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Test Catalog

Test ID: PHAGP    
Phagocytic Primary Immunodeficiency (PID) Gene Panel, 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 primary immunodeficiency due to phagocytic defects, chronic granulomatous disease, or related disorders

 

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 primary immunodeficiency due to phagocytic defects, chronic granulomatous disease, or related disorders 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 evaluate for the genes listed on the panel.

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 and cryopreservation 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

Primary immunodeficiencies (PID) that affect the function of phagocytes (neutrophils, monocytes, macrophages, and eosinophils) predispose patients to a narrow spectrum of specific infections as a result of impaired killing of bacteria and fungi.

 

Chronic granulomatous disease (CGD), due to impaired production of reactive oxygen intermediates, is characterized by infections (ie, Staphylococcus aureus, Burkholderia cepacia complex, Serratia marcescens, Nocardia, and Aspergillus sp.) that involve the skin, lungs, lymph nodes, liver, and bones, although any organ or tissue can be affected. Patients may also experience immune dysregulation, resulting in granuloma formation, colitis, and other inflammatory disorders. While most affected individuals are diagnosed prior to 5 years of age, patients may present into late adulthood. Tests that measure neutrophil superoxide production by nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, including the dihydrorhodamine (DHR) or nitroblue tetrazolium (NBT) tests, may be used in establishing a diagnosis. X-linked CGD, the most common form, is caused by pathogenic variants in CYBB. In some cases, a contiguous gene deletion may result in CGD along with McLeod neuroacanthocytosis syndrome. In cases of a large contiguous gene deletion, patients may also inherit RPGR-related retinitis pigmentosa, Duchenne muscular dystrophy, and ornithine transcarbamylase deficiency. A chromosomal microarray may be indicated if a contiguous gene deletion is suspected. In addition to the X-linked form, CGD may also be inherited in an autosomal recessive pattern, due to biallelic pathogenic variants in the other genes that encode the remainder of the subunits of phagocyte NADPH, including CYBA, NCF1, NCF2, and NCF4 (Note: NCF1 is not currently included on this panel). Similarly to CGD, complete glucose 6-phosphate dehydrogenase (G6PD) deficiency can result in an increased susceptibility to infection due to impaired neutrophil respiratory burst. G6PD deficiency is also inherited in an X-linked pattern due to pathogenic variants in G6PD. Chronic nonspherocytic hemolytic anemia occurs in severe deficiency, while acute hemolytic episodes (typically triggered by some medications, ingestion of fava beans, viral or bacterial infections, etc) are observed in less severe G6PD deficiency. Patients with myeloperoxidase deficiency also show a reduced ability of the neutrophil to generate a respiratory burst, as evidenced by abnormal DHR results, but show normal superoxide production levels and NBT staining.

 

Neutrophils contain azurophilic (or primary) granules, specific (or secondary) granules, and tertiary granules that contain antimicrobial substances. Azurophilic granules contain myeloperoxidase, bactericidal/permeability-increasing protein, defensins, neutrophil elastase, and cathepsin G. Specific granules contain lactoferrin, lysozyme, NADPH oxidase, alkaline phosphatase, collagenase, histaminase, and cathelicidin. Tertiary granules contain cathepsin, gelatinase, and collagenase. Deficiency of myeloperoxidase can occur as an autosomal recessive condition due to variants in myeloperoxidase (MPO) and results in a susceptibility to Candida infections. Papillon-Lefevre Syndrome (PALS) is an autosomal recessive disorder due to pathogenic variants in CTSC (lysosomal cysteine protease cathepsin C, also known as dipeptidyl peptidase I [DPPI]). DPPI is necessary for posttranslational modification of the serine proteases in the neutrophil azurophilic granules, activation of granzymes A and B of cytotoxic lymphocytes, and activation of mast cell chymases. PALS typically presents with severe periodontal disease and keratosis palmoplantaris, along with mild immunodeficiency. In specific granule deficiency (SGD), neutrophils lack expression of secondary and tertiary granule proteins, have an atypical bilobed nuclear morphology, and demonstrate defects in chemotaxis and bactericidal activity. SGD is due to pathogenic variants in CEBPE, which is a myeloid-specific transcription factor.

 

Leukocyte adhesion deficiencies (LAD) are characterized by recurrent bacterial infections due to reduced ability of neutrophils to adhere to various substances and migrate to sites of infection, as well as defective phagocytic and respiratory burst response to bacteria and yeast. Patients often are first noticed due to omphalitis, but later gingivitis/periodontitis, pneumonia, peritonitis, and deep abscesses may develop. LAD can be caused by pathogenic variants in ITGB2, which encodes for the CD18 antigen (LAD1); and SLC35C1, which encodes for a GDP-fucose transporter (LAD2) (Note: SLC35C1 is not currently included on this panel) or FERMT3 (LAD3). Although the neutrophil functional studies are similar between LAD1 and LAD2, the clinical course in LAD2 is milder, though patients may also present with other features (ie, mental and growth retardation) due to abnormal fucose metabolism. LAD3 presents similarly to LAD1, but platelets are also affected resulting in clotting defects. Pathogenic variants in RASGRP2 (also inherited in a recessive pattern) mimic the phenotype of LAD3. Recessively inherited defects in PMM2 (congenital disorder of glycosylation type IA) show diminished neutrophil chemotaxis resulting in severe infections.

 

Granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulates the formation of colonies of neutrophils and macrophages from bone marrow precursors, but is also required for proper neutrophil function. Recessive inheritance of pathogenic variants in CSF2RA, which encodes for the alpha chain of the GM-CSF receptor, disrupts GM-CSF signaling and results in defects in neutrophil adhesion, phagocytosis, superoxide formation, and microbial killing. Clinically, this manifests as pulmonary alveolar proteinosis and increased susceptibility to infections (pulmonary and extrapulmonary).

 

The fMet-Leu-Phe receptor, encoded by FPR1, is located on the cell surface and is involved in chemotaxis phagocytic cells. Variants in FPR1 may present with aggressive periodontitis and FPR1 governs neutrophil function during acute inflammation.

 

Netherton syndrome (NS), due to pathogenic variants in SPINK5 encoding LEKTI (lymphoepithelial Kazal-type-related inhibitor), is characterized by extensive skin inflammation, hair abnormalities, atopic manifestations, and recurrent bacterial infections. Although various immunologic defects have been suggested to contribute to the immune deficiency, in some cases NK cells demonstrate an immature phenotype with impaired degranulation and cytotoxic effects. Patients may also have decreased circulating B-cells and elevated IgE and IgA.

 

Table1. Genes included in the Phagocytic / Chronic Granulomatous Disease PID Gene Panel

GENE SYMBOL (ALIAS)

PROTEIN

OMIM

INHERITANCE

PHENOTYPE DISORDER

CEBPE

CCAAT/enhancer-binding protein epsilon

600749

AR

Specific granule deficiency

CSF2RA

Granulocyte-macrophage colony-stimulating factor receptor subunit alpha isoform a precursor

306250

XL

Pulmonary surfactant metabolism dysfunction 4 (SMDP4),

pulmonary alveolar proteinosis

CTSC

Dipeptidyl peptidase 1 isoform a preproprotein

602365

AR

Haim-Munk syndrome, Papillon-Lefevre syndrome, Periodontitis 1, juvenile

CYBA

Cytochrome b-245 light chain

608508

AR

Chronic granulomatous disease

CYBB

Cytochrome b-245 heavy chain

300481

XL

Chronic granulomatous disease, immunodeficiency 34, mycobacteriosis

FERMT3

Fermitin family homolog 3 short form

607901

AR

Leukocyte adhesion deficiency, type III

FPR1

fMet-Leu-Phe receptor

136537

AR

Juvenile periodontitis

G6PD

Glucose-6-phosphate 1-dehydrogenase isoform b

305900

XL

Hemolytic anemia, chronic granulomatous disease

ITGB2

Integrin beta-2 precursor

600065

AR

Leukocyte adhesion deficiency type 1

MPO

Myeloperoxidase precursor

606989

AR

Myeloperoxidase deficiency

NCF2

Neutrophil cytosol factor 2 isoform 1

608515

AR

Chronic granulomatous disease

NCF4

Neutrophil cytosol factor 4 isoform 2

601488

AR

Chronic granulomatous disease

PMM2 (CDG1)

Phosphomannomutase 2

601785

AR

Congenital disorder of glycosylation, type Ia

RASGRP2

RAS guanyl-releasing protein 2 isoform a

605577

AR

Bleeding disorder, platelet-type, 18, LAD-III

SPINK5

Serine protease inhibitor Kazal-type 5 isoform b preproprotein

605010

AD/AR

Atopy(AD), Netherton syndrome (AR)

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

Clinical Correlations:

This panel contains genes that are primarily associated with a phagocytic defect (including chronic granulomatous disease). Although leukocyte adhesion deficiency types 1 and 3 are included, type 2 is not. In addition, due to phenotypic overlap, PMM2 is included in this panel.

 

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 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 for this patient 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 this patient's results.

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

1. Picard C, Gaspar HB, Al-Herz W, Bousfina A, 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

2. Roos D, de Boer M: Molecular diagnosis of chronic granulomatous disease. Clin Exp Immunol. 2014;175:139-149

3. Hanna S, Etzioni A: Leukocyte adhesion deficiencies. Ann N Y Acad Sci. 2012;1250:50-55

4. Taqhizade-Mortezaee F, Esmaeli B, Badalzadeh M, et al: Investigation of ITGB2 Gene in 12 New Cases of Leukocyte Adhesion Deficiency-Type I Revealed Four Novel Mutations from Iran, Archives of Iranian Med. 2015;18:11:760-764

5. Trapnell BC, Carey BC, Uchida K, Suzuki T: Pulmonary alveolar proteinosis, a primary immunodeficiency of impaired GM-CSF stimulation of macrophages. Curr Opin Immunol. 2009;21(5):514-521

6. Gombart AF, Koeffler HP: Neutrophil specific granule deficiency and mutations in the gene encoding transcription factor C/EBP(epsilon). Curr Opin Hematol. 2002;9(1):36-42

7. Nagy N, Valyi P, Csoma Z, et al: CTSC and Papillon-Lefevre syndrome: detection of recurrent mutations in Hungarian patients, a review of published variants and database update, Mol Gen and Genomic Med. 2014;2(3):217-228

8. Lozano ML, Cook A, Bastida JM, et al: Novel mutations in RASGRP2, which encodes CALDAG-GEF1, abrogate Rap1 activation, causing platelet dysfunction. Blood. 2016;128:1282-1289

9. Pasvolsky R, Feigelson SW, Kilic SS, et al: A LAD-III syndrome is associated with defective expression of the Rap1 activator, CALDAG-GEF1, in lymphocytes, neutrophils and platelets. J Exp Med. 2007;204:1571-1582

10. Notarangelo LD, Pessach I: Out of breath: GM-CSFRa mutations disrupt surfactant homeostasis. J Exp Med. 2008;205:2693-2697

11. Kuhns DB, Alvord WG, Heller T: Residual NADPH oxidase and survival in Chronic Granulomatous Disease. New Engl J Med. 2010;363:2600-2610

12. Dorward DA, Lucas CD, Chapman GB, et al: The role of formylated peptides and formyl peptide receptor 1 in governing neutrophil function during acute inflammation. Am J Pathol. 2015;185:1173-1184

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