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Test Code SCCNP Severe Congenital and Cyclic Neutropenia Gene Panel, Varies


Ordering Guidance


Targeted testing for familial variants (also called site-specific or known variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about testing option, call 800-533-1710.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Specimen Required


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.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

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

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

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

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

 

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.

Specimen Volume: 4-mm punch

Specimen Stability Information: Refrigerated (preferred)/Ambient

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks is required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Cultured fibroblasts

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured fibroblast cells from a skin biopsy from another laboratory. Cultured cells from a prenatal specimen will not be accepted.

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

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks is required to culture fibroblasts before genetic testing can occur.


Forms

1. 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:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

2. Molecular Genetics: Congenital Inherited Diseases Patient Information (T521)

3. Congenital Neutropenia, Bone Marrow Failure, Telomere Defects, and Pulmonary Fibrosis (IPF) Patient Information

Secondary ID

619872

Useful For

Providing a genetic evaluation for patients with a personal or family history suggestive of severe congenital neutropenia and/or cyclic neutropenia

 

Establishing a diagnosis of an inherited congenital neutropenia and, in some cases, allowing for appropriate management and surveillance for disease features based on the gene involved

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
CULFB Fibroblast Culture for Genetic Test Yes No

Testing Algorithm

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.

Method Name

Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing

Reporting Name

Congenital Neutropenia GenePanel

Specimen Type

Varies

Specimen Minimum Volume

Blood: 1 mL; Skin biopsy or cultured fibroblasts: See Specimen Required

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

Inherited congenital neutropenia refers to a subset of primary immunodeficiencies impacting neutrophil maturation and function. The severity of the clinical manifestations in these disorders typically reflects the degree of neutropenia. Most cases of neutropenia are due to acquired (non-genetic) causes. Severe congenital neutropenia (SCN) is characterized by chronically low neutrophil count and recurrent, often life-threatening infections beginning in the first few months of life. Some individuals with SCN may also have an increased risk for myelodysplastic syndrome or acute myelogenous leukemia.(1-3) Cyclic neutropenia (CN) is characterized by periods of severe neutropenia and infections that last 3 to 5 days and recur at regular intervals.(1-5) Individuals with SCN or CN may also exhibit recurrent fevers, sinusitis, gingivitis, cellulitis, oral ulcers, colonic ulcers, and other manifestations of chronic infections.(1-5) Bone marrow biopsy on affected individuals may show arrest in myelopoiesis at the promyelocyte/myelocyte stage.(1-3)

 

The prevalence of inherited severe congenital neutropenia and cyclic neutropenia is estimated to range from 1:500,000 to 1:100,000 live births.(1-5) The genetic etiology of inherited congenital neutropenia is most commonly due to disease-causing variants in genes that play a role in neutrophil differentiation.(1) Inheritance can be autosomal recessive, autosomal dominant, or X-linked.

 

The most common causes of isolated congenital neutropenia are disease-causing variants in the ELANE and HAX1 genes, which encode neutrophil elastase and HCLS1(hematopoietic cell-specific Lyn substrate)-associated protein X-1, respectively. Autosomal dominant ELANE-related neutropenia is the most common cause of congenital neutropenia in children and may present with oral/colonic ulcers, recurrent upper and lower respiratory infections, and various infections of the soft tissue.(2,4,6) In addition, most cases of cyclic neutropenia are due to disease-causing variants in ELANE. Autosomal recessive Kostmann disease, caused by variants in the HAX1 gene, is the second most common cause of congenital neutropenia in children and presents similarly to ELANE-related neutropenia.(2,4,6) X-linked WAS-related disorders lead to a spectrum of congenital neutropenia phenotypes including Wiskott-Aldrich syndrome and X-linked congenital neutropenia.(5,6) Isolated severe congenital neutropenia may more rarely be due to disease-causing variants in several additional genes including CSF3R, CXCR2, GFI1 and WIPF1.(1,6)

 

Severe neutropenia may also be present as part of a multisystem disorder.(1) This panel assesses for many conditions in which neutropenia is seen in conjunction with extra-hematologic features, including but not limited to:

-Shwachman-Diamond syndrome, an autosomal dominant condition due to disease-causing variants in the SBDS gene, is also characterized by exocrine pancreatic dysfunction, bone abnormalities, and hematologic abnormalities.

-GATA2-deficieny (monocytopenia and mycobacterial infection [MonoMAC] syndrome), an autosomal dominant condition due to disease-causing variants in the GATA2 gene, demonstrates a wide spectrum of clinical presentations ranging from mild chronic neutropenia with monocytopenia to Emberger syndrome and predisposition to acute myeloid malignancy.

-Barth syndrome, an X-linked condition due to disease-causing variants in the TAZ gene, is also characterized cardiomyopathy, skeletal myopathy, growth delay, and distinctive facial features.

-Cohen syndrome, an autosomal recessive condition due to disease-causing variants in the VSP13B gene, is also characterized by hypotonia, developmental delays, microcephaly, failure to thrive in infancy, truncal obesity, ophthalmologic findings, joint hypermobility, a cheerful disposition, and characteristic facial features.

-WHIM (warts, hypogammaglobulinemia, infections, and myelokathexis) syndrome, an autosomal dominant condition caused by variants in the CXCR4 gene, is also characterized by hypogammaglobulinemia and susceptibility to human papillomavirus.

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(7) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Method Description

Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions/insertions (delins) less than 40 base pairs (bp), and above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.

 

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. See Targeted Genes and Methodology Details for Severe Congenital and Cyclic Neutropenia Gene Panel for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.(Unpublished Mayo method)

 

Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.

 

Genes analyzed: AK2, AP3B1, AP3D1, CD40LG, CEBPE, CLPB, CSF3R, CXCR2, CXCR4, DNAJC21, EFL1, ELANE, G6PC3, GATA2, GFI1, GINS1, HAX1, JAGN1, LYST, RAC2, SBDS, SLC37A4, SMARCD2, SRP54, TAZ(TAFAZZIN), USB1, VPS13B, VPS45, WAS, and WIPF1

Day(s) Performed

Varies

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

81443

88233- Tissue culture, skin, solid tissue biopsy (if appropriate)

88240- Cryopreservation (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
SCCNP Congenital Neutropenia GenePanel In Process

 

Result ID Test Result Name Result LOINC Value
619873 Test Description 62364-5
619874 Specimen 31208-2
619875 Source 31208-2
619876 Result Summary 50397-9
619877 Result 82939-0
619878 Interpretation 69047-9
619879 Additional Results 82939-0
619880 Resources 99622-3
619881 Additional Information 48767-8
619882 Method 85069-3
619883 Genes Analyzed 82939-0
619884 Disclaimer 62364-5
619885 Released By 18771-6