Test Id : SCDGP

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.

Targeted testing for familial variants (also called site-specific or known mutations testing) is available for the genes on this panel. See FMTT / Familial Mutation, Targeted Testing, Varies.

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.

Submit only 1 of the following specimens:

Preferred:

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 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

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: 2 to 5 blood spots

Collection Instructions:

1. An alternative blood collection option for a patient older than 1 year of age is fingerstick. See How to Collect Dried Blood Spot Samples 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. Due to lower concentration of DNA yielded from blood spot, it is possible that additional specimen may be required to complete testing.

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

• Informed Consent for Genetic Testing
• Primary Immunodeficiencies Patient Information
• Informed Consent for Genetic Testing (Spanish)

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:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Primary Immunodeficiencies Patient Information (T791) is recommended.

Whole blood: 1 mL; Blood spots: 2 spots; For the other specimen types: See Specimen Required

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of:

-Severe combined immunodeficiency (SCID)

-Combined immunodeficiency (CID)

-T-cell lymphopenia/deficiency

-Bare lymphocyte syndrome (BLS)

-Epstein-Barr virus-associated primary immunodeficiency disorder (EBV-associated PIDD)

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

Identifying pathogenic variants within genes known to be associated SCID, CID, T-cell lymphopenia/deficiency, BLS, or EBV-associated PIDD allowing for predictive testing of at-risk family members

This test includes next-generation sequencing and supplemental Sanger sequencing to test for variants in the ADA(ADA1), ADA2 (CECR1), AK2, ATM, CD247(CD3Z), CD27, CD3D, CD3E, CD3G, CD8A, CHD7, CIITA, CORO1A, CTPS1, DCLRE1C(ARTEMIS), FOXN1, GATA2, IKBKB, IKBKG(NEMO), IL21, IL21R, IL2RG, IL7R, ITK, JAK3, LCK, LIG4, MAGT1, MALT1, MTHFD1, NFKBIA(IKBA), NHEJ1, ORAI1, PNP, PRKDC, PTPRC(CD45), RAC2, RAG1, RAG2, RBM8A, RFX5, RFXANK, RFXAP, RHOH, RMRP, SEMA3E, SH2D1A, SLC46A1, STAT5B, STIM1, STK4, TAP1, TAP2, TAPBP, TAZ, TBX1, TNFRSF4(OX40), TRAC, TTC7A,WAS, WIPF1, XIAP(BIRC4), ZAP70 genes.

This test uses Sanger sequencing to test for variants in certain exons of the following genes:

IKBKG (NEMO) Exons 3-10; The recurrent IKBKG ~11.7 kilobase deletion associated with incontinentia pigmenti is not detected.

CORO1A Exon 11

STAT5B Exons 6-8

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

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.

Severe combined immunodeficiency (SCID) is characterized by the absence or dysfunction of T lymphocytes, which affects both cellular and humoral adaptive immunity resulting in a severe form of this inherited primary immunodeficiency disorder that may be life-threatening. In classic form, SCID presents in infancy with persistent respiratory and gastrointestinal infections, failure to thrive, or graft-versus-host disease (due to engraftment of maternal T cells). The absence of lymphoid tissue, immunoglobulins, and T lymphocytes may also be noted. Typically, patients will have less than 300 autologous CD3 T cells/mcL blood and will require immediate medical intervention.

Atypical or "leaky" SCID tends to present later (ie, over 12 months of age) with recurrent, severe, and prolonged viral infections, bronchiectasis, autoimmune manifestations including cytopenias, and failure to thrive. Patients may display partial or restricted antigen-specific antibody responses. Leaky SCID is also related to hypomorphic variants in genes normally associated with classic SCID, as indicated above.

Omenn syndrome, a form of leaky SCID that typically presents in infancy, is characterized by erythroderma, alopecia, hepatosplenomegaly, and lymphadenopathy. Laboratory findings may include elevated IgE, eosinophilia, and lymphocytosis. Omenn syndrome is due to genetic variants in at least 7 different genes that allow for partial activity, although disease severity is likely only partially attributable to genotype. While RAG1 and RAG2 hypomorphic variants are most often associated with leaky SCID or Omenn syndrome, patients may have variants affecting other genes/proteins, such as Artemis or interleukin-7 receptor (IL-7R) alpha. There may be forms of leaky SCID with hypomorphic variants in these genes that do not have the associated Omenn syndrome phenotype.

SCID can be classified as T-B+ or T-B- SCID, with further subdivision possible based on the presence or absence of NK cells. T-B+ SCID, characterized by impaired development of mature T-cells along with present but non-functional B-cells, is most often caused by genetic variants that affect cytokine-mediated signaling. X-linked SCID is due to mutations in the IL2RG gene, which encodes the common gamma chain that is a part of the IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21 receptors. Autosomal recessive forms due to variants in JAK3 or IL7R also disrupt cytokine signaling. Genetic variants in one of the four CD3 genes (CD3G, CD3D, CD3E, and CD247[CD3Z]) inhibit CD3 signaling and also cause T-B+ SCID. T-B+ SCID may also be due to coronin-1A deficiency causing disruption of thymic egress of T cells and defective T cell locomotion, or due to CD45 deficiency (caused by variants in PTPRC). Patients with coronin-1A deficiency may also have other syndromic manifestations.

T-B- SCID is typically characterized by a defect in V(D)J recombination. V(D)J recombination begins with proteins encoded by RAG1 and RAG2 forming a heterodimer and making a single-stranded nick and forming hairpin structured ends between a coding element (V, D, or J segment) and the recombination signal sequence. Then, in the processing phase, the DNA-protein kinase complex (including a protein encoded by PRKDC) binds to and opens the hairpin structure by phosphorylating Artemis (encoded by DCLRE1C). Prior to ligation of the open ends by LIG4/XRCC4 and Cernunnos/XLF (encoded by NHEJ1), additional editing takes place. Adenosine deaminase deficiency, which results in accumulation of metabolic by-products that are toxic to lymphocytes, and results in T-B- and NK- SCID. It accounts for approximately 15% of cases and is inherited as an autosomal recessive condition, which may include neurological problems (ie, cognitive impairment, hearing/visual impairment, and movement disorders) in addition to SCID. Reticular dysgenesis, due to genetic variants in AK2, is the most severe form of combined immunodeficiency and is characterized by congenital agranulocytosis, lymphopenia, lymphoid and thymic hypoplasia, along with bilateral sensorineural deafness.

Subsets of T cells may be decreased due to genetic variants in certain genes, without an appreciable effect on other T cell subsets. For example, genetic variants in CD8A, ZAP70, TAP1, TAP2, or TAPBP can result in absent or reduced CD8+ T cells in the presence of normal quantity of CD4+ T cells. In contrast, genetic variants in CIITA, RFXANK, RFX5, or RFXAP result in absent or reduced CD4+ T cells. These genes are associated with bare lymphocyte syndromes types 1 and 2 respectively, or major histocompatibility complex (MHC) class I and II deficiencies. In addition, variants in ITK, MAGT1, RHOH, STK4, TRAC, LCK, MALT1, IL21, IL21R, TNFRSR4 (OX40), IKBKB, CD27, or CTPS1 are thought to generally result in combined immunodeficiency that is generally less clinically profound than SCID.

Several combined immunodeficiencies are associated other features and syndromes. Variants in WAS and WIPF1 present with combined immunodeficiency and congenital thrombocytopenia, while variants in RBM8A are associated with thrombocytopenia-absent radius syndrome. DNA repair defects are commonly observed along with combined immunodeficiency in ataxia-telangiectasia (due to variants in ATM). Thymic defects with additional congenital anomalies may be observed in DiGeorge syndrome (represented on this panel by TBX1), CHARGE syndrome (due to variants in CHD7 or SEMA3E), and patients with genetic variants in FOXN1. Immune-osseous dysplasias along with combined immunodeficiency may be observed in cartilage hair hypoplasia (due to variants in RMRP), while those with variants in STAT5B may have growth hormone insensitivity. Combined immunodeficiency (CID) along with defects of vitamin B12 and folate metabolism may be observed in patients with genetic variants in SLC46A1 or MTHFD1. Anhidrotic ectodermal dysplasia with immunodeficiency results from genetic variants in IKBKG (NEMO) or NFKBIA (IKBA). Calcium channel defects are an associated feature in those with variants in ORAI1 or STIM1. In addition to CID, patients with variants in TTC7A may have multiple intestinal atresias. Barth syndrome along with combined immunodeficiency can be observed in patients with variants in TAZ. Some of these defects can be identified by newborn screening (NBS) for SCID, while others do not present with severe enough T cell lymphopenia in the neonatal period to be identified by NBS.

Table. Genes included in this test

ADA=adenosine deaminase

AD=autosomal dominant

AR=autosomal recessive

GOF=gain of function

MHC=major histocompatibility complex

XL=X-linked

An interpretive report will be provided.

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.

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 (ie, 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) 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.

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 Jan;38(1):96-128. doi: 10.1007/s10875-017-0464-9

2. Shearer WT, Dunn E, Notarangelo LD, et al: Establishing diagnostic criteria for severe combined immunodeficiency disease (SCID), leaky SCID, and Omenn Syndrome: The Primary Immune Deficiency Treatment Consortium experience. J Allergy Clin Immunol. 2014 Apr;133(4):1092-1098. doi: 10.1016/j.jaci.2013.09.044

3. Bousfiha AA, Jeddane L, Ailal F, 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

4. Raje N, Soden S, Swanson D, Ciaccio CE, Kingsmore SF, Dinwiddie DL: Utility of next generation sequencing in clinical primary immunodeficiencies. Curr Allergy Asthma Rep. 2014 Oct;14(10):468

5. Taylor GS, Long HM, Brooks JM, Rickinson AB, Hislop AD: The immunology of Epstein-Barr virus-induced disease. Annu Rev Immunol. 2015;33:787-821. doi: 10.1146/annurev-immunol-032414-112326

6. DeSandro A, Nagarajan UM, Boss JM: The bare lymphocyte syndrome: Molecular clues to the transcriptional regulation of major histocompatability complex class II genes. Am J Hum Genet. 1999 Aug;65(2):279-286. doi: 10.1086/302519

7. Walkovich K, Vander Lugt M: ZAP70-related combined immunodeficiency. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2009. Updated June 8, 2017. Accessed November 27, 2017. Available at www.ncbi.nlm.nih.gov/books/NBK20221/

8. Hershfield M: Adenosine deaminase deficiency. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2006. Updated March 16, 2017. Accessed November 27, 2017. Available at www.ncbi.nlm.nih.gov/books/NBK1483/

9. Allenspach E, Rawlings DJ, Scharenberg AM: X-linked severe combined immunodeficiency. In: Pagon RA, Adam MP, Ardinger HH, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2003. Updated April 14, 2016. Accessed November 27, 2017. Available at www.ncbi.nlm.nih.gov/books/NBK1410/

10. Crequer A, Picard C, Patin E, et al: Inherited MST1 deficiency underlies susceptibility to EV-HPV infections. PLoS One. 2012;7(8):e44010

11. Kwan A, Abraham RS, Currier R, et al: Newborn screening for severe combined immunodeficiency in 11 screening programs in the United States. JAMA. 2014 Aug 20;312(7):729-738. doi: 10.1001/jama.2014.9132

• Informed Consent for Genetic Testing
• Primary Immunodeficiencies Patient Information
• Informed Consent for Genetic Testing (Spanish)

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 is performed in select regions including CORO1A (exon 11), IKBKG (exons 3-10), and STAT5B (exons 6-8). Additional 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: ADA(ADA1), ADA2 (CECR1), AK2, ATM, CD247(CD3Z), CD27, CD3D, CD3E, CD3G, CD8A, CHD7, CIITA, CORO1A, CTPS1, DCLRE1C(ARTEMIS), FOXN1, GATA2, IKBKB, IKBKG(NEMO), IL21, IL21R, IL2RG, IL7R, ITK, JAK3, LCK, LIG4, MAGT1, MALT1, MTHFD1, NFKBIA(IKBA), NHEJ1, ORAI1, PNP, PRKDC, PTPRC(CD45), RAC2, RAG1, RAG2, RBM8A, RFX5, RFXANK, RFXAP, RHOH, RMRP, SEMA3E, SH2D1A, SLC46A1, STAT5B, STIM1, STK4, TAP1, TAP2, TAPBP, TAZ, TBX1, TNFRSF4(OX40), TRAC, TTC7A, WAS, WIPF1, XIAP(BIRC4), ZAP70

Monday

• 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.

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.

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