Severe Congenital Neutropenia via the GFI1 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 8623 | GFI1 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).
Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).
The Sanger Sequencing method for this test is NY State approved.
For Sanger Sequencing click here.Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
Severe congenital neutropenia comprises a heterogeneous group of disorders of myelopoiesis with varying symptoms and patterns of inheritance. SCN is characterized by absolute neutrophil counts (ANC) consistently below 500/μl and severe systemic bacterial infections beginning in early infancy (Boxer and Newburger. Pediatr Blood Cancer 49:609-614, 2007). Patients typically have recurrent fevers and develop sinusitis, gingivitis, and other soft tissue infections. A hallmark of SCN is bone marrow "maturation arrest;" neutrophils differentiate only to the promyelocyte/myelocyte stage (Kostman. Acta Paediatr Scand 64:362-368, 1975). About 95% of patients respond to treatment with recombinant granulocyte-colony stimulating factor (G-CSF) with an increase in ANC (Bellanne-Chantelot et al. Blood 103:4119-4125, 2004; Freedman et al. Blood 96:429-436, 2000); however, treated patients are still at risk of sepsis (Donini et al. Blood 109:4716-4723, 2007). SCN is a premalignant condition; patients are at an elevated risk of developing myelodysplastic syndrome and acute myeloblastic leukemia (MDS/AML). The risk of malignancy increases upon G-CSF treatment (Gilman et al. Blood 36:576-585, 1970; Freedman et al. Blood 96:429-436, 2000; Rosenberg et al Blood 107:4628-4635, 2006). In contrast to SCN, MDS/AML have not been diagnosed in patients with cyclic or idiopathic neutropenia.
Genetics
Variants in the GFI1 gene (OMIM 600871) cause a rare form of autosomal dominant SCN. GFI1 encodes growth factor independent-1, a zinc finger protein with transcriptional repressor function that helps regulate cell type differentiation. Mutant GFI1 acts in a dominant negative manner and blocks granulopoiesis (Zarebski et al. Immunity 28:370-380, 2008). Causative missense variants in the zinc finger domain of GFI1 have been reported in only a few families and individuals (Person et al. Nat Genet 34:308-312, 2003; Hochberg et al. Pediatr Blood Cancer 50:630-632, 2008; Xia et al. Br J Haematol 147:535-542, 2009). The GFI1 phenotype includes a circulating population of immature myeloid cells and immunodeficient lymphocytes (Person et al. Nat Genet 34:308-312, 2003).
Clinical Sensitivity - Sequencing with CNV PGxome
Variants in the GFI1 gene are a rare cause of SCN.
Thus far, no gross deletions or duplications have been reported in GFI1 (Human Gene Mutation Database).
Testing Strategy
This test provides full coverage of all coding exons of the GFI1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).
Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).
Indications for Test
Patients with recurring bacterial infections, a family history of SCN, or neutropenia unrelated to other syndromes (e.g. Chediak-Higashi syndrome, Hermansky Pudlak syndrome, or Griscelli syndrome).
Patients with recurring bacterial infections, a family history of SCN, or neutropenia unrelated to other syndromes (e.g. Chediak-Higashi syndrome, Hermansky Pudlak syndrome, or Griscelli syndrome).
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| GFI1 | 600871 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
| Name | Inheritance | OMIM ID |
|---|---|---|
| Neutropenia, Nonimmune Chronic Idiopathic, Of Adults | AD | 607847 |
| Neutropenia, Severe Congenital, 2, Autosomal Dominant | AD | 613107 |
Related Test
| Name |
|---|
| Severe Congenital Neutropenia and Neutrophilia via the CSF3R Gene |
Citations
- Bellanne-Chantelot C. 2004. Mutations in the ELA2 gene correlate with more severe expression of neutropenia: a study of 81 patients from the French Neutropenia Register. Blood 103: 4119–4125. PubMed ID: 14962902
- Boxer LA, Newburger PE. 2007. A molecular classification of congenital neutropenia syndromes. Pediatric Blood & Cancer 49: 609–614. PubMed ID: 17584878
- Donini M, Fontana S, Savoldi G, Vermi W, Tassone L, Gentili F, Zenaro E, Ferrari D, Notarangelo LD, Porta F, Facchetti F, Notarangelo LD, et al. 2007. G-CSF treatment of severe congenital neutropenia reverses neutropenia but does not correct the underlying functional deficiency of the neutrophil in defending against microorganisms. Blood 109: 4716–4723. PubMed ID: 17311988
- Freedman MH, Bonilla MA, Fier C, Bolyard AA, Scarlata D, Boxer LA, Brown S, Cham B, Kannourakis G, Kinsey SE. 2000. Myelodysplasia syndrome and acute myeloid leukemia in patients with congenital neutropenia receiving G-CSF therapy. Blood 96: 429–436. PubMed ID: 10887102
- Gilman PA, Jackson DP, Guild HG. 1970. Congenital agranulocytosis: prolonged survival and terminal acute leukemia. Blood 36: 576–585. PubMed ID: 4319697
- Hochberg, J. C., et.al. (2008). "Mosaic tetraploidy and transient GFI1 mutation in a patient with severe chronic neutropenia." Pediatr Blood Cancer 50(3): 630-2. PubMed ID: 17096407
- Human Gene Mutation Database (Bio-base).
- Kostman R. 1975. Infantile genetic agranulocytosis. A review with presentation of ten new cases. Acta Paediatr Scand 64: 362–368. PubMed ID: 1130195
- Person, R. E., et.al. (2003). "Mutations in proto-oncogene GFI1 cause human neutropenia and target ELA2." Nat Genet 34(3): 308-12. PubMed ID: 12778173
- Rosenberg PS. 2006. The incidence of leukemia and mortality from sepsis in patients with severe congenital neutropenia receiving long-term G-CSF therapy. Blood 107: 4628–4635. PubMed ID: 16497969
- Xia J, Bolyard AA, Rodger E, Stein S, Aprikyan AA, Dale DC, Link DC. 2009. Prevalence of mutations in ELANE , GFI1 , HAX1 , SBDS , WAS and G6PC3 in patients with severe congenital neutropenia. British Journal of Haematology 147: 535–542. PubMed ID: 19775295
- Zarebski, A., et.al. (2008). "Mutations in growth factor independent-1 associated with human neutropenia block murine granulopoiesis through colony stimulating factor-1." Immunity 28(3): 370-80. PubMed ID: 18328744
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
PGxome (Exome) Sequencing Panel
PGnome (Genome) Sequencing Panel
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ORDER OPTIONS
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2) Select Additional Test Options
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