Skin biopsy or two T25 flasks of cultured fibroblasts from skin*
Blood – 2-3 mL in an EDTA (purple top) tube.
Bone Marrow - 2-3 mL in an EDTA (purple top) tube.
Saliva – please contact the lab regarding the availability of collection kits by emailing DGDGeneticCounselor@chop.edu.
DNA – 3 ug of DNA with a concentration of at least 50 ng/ul
*If the individual being tested has suspected or confirmed myelodysplasia or leukemia/lymphoma, or if the individual is the recipient of a donor (allogenic) bone marrow transplant, cultured fibroblasts from skin are the preferred specimen to assess for constitutional genetic variants.
Specimen Preparation
Please provide detailed clinical history and features. For more information contact the lab at 6-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
Unacceptable Conditions
Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.
Storage/Transport Temperature
For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day.
For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.
Please contact the lab (267-426-1447) with questions regarding non-blood specimens.
Volume Required
2-3 mL of blood or 3 ug of DNA with a concentration of at least 50 ng/ul
Minimum Required
1 mL of whole blood
Phlebotomy Draw
Yes
Clinical Features
Clinical symptoms of inherited neutropenia include recurrent infections and fevers, inflammation of skin and gums, osteopenia and leukemia.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
28 days
Detection Rate
The diagnostic yield for comprehensive NGS panels is not yet well-established, and depends on the panel's gene content and the patient's clinical features. Estimated detection rates are provided for pathogenic variants in the genes on this panel that can be identified by gene sequencing for probands meeting the clinical diagnostic criteria for specific disorders:
There are many syndromes associated with inherited neutropenia with phenotypic overlap; therefore, a genetic diagnosis is beneficial for management options [Donadieu 2011, PMID: 21595885].
Genomic DNA was extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing was performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis were based on the GRCh38 reference sequence. Sequencing data was processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants.
Molecular Testing Notes
The inherited neutropenia panel includes analysis of the following genes: AP3B1, CSF3R, CXCR4*, ELANE*, G6PC3, GATA1, GATA2, GFI1*, HAX1, LAMTOR2, LYST, RAB27A, RAC2*, RMRP, SBDS, SLC37A4, TAFAZZIN, USB1, VPS13B, VPS45, WAS, WIPF1
* Sequence analysis only is performed for these genes.
CPT Codes
81406x3, 81408, 81479
Collection
Collect
Skin biopsy or two T25 flasks of cultured fibroblasts from skin*
Blood – 2-3 mL in an EDTA (purple top) tube.
Bone Marrow - 2-3 mL in an EDTA (purple top) tube.
Saliva – please contact the lab regarding the availability of collection kits by emailing DGDGeneticCounselor@chop.edu.
DNA – 3 ug of DNA with a concentration of at least 50 ng/ul
*If the individual being tested has suspected or confirmed myelodysplasia or leukemia/lymphoma, or if the individual is the recipient of a donor (allogenic) bone marrow transplant, cultured fibroblasts from skin are the preferred specimen to assess for constitutional genetic variants.
Specimen Preparation
Please provide detailed clinical history and features. For more information contact the lab at 6-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
Unacceptable Conditions
Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.
Storage/Transport Temperature
For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day.
For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.
Please contact the lab (267-426-1447) with questions regarding non-blood specimens.
Volume Required
2-3 mL of blood or 3 ug of DNA with a concentration of at least 50 ng/ul
Minimum Required
1 mL of whole blood
Phlebotomy Draw
Yes
Ordering
Clinical Features
Clinical symptoms of inherited neutropenia include recurrent infections and fevers, inflammation of skin and gums, osteopenia and leukemia.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
28 days
Detection Rate
The diagnostic yield for comprehensive NGS panels is not yet well-established, and depends on the panel's gene content and the patient's clinical features. Estimated detection rates are provided for pathogenic variants in the genes on this panel that can be identified by gene sequencing for probands meeting the clinical diagnostic criteria for specific disorders:
There are many syndromes associated with inherited neutropenia with phenotypic overlap; therefore, a genetic diagnosis is beneficial for management options [Donadieu 2011, PMID: 21595885].
Genomic DNA was extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing was performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis were based on the GRCh38 reference sequence. Sequencing data was processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants.
Molecular Testing Notes
The inherited neutropenia panel includes analysis of the following genes: AP3B1, CSF3R, CXCR4*, ELANE*, G6PC3, GATA1, GATA2, GFI1*, HAX1, LAMTOR2, LYST, RAB27A, RAC2*, RMRP, SBDS, SLC37A4, TAFAZZIN, USB1, VPS13B, VPS45, WAS, WIPF1
* Sequence analysis only is performed for these genes.
