 50397-9
92333 Result Details 82939-0
92334 Interpretation 69047-9
92335 Additional Information 48767-8
92336 Method 49549-9
92337 Disclaimer 62364-5
92338 Reviewed by 18771-6