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GATA-Binding Protein 2, Gene Analysis, NGS, Varies
MessageSendout, Mayo test code: GATAS
Test Code
LAB1238017
Alias/See Also
NextGen Sequencing Test
Dendritic cell lymphopenia
Dendritic cell, monocyte, B and NK lymphoid (DCML) deficiency
Emberger syndrome
GATA2
GATA2 haploinsufficiency
Immunodeficiency 21
Lymphedema
Monocytopenia and mycobacterial infection (MonoMAC) syndrome
Mycobacterial infections
Myelodysplastic syndrome
Next Gen Sequencing Test
NK cell lymphopenia
Pulmonary alveolar proteinosis (PAP)
Warts
WILD syndrome
B-cell lymphopenia
Dendritic cell, monocyte, B- and natural killer-lymphoid deficiency
Monocytopenia and mycobacterial infection syndrome
Natural killer-cell lymphopenia
GATAS
Dendritic cell lymphopenia
Dendritic cell, monocyte, B and NK lymphoid (DCML) deficiency
Emberger syndrome
GATA2
GATA2 haploinsufficiency
Immunodeficiency 21
Lymphedema
Monocytopenia and mycobacterial infection (MonoMAC) syndrome
Mycobacterial infections
Myelodysplastic syndrome
Next Gen Sequencing Test
NK cell lymphopenia
Pulmonary alveolar proteinosis (PAP)
Warts
WILD syndrome
B-cell lymphopenia
Dendritic cell, monocyte, B- and natural killer-lymphoid deficiency
Monocytopenia and mycobacterial infection syndrome
Natural killer-cell lymphopenia
GATAS
CPT Codes
81479
Includes
For skin biopsy or cultured fibroblast specimens, fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.
Preferred Specimen
Blood: 3 mL whole from from a lavender EDTA tube.
Skin biopsy: 4 mm punch in a sterile container with any standard cell culture media. The solultion should be supplemented with 1% penicillin and streptomycin.
Cultured fibroblasts: 2 flasks from a skin biopsy.
Skin biopsy: 4 mm punch in a sterile container with any standard cell culture media. The solultion should be supplemented with 1% penicillin and streptomycin.
Cultured fibroblasts: 2 flasks from a skin biopsy.
Patient Preparation
A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.
Minimum Volume
Blood: 1 mL
Other Acceptable Specimens
Blood: Pink EDTA or yellow ACD tube
Transport Container
Blood: original container
Transport Temperature
Blood: Ambient
Skin biopsy: Refrigerated
Cultured fibroblasts: Ambient
Skin biopsy: Refrigerated
Cultured fibroblasts: Ambient
Specimen Stability
Varies
Reject Criteria (Eg, hemolysis? Lipemia? Thaw/Other?)
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.
Methodology
Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing
FDA Status
Approved
Setup Schedule
Varies
Report Available
28-42 days
Limitations
Clinical Correlations:
Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.
If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.
To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact Mayo Clinic Laboratories genetic counselors at 800-533-1710.
Technical Limitations:
Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.
There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.
This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.
Deletion/Duplication Analysis:
This analysis targets single and multi-exon deletions/duplications; however, in some instances, single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.
This test is not designed to detect low levels of mosaicism or to differentiate between somatic and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.
For detailed information regarding gene specific performance and technical limitations, see Method Description or contact a laboratory genetic counselor.
If the patient has had an allogeneic hematopoietic stem cell transplant or a recent non-leukoreduced blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant.
Reclassification of Variants:
Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages health care providers to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time. Due to broadening genetic knowledge, it is possible that the laboratory may discover new information of relevance to the patient. Should that occur, the laboratory may issue an amended report.
Variant Evaluation:
Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline.(1) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.
Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.
Rarely, incidental or secondary findings may implicate another predisposition or presence of active disease. These findings will be carefully reviewed to determine whether they will be reported.
Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.
If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.
To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact Mayo Clinic Laboratories genetic counselors at 800-533-1710.
Technical Limitations:
Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.
There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.
This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.
Deletion/Duplication Analysis:
This analysis targets single and multi-exon deletions/duplications; however, in some instances, single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.
This test is not designed to detect low levels of mosaicism or to differentiate between somatic and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.
For detailed information regarding gene specific performance and technical limitations, see Method Description or contact a laboratory genetic counselor.
If the patient has had an allogeneic hematopoietic stem cell transplant or a recent non-leukoreduced blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant.
Reclassification of Variants:
Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages health care providers to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time. Due to broadening genetic knowledge, it is possible that the laboratory may discover new information of relevance to the patient. Should that occur, the laboratory may issue an amended report.
Variant Evaluation:
Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline.(1) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.
Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.
Rarely, incidental or secondary findings may implicate another predisposition or presence of active disease. These findings will be carefully reviewed to determine whether they will be reported.
Reference Range
Included with report
Clinical Significance
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
Screening family members of patients with confirmed GATA2 deficiency
Performing Laboratory
Mayo Clinic Laboratories, Rochester, Minnesota
Additional Information
GATA-Binding Protein 2, GATA2, Full Gene Analysis, Next-Generation Sequencing, Varies
