Test Catalog

Test Id : SCNGP

Congenital Neutropenia, Primary Immunodeficiency Disorder Panel (18 genes), Next-Generation Sequencing, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of congenital neutropenia, cyclic neutropenia, or other primary immunodeficiency disorder (PIDD) presenting with significant neutropenia

 

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

 

Identifying variants within genes known to be associated with PIDD characterized by significant neutropenia allowing for predictive testing of at-risk family members

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test includes next-generation sequencing and supplemental Sanger sequencing to test for variants in the AP3B1(HP2), CSF3R, CXCR4, ELANE(ELA2), G6PC3, GATA2, GFI1, HAX1, LAMTOR2(MAPBPIP), RAC2, SBDS, SLC37A4, TAZ, USB1(C16ORF57), VPS13B(COH1), VPS45, WAS, and WIPF1 genes.

 

Identification of a pathogenic variant may assist with prognosis, clinical management, familial screening, and genetic counseling.

Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial tests.

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

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

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

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Congenital Neutropenia PID Panel

Aliases
Lists additional common names for a test, as an aid in searching

AP3B1(HP2)

Barth syndrome

Cohen syndrome

CSF3R

CXCR4

Cyclic neutropenia

Dursun syndrome

ELANE(ELA2)

Emberger syndrome

G6PC3

GATA2

GFI1

Glycogen storage disease Ib and Ic

HAX1

Hermansky-Pudlak syndrome 2

Immunodeficiency 21

LAMTOR2(MAPBPIP)

Myelokathexis Nonimmune chronic idiopathic

Neutrophil functional defects

RAC2

SBDS

Severe congenital neutropenia

Shwachman-Diamond syndrome

SLC37A4

TAZ

USB1(C16ORF57)

VPS13B(COH1)

VPS45

X-linked severe congenital neutropenia

X-linked thrombocytopenia

WAS

WHIM syndrome

WIPF1

Wiskott-Aldrich syndrome 2

Next Gen Sequencing Test

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

Necessary Information

1. Primary Immunodeficiencies Patient Information (T791) is strongly recommended, but not required, to be filled out and sent with the specimen. This information aids in providing a more thorough interpretation of test results. Ordering providers are strongly encouraged to complete the form and send it with the specimen.

2. Include physician name and phone number with specimen.

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Patient Preparation: A previous bone marrow transplant from an allogenic donor or a recent (ie, <6 weeks from time of sample collection) heterologous blood transfusion 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:

 

Preferred:

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 5 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 14 days

Additional Information: For patients with severe neutropenia, DNA yield may be insufficient for testing. Consider sending additional volume or an alternate specimen type.

 

Specimen Type: Blood spot

Supplies: Card-Blood Spot Collection Filter Paper (T493)

Container/Tube:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: Whatman FTA Classic paper, PerkinElmer 226 (formerly Ahlstrom 226) filter paper, or blood spot collection card

Specimen Volume: 5 Blood spots

Collection Instructions:

1. An alternative blood collection option for a patient 1 year of age or older is a fingerstick. For infants younger than 1 year, a heel stick should be used. See Dried Blood Spot Collection Tutorial for how to collect blood spots via fingerstick.

2. Let blood dry on the filter paper at ambient temperature in a horizontal position for a minimum of 3 hours.

3. Do not expose specimen to heat or direct sunlight.

4. Do not stack wet specimens.

5. Keep specimen dry.

Specimen Stability Information: Ambient (preferred)/Refrigerated

Additional Information:

1. For patients with severe neutropenia, DNA yield may be insufficient for testing. Consider sending additional volume or an alternate specimen type.

2. For collection instructions, see Blood Spot Collection Instructions.

3. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777).

4. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800).

 

Specimen Type: Peripheral blood mononuclear cells (PBMC)

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

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

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

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: Extracted 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

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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 in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Primary Immunodeficiencies Patient Information (T791) is recommended. See Special Instructions.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

Whole blood: 1 mL

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

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

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of congenital neutropenia, cyclic neutropenia, or other primary immunodeficiency disorder (PIDD) presenting with significant neutropenia

 

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

 

Identifying variants within genes known to be associated with PIDD characterized by significant neutropenia allowing for predictive testing of at-risk family members

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test includes next-generation sequencing and supplemental Sanger sequencing to test for variants in the AP3B1(HP2), CSF3R, CXCR4, ELANE(ELA2), G6PC3, GATA2, GFI1, HAX1, LAMTOR2(MAPBPIP), RAC2, SBDS, SLC37A4, TAZ, USB1(C16ORF57), VPS13B(COH1), VPS45, WAS, and WIPF1 genes.

 

Identification of a pathogenic variant may assist with prognosis, clinical management, familial screening, and genetic counseling.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Severe congenital neutropenia is a primary immunodeficiency disorder that is characterized by severe and recurrent bacterial infections, such as otitis media, bronchitis, pneumonia, osteomyelitis, and cellulitis, typically with the absence of pus at the infected site. Susceptibility to fungal infections may also be observed. Neutropenia may be an isolated finding or may be part of a syndrome. This panel includes genes associated with neutropenia as a major presenting feature; other panels may be more appropriate when neutropenia is identified but not as the main finding.

 

Pathogenic variants in ELANE, which encodes neutrophil elastase, can result in severe congenital neutropenia type 1 (SCN1) or cyclic neutropenia. SCN1 often presents immediately with omphalitis, while diarrhea, pneumonia, and deep abscesses affecting the liver, lungs, or subcutaneous tissues are noted within the first year. Patients are at risk for development of myelodysplastic syndrome or acute myelogenous leukemia, presumably due to acquired mutations in CSF3R (which may also be identified in the presence of congenital neutropenia due to variants in genes other than ELANE, see below). Biallelic mutations in CSF3R have also been recently reported to be associated with severe congenital neutropenia. Cyclic neutropenia typically presents in the first year of life with 3-week-long oscillations in cell counts along with intervals of fever, oral ulcerations, and ulcerations; between intervals, patients are generally healthy. Unlike SCN1, cyclic neutropenia is not associated with risk of malignancy. Both SCN1 and cyclic neutropenia are inherited in an autosomal dominant pattern from an affected parent, although de novo variants have been identified. Studies have demonstrated pathogenic variants in ELANE in nearly 100% of cases with well-documented classical cyclic neutropenia, while in some cases with atypical presentations (ie, oscillations that are not 3 weeks) a variant in ELANE is not identified. ELANE variants are identified in 38% to 80% of cases of congenital neutropenia, depending on the criteria used to identify patients. Although there is some overlap, generally, variants at the active site of neutrophil elastase result in cyclic neutropenia, while variants that prevent normal folding or packaging of the enzyme cause congenital neutropenia.

 

In addition to variants in ELANE, severe congenital neutropenia, where the predominant finding is neutropenia, can be inherited as a result of pathogenic variants in other genes. Dominant variants in GFI1 (encoding growth factor independent 1) result in severe congenital neutropenia type 2 (SCN2). Pathogenic variants in G6PC3 (encoding glucose-6-phosphate 3), which are inherited in an autosomal recessive manner, can result in a phenotypic spectrum from isolated/nonsyndromic severe congenital neutropenia to classic G6PC3 deficiency (severe neutropenia along with cardiovascular and urogenital abnormalities) to severe G6PC3 deficiency (also known as Dursun syndrome, which includes features of classic G6PC3 deficiency along with severe lymphopenia, primary pulmonary hypertension, thymic hypoplasia, among other features). Kostmann disease or severe congenital neutropenia type 3 (SCN3) is due to recessive inheritance of pathogenic variants in HAX1 (which encodes HCLS1-associated protein X-1) and may result in seizures and developmental delay in addition to neutropenia. Along with neutropenia, variants in VPS45 inherited in an autosomal recessive manner (also known as severe congenital neutropenia type 5 [SNC5]) are associated with neutrophil dysfunction, bone marrow fibrosis, and nephromegaly due to renal extramedullary hematopoiesis. While loss-of-function variants in WAS, which is located on the X chromosome, cause Wiskott-Aldrich syndrome (characterized by thrombocytopenia, eczema, and recurrent infections), gain-of-function variants affecting the autoinhibitory structure of the protein, have been associated with congenital neutropenia, along with variable lymphopenia, decreased lymphocyte proliferation, and impaired phagocyte activity. Pathogenic variants in WIPF1 can present with similar findings to Wiskott-Aldrich syndrome.

 

Severe neutropenia may also be present as part of a multisystem disorder. Barth syndrome, due to pathogenic variants in TAZ, which is located on the X-chromosome, is characterized by neutropenia, cardio- and skeletal myopathy, growth delay, and distinctive facial features. Biallelic variants in C16orf57 manifest as poikiloderma with neutropenia; the neutropenia may be cyclical. In Cohen syndrome, an autosomal recessive disorder due to variants in COH1 (also known as VPS13B), neutropenia is accompanied by hypotonia, developmental delays, microcephaly, failure to thrive in infancy, truncal obesity in adolescent years, ophthalmologic findings, joint hypermobility, a cheerful disposition, and characteristic facial features. Glycogen storage disease type I (GSDI), caused by biallelic pathogenic variants in either G6PC or SLC37A4, when untreated can result in chronic neutropenia and impaired neutrophil and monocyte function, as well as the characteristic findings that include accumulation of glycogen and fat in the liver and kidneys. Pathogenic variants in LAMTOR2/MAPBPIP have been shown to result in neutropenia, decreased cytotoxic activity of CD8+ T cells, short stature, and hypopigmented skin. Persistent or intermittent neutropenia is often a presenting feature of Shwachman-Diamond syndrome (SDS), which is also characterized by exocrine pancreatic dysfunction (with malabsorption, malnutrition, and growth failure), bone abnormalities, and hematologic abnormalities (single- or multilineage cytopenias along with predisposition to myelodysplastic syndrome and acute myelogenous leukemia). SDS is an autosomal recessive disorder due to pathogenic variants in SBDS. Warts, hypogammaglobulinemia, immunodeficiency, and myelokathexis (WHIM) syndrome is characterized by neutropenia in addition to hypogammaglobulinemia, and susceptibility to human papillomavirus. It is due to autosomal dominant pathogenic variants in CXCR4. Although most forms of Hermansky-Pudlak syndrome do not include significant neutropenia, type 2 caused by variants in AP3B1 can be associated with persistent neutropenia and increased infections in addition to the typical findings of tyrosinase-positive oculocutaneous albinism, platelet storage pool deficiency, pulmonary fibrosis, and granulomatous colitis. Few patients with RAC2 pathogenic variants have been identified, but neutrophil dysfunction appears to be a feature, though CD11b expression and specific granule release appear to be preserved. Both individuals with dominant and individuals with recessive inheritance have been identified, with and without additional associated phenotypic findings.

 

GATA-binding protein (GATA2) deficiency demonstrates a wide spectrum of clinical presentations, including neutropenia. Most variants appear to arise de novo (spontaneously) and are then transmitted in an autosomal dominant manner. If the clinical phenotype strongly suggests GATA2 deficiency, this gene is available as a stand-alone test (see GATA2 / GATA-Binding Protein 2 [GATA2], Full Gene, Next-Generation Sequencing, Varies). This panel does not evaluate for somatic (acquired) ASXL1 variants associated with GATA2 deficiency.

 

Genes included in this test

Gene (alias)

Protein

OMIM

Incidence

Inheritance

Phenotype disorder

AP3B1

AP-3 complex subunit beta-1 isoform 1

603401

Rare

AR

Hermansky-Pudlak syndrome 2

CSF3R

Granulocyte colony-stimulating factor receptor isoform a precursor

138971

 

AR, acquired

Severe congenital neutropenia

CXCR4

C-X-C chemokine receptor type 4 isoform b

162643

 

AD

Myelokathexis, isolated, WHIM syndrome (AD)

ELANE

Neutrophil elastase preproprotein

130130

 2:1,000,000-3:1,000,000 (SCN); 1:1,000,000 (cyclic neutropenia)

AD

Severe congenital neutropenia (SCN), cyclic neutropenia

G6PC3

Glucose-6-phosphatase 3

611045

 

AR

Dursun syndrome, severe congenital neutropenia (SCN) 4

GATA2

Endothelial transcription factor GATA-2 isoform 1

137295

 

AD

Immunodeficiency 21, Emberger syndrome, susceptibility to acute myeloid leukemia and myelodysplastic syndrome

GFI1

Zinc finger protein Gfi-1

600871

 

AD

Severe congenital neutropenia (SCN) 2(AD), nonimmune chronic idiopathic neutropenia of adults

HAX1

HCLS1-associated protein X-1 isoform a

605998

 

AR

Severe congenital neutropenia (SCN) 3

LAMTOR2 (MAPBPIP)

Ragulator complex protein LAMTOR2 isoform 1

610389

 

AR

Immunodeficiency due to defect in MAPBP-interacting protein

RAC2

ras-Related C3 botulinum toxin substrate 2

602049

 

AD/AR

Neutrophil functional defects

SBDS

Ribosome maturation protein SBDS

607444

 

AR

Shwachman-Diamond syndrome, susceptibility to aplastic anemia

SLC37A4

Ddipeptidyl peptidase 1 isoform a preproprotein

602671

 

AR

Glycogen storage disease Ib and 1c

TAZ

Tafazzin isoform 1

300394

 

XL

Barth syndrome

USB1 (C16ORF57)

U6 snRNA phosphodiesterase isoform 1

613276

Rare

AR

Poikiloderma with neutropenia  

VPS13B (COH1)

Vacuolar protein sorting-associated protein 13B isoform 5

607817

 

AR

Cohen syndrome

VPS45

Vacuolar protein sorting-associated protein 45 isoform 1

610035

 

AR

Severe congenital neutropenia (SCN) 5

WAS

(Gain-of-function mutations)

Wiskott-Aldrich syndrome protein

300392

 

XL (gain of function)

Neutropenia, severe congenital, X-linked, thrombocytopenia, X-linked

WIPF1

WAS/WASL-interacting protein family member 1

602357

 

In progress

Wiskott-Aldrich syndrome 2

 

AD=autosomal dominant

AR=autosomal recessive

XL=X-linked

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

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

 

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 predictions made by these tools may change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

The majority of DNA extracted from whole blood is derived from neutrophils. Therefore, blood specimens collected from patients with severe neutropenia may yield limited quantity of DNA that is insufficient for testing. When ordering this test for patients with severe neutropenia, please consider timing the collection when the patient has a higher neutrophil count, submitting an alternate specimen type, or collecting additional blood volume.

 

Clinical Correlations:

Some individuals who have involvement of one or more of the genes on the panel may have a variant that is not identified by the methods performed (eg, promoter variants, deep intronic variants). The absence of a variant, therefore, does not eliminate the possibility of disease. Test results should be interpreted in context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

For predictive testing of asymptomatic individuals, it is often useful to first test an affected family member. Identification of a pathogenic variant in an affected individual allows for more informative testing of at-risk individuals.

 

Technical Limitations:

Next-generation sequencing may not detect all types of genetic variants. The variant detection software has lower detection efficiency for insertion/deletion variants as compared to single nucleotide variants. Therefore, small deletions and insertions greater than 8 nucleotides in length may not be detected by this test. Copy Number variations (CNV) are not currently reported for any of the genes on this panel. Additionally, rare alterations (polymorphisms) may be present that could lead to false-negative or false-positive results. In some cases, DNA variants of undetermined significance may be identified. If results do not match clinical findings, consider alternative methods for analyzing these genes, such as Sanger sequencing or large deletion/duplication analysis. If the patient has had an allogeneic blood or bone marrow transplant or a recent (ie, <6 weeks from time of sample collection) heterologous blood transfusion, results may be inaccurate due to the presence of donor DNA. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

 

Reclassification of Variants-Policy:

At this time, it is not standard practice for the laboratory to systematically review likely deleterious alterations or variants of uncertain significance that are detected and reported. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time. Consultation with a healthcare provider, or team of healthcare providers, with expertise in genetics and primary immunodeficiencies, is recommended for interpretation of this result.

 

A list of benign and likely benign variants detected is available from the lab upon request.

 

Contact the laboratory if additional information is required regarding the transcript or human genome assembly used for the analysis of results.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Picard C, Gaspar HB, Al-Herz W, et al: International Union of Immunological Societies: 2017 Primary Immunodeficiency Disease Committee report on inborn errors of immunity, J Clin Immunol. 2018;38:96-128. doi: 10.1007/s10875-017-0464-9

2. Donadieu J, Fenneteau O, Beaupain B, Mahlaoui N, Bellanne Chantelot C: Congenital neutropenia: diagnosis, molecular bases and patient management. Orphanet J Rare Dis. 2011;6:26. doi: 10.1186/1750-1172-6-26

3. Boxer LA, Stein S, Buckley D, et al: Strong evidence for autosomal dominant inheritance of severe congenital neutropenia associated with ELA2 mutations. J Pediatr. 2006;148:633-636

4. Beel K, Bandenberghe P: G-CSF receptor (CSF3R) mutations in X-linked neutropenia evolving to acute myeloid leukemia or myelodysplasia. Haematologica. 2009;94(10):1449-1452

5. Klein C: Genetic defects in severe congenital neutropenia: emerging insights into life and death of human neutrophil granulocytes. Ann Rev Immunol. 2011;29:399-413

6. Albert MH, Notarangelo LD, Ochs HD: Clinical spectrum, pathophysiology and treatment of the Wiskott-Aldrich syndrome. Cur Opin Hematol. 2011;18(1):42-48

7. Concolino D, Roversi G, Muzzi GL, et al: Clericuzio-type poikiloderma with neutropenia syndrome in three sibs with mutations in the C16orf57 gene: delineation of the phenotype. Am J Med Genet. 2010;152A(10):2588-2594

8. Bohn G, Allroth A, Brandea G, et al: A novel human primary immunodeficiency syndrome caused by deficiency of endosomal adaptor protein p14. Nature Med. 2007;13(1):38-45

9. Triot A, Jarvinen PM, Arostegui JI, et al: Inherited biallelic CSF3R mutations in severe congenital neutropenia. Blood. 2014;123:3811-3817

10. Bousifiha AA, et al: A phenotypic approach for IUIS PID classification and diagnosis: guidelines for clinicians at the bedside. J Clin Immunol. 2013;Aug;33(6):1078-1087

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Next-generation sequencing (NGS) is performed using an Illumina instrument with paired-end reads. The DNA is prepared for NGS using a custom Agilent SureSelect Target Enrichment System. Data is analyzed with a bioinformatics software pipeline. Supplemental Sanger sequencing may be performed occasionally in regions where NGS is insufficient for data capture or not specific enough to correctly identify a variant.(Unpublished Mayo method)

 

Genes analyzed: AP3B1(HP2), CSF3R, CXCR4, ELANE(ELA2), G6PC3, GATA2, GFI1, HAX1, LAMTOR2(MAPBPIP), RAC2, SBDS, SLC37A4, TAZ, USB1(C16ORF57), VPS13B(COH1), VPS45, WAS, WIPF1

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Monday 

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

4 to 8 weeks

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Extracted DNA: 2 months

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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 US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81443

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
SCNGP Congenital Neutropenia PID Panel In Process
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
BA3910 Gene(s) Evaluated 48018-6
BA3911 Result Summary 50397-9
BA3912 Result Details 82939-0
BA3913 Interpretation 69047-9
BA3914 Additional Information 48767-8
BA3915 Method 85069-3
BA3916 Disclaimer 62364-5
BA3917 Reviewed by 18771-6

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports