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26470 Congenital Neutropenia, Primary Immunodeficiency Disorder Panel (18 genes), Next-Generation Sequencing, Varies (SCNGP)

Congenital Neutropenia, Primary Immunodeficiency Disorder Panel (18 genes), Next-Generation Sequencing, Varies (SCNGP)
Test Code: SCNGPSO
Synonyms/Keywords

​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

Test Components

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.

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.

Useful For

​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

Specimen Requirements
Specimen TypePreferred Container/TubeAcceptable Container/TubeSpecimen VolumeSpecimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no repeat)
​Whole Blood​EDTA Lavender Top Tube (LTT)​5 mL​1 mL
​Cultured Fibroblasts​T-75 or T-25 flask​1 Full T-75 or 2 fll T-25 flasks
​Skin Biopsy​Sterile Container with any standard cell culture media (eg, minimal essential media, RPMI 1640).  The solution should be supplemented with 1% penicillin and streptomycin.  ​4-mm punch
Collection Processing Instructions

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.

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.

Special Notes:

Whole Blood:

1. Invert several times to mix blood.

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

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

Cultured Fibroblasts:

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.

Skin Biopsy: 

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 Stability Information
Specimen TypeTemperatureTime
​Whole Blood ​​Ambient (preferred)​4 days
​Refrigerated​14 days
​Cultured Fibroblasts ​​Ambient (preferred)
​Refrigerated​<24 hours
​Skin Biopsy ​​Refrigerated (preferred)
​Ambient
Rejection Criteria
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.
Performing Laboratory Information
Performing LocationDay(s) Test PerformedReport AvailableMethodology/Instrumentation
​Mayo Clinic Laboratories​Monday​4 to 8 weeks​Custom Sequence Capture and Targeted Next-Generation Sequencing followed by Polymerase Chain Reaction (PCR) and Supplemental Sanger Sequencing
Reference Lab
Reference Range Information
Performing LocationReference Range
​Mayo Clinic Laboratories​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 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.

Outreach CPTs
CPTModifier
(if needed)
QuantityDescriptionComments
​81433​1
​88233​1​Fibroblast Culture ​if needed
​88240​1​Cryopreservation for biochemical studies​if needed
Synonyms/Keywords

​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

Test Components

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.

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.

Ordering Applications
Ordering ApplicationDescription
​COM​Congenital Neutropenia Immune Disorders 18 genes (SCNGP)
​Cerner​Congenital Neutropenia, Primary Immunodificiency Disorder Panel (SCNGP)
If the ordering application you are looking for is not listed, contact your local laboratory for assistance.
Specimen Requirements
Specimen TypePreferred Container/TubeAcceptable Container/TubeSpecimen VolumeSpecimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no repeat)
​Whole Blood​EDTA Lavender Top Tube (LTT)​5 mL​1 mL
​Cultured Fibroblasts​T-75 or T-25 flask​1 Full T-75 or 2 fll T-25 flasks
​Skin Biopsy​Sterile Container with any standard cell culture media (eg, minimal essential media, RPMI 1640).  The solution should be supplemented with 1% penicillin and streptomycin.  ​4-mm punch
Collection Processing

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.

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.

Special Notes:

Whole Blood:

1. Invert several times to mix blood.

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

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

Cultured Fibroblasts:

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.

Skin Biopsy: 

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 Stability Information
Specimen TypeTemperatureTime
​Whole Blood ​​Ambient (preferred)​4 days
​Refrigerated​14 days
​Cultured Fibroblasts ​​Ambient (preferred)
​Refrigerated​<24 hours
​Skin Biopsy ​​Refrigerated (preferred)
​Ambient
Rejection Criteria
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.
Useful For

​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

Test Components

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.

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.

Reference Range Information
Performing LocationReference Range
​Mayo Clinic Laboratories​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 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.

For more information visit:
Performing Laboratory Information
Performing LocationDay(s) Test PerformedReport AvailableMethodology/Instrumentation
​Mayo Clinic Laboratories​Monday​4 to 8 weeks​Custom Sequence Capture and Targeted Next-Generation Sequencing followed by Polymerase Chain Reaction (PCR) and Supplemental Sanger Sequencing
Reference Lab
For billing questions, see Contacts
Outreach CPTs
CPTModifier
(if needed)
QuantityDescriptionComments
​81433​1
​88233​1​Fibroblast Culture ​if needed
​88240​1​Cryopreservation for biochemical studies​if needed
For most current information refer to the Marshfield Laboratory online reference manual.