Test Catalog

Test Id : COMID

Combined Humoral and Cell-Mediated Immunodeficiency 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 a hereditary combined humoral and cell-mediated immunodeficiency (CID)

 

Establishing a diagnosis of a combined immunodeficiency associated with known causal genes

 

Identifying variants within genes known to be associated with inherited CID, allowing for predictive testing of at-risk family members and/or determination of targeted management (anticipatory guidance, management changes, specific therapies)

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 117 genes associated with hereditary combined immunodeficiency: ADA, AK2, ARPC1B, ATM, BCL10, BCL11B, BLM, CARD11, CD247, CD28, CD3D, CD3E, CD3G, CD40, CD40LG, CD70, CD8A, CDCA7, CHD7, CIITA, CORO1A, CTLA4, DCLRE1C, DNMT3B, DOCK2, DOCK8, EPG5, ERCC6L2, EXTL3, FCHO1, FOXN1, GINS1, HELLS, ICOS, ICOSLG, IKBKB, IKBKG, IKZF1, IL21, IL21R, IL2RA, IL2RB, IL2RG, IL7R, ITK, ITPKB, JAK3, KDM6A, KMT2A, KMT2D, LAT, LCK, LCP2, LIG1, LIG4, LRBA, MAGT1, MALT1, MAP3K14, MCM10, MSN, MTHFD1, MYSM1, NBN, NFKBIA, NHEJ1, NSMCE3, ORAI1, PAX1, PGM3, PNP, POLD1, POLE, POLE2, PRKDC, PSMB9, PTPRC, RAC2, RAG1, RAG2, RASGRP1, RBCK1, REL, RELA, RELB, RFX5, RFXANK, RFXAP, RHOH, RMRP (NME1), RNF168, RNF31, RNU4ATAC, SEC61A1, SEMA3E, SH2D1A, SKIV2L (SKIC2), SMARCAL1, SP110, STAT3, STAT5B, STIM1, STK4, TAP1, TAP2, TAPBP, TAZ (TAFAZZIN), TBX1, TFRC, TNFRSF4, TRAC, TTC37 (SKIC3), TTC7A, WAS, WIPF1, ZAP70, and ZBTB24. See Targeted Genes and Methodology Details for Combined Humoral and Cell-Mediated Immunodeficiency Gene Panel and Method Description for additional details.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, recurrence risk assessment, familial screening, and genetic counseling for hereditary combined immunodeficiency.

Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial tests.

Test Id Reporting Name Available Separately Always Performed
CULAF Amniotic Fluid Culture/Genetic Test Yes No
_STR1 Comp Analysis using STR (Bill only) No, (Bill only) No
_STR2 Add'l comp analysis w/STR (Bill Only) No, (Bill only) No
CULFB Fibroblast Culture for Genetic Test Yes No
MATCC Maternal Cell Contamination, B Yes No

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Skin biopsy:

For skin biopsy or cultured fibroblast specimens, fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

 

Cord blood:

For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.

Method Name
A short description of the method used to perform the test

Sequence Capture and Amplicon-Based Next-Generation Sequencing (NGS), followed by Polymerase Chain Reaction (PCR)/Quantitative Real-Time Polymerase Chain Reaction (qPCR) and Sanger Sequencing as needed

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Combined Immunodeficiency GenePanel

Aliases
Lists additional common names for a test, as an aid in searching

NextGen Sequencing Test

CD3 delta deficiency

CD3 epsilon deficiency

CD3 zeta deficiency

CD3 lambda deficiency

CD40 deficiency

CD40 ligand (CD154) deficiency

CD40L deficiency

CD45 deficiency

CD70 deficiency

CD8 deficiency

Cernunnos/XLF deficiency

CHARGE syndrome

Combined immunodeficiency (CID)

Coronin-1A deficiency

c-Rel deficiency

CTLA4 haploinsufficiency (ALPS-V)

DCLRE1C (Artemis) deficiency

DNA ligase IV deficiency

DOCK2 deficiency

DOCK8 deficiency

Ectodermodysplasia with immunodeficiency (EDA-ID) due to IKBA GOF mutation

EDA-ID due to NEMO/IKBKG deficiency (ectodermal dysplasia, immune deficiency)

EPG5 deficiency (Vici syndrome)

Epidermodysplasia verruciformis

ERCC6L2 (Hebo deficiency)

FCHO1 deficiency

FOXN1 haploinsufficiency

Gamma c deficiency (common gamma chain SCID, CD132 deficiency)

GINS1 deficiency

Hepatic veno-occlusive disease with immunodeficiency (VODI)

HLA class I deficiency

HOIL1 deficiency

HOIP deficiency

Hyper-IgE syndrome

Hyper-IgM syndrome

ICOS deficiency

ICOSL deficiency

IKAROS deficiency

IKBKB deficiency

IL-21 deficiency

IL-21R deficiency

IL2-inducible T-cell kinase deficiency

IL7R alpha deficiency

IL7Ra deficiency

Immunodeficiency

Immunodeficiency with centromeric instability and facial anomalies (ICF types 1, 2, 3, 4)

Immunodeficiency with multiple intestinal atresias

Immunodeficiency, X-linked with magnesium defect, Epstein-Barr virus infection and neoplasia

Immunoskeletal dysplasia with neurodevelopmental abnormalities (EXTL3 deficiency)

ITK deficiency

JAK3 deficiency

Kabuki syndrome 1

Kabuki syndrome 2

KMT2A deficiency (Wiedemann-Steiner syndrome)

LAT deficiency

LCK deficiency

Leaky SCID

LIG4 syndrome

Ligase I deficiency

LRBA deficiency

lymphoproliferative syndrome 1

MALT1 deficiency

Methylene-tetrahydrofolate dehydrogenase 1 (MTHFD1) deficiency

MHC class I deficiency

MHC class II deficiency

MHC class II deficiency group B

MHC class II deficiency group C

MHC class II deficiency group D

Moesin deficiency

MOPD1 deficiency (Roifman syndrome)

MTHFD1 deficiency

MYSM1 deficiency

Nijmegen breakage syndrome

NIK deficiency

NK-cell deficiency

NSMCE3 deficiency

Omenn syndrome

ORAI-1 deficiency

OX40 deficiency

PGM3 deficiency

POLE1 (Polymerase epsilon subunit 1) deficiency (FILS syndrome)

POLE2 (Polymerase epsilon subunit 2) deficiency

Polymerase delta deficiency

Purine nucleoside phosphorylase (PNP) deficiency

Rac2 deficiency

RAG deficiency

RASGRP1 deficiency

RelA haploinsufficiency

RelB deficiency

Reticular dysgenesis

RHOH deficiency

RNF168 deficiency (Radiosensitivity, Immune Deficiency, Dysmorphic features, Learning difficulties [RIDDLE] syndrome)

SAP deficiency (XLP1)

Schimke immuno-osseous dysplasia

SEC61A1 deficiency

Severe combined immunodeficiency

Severe combined immunodeficiency (SCID)

severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive

STAT3 GOF mutation

STAT5b deficiency

STIM1 deficiency

STK4 deficiency

Tapasin deficiency

T-B+ severe combined immunodeficiency due to gamma chain deficiency

T-B+ severe combined immunodeficiency due to JAK3 deficiency

T-B+NK severe combined immunodeficiency

TBX1 deficiency

TCR alpha deficiency

TCRa deficiency

TFRC deficiency

Tricho-Hepato-Enteric Syndrome (THES)

Winged helix nude FOXN1 deficiency

WIP deficiency

Wiskott-Aldrich syndrome

X-linked magnesium EBV and neoplasia (XMEN)

X-linked neutropenia/myelodysplasia

ZAP-70 deficiency

Adenosine deaminase (ADA) deficiency

AD-HIES STAT3 deficiency (Job syndrome)

AK2 defect

Arp2/3-mediated filament branching defect

Ataxia-telangiectasia

Atypical SCID

Autoimmune lymphoproliferative syndrome with autoimmune cytopenias

Bare lymphocyte syndrome

Bare lymphocyte syndrome, complementation group A

Barth Syndrome (3-Methylglutaconic aciduria type II)

BCL10 deficiency

BCL11B deficiency

CARD11 deficiency

CARD11 GOF

Cartilage hair hypoplasia (CHH)

CD122 deficiency

CD247 deficiency

CD25 deficiency

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Skin biopsy:

For skin biopsy or cultured fibroblast specimens, fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

 

Cord blood:

For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

Patients who have had a previous bone marrow transplant from an allogenic donor should not have testing performed on blood, bone marrow, or saliva because any results generated will reflect the genome of the donor rather than the recipient. Testing on patients who have an active hematologic malignancy or hematologic disorder with clonal proliferation may identify both somatic mutations and germline variants, which may result in test failure or necessitate follow-up testing to determine whether the detected variant is germline or somatic. For these patients, testing a skin biopsy or cultured fibroblasts is recommended. For instructions for testing patients who have received a bone marrow transplant or have an active hematologic disorder, call 800-533-1710. For more information see Cautions.

 

Customization of this panel and single gene analysis for any gene present on this panel are available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies. To modify this panel via CGPH, use the Inborn Errors of Immunity/Bone Marrow Failure/Telomeropathy/Pulmonary Fibrosis/Very Early Onset IBD/Pancreatitis disease state for step 1 on the Custom Gene Ordering Tool.

 

Targeted testing for familial variants (also called site-specific or known variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.

Additional Testing Requirements

For cord blood specimens: Maternal cell contamination (MCC) studies are available. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on both the cord blood and maternal specimens under separate order numbers. Cord blood testing will proceed without MCC studies, but results may be compromised if MCC is present.

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
MG148 Is this Bone Marrow Yes
No

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor will interfere with testing. For information about testing patients who have received a hematopoietic stem cell transplant, call 800-533-1710.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Green top (sodium heparin)

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 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

 

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.

Specimen Volume: 4-mm Punch

Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours

Additional Information:

1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.

2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical and Molecular Testing, Tissue. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Cultured fibroblasts

Source: Skin

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured fibroblast cells from a skin biopsy from another laboratory. Cultured cells from a prenatal specimen will not be accepted.

Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours

Additional Information:

1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.

2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical and Molecular Testing, Tissue. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Extracted DNA

Container/Tube:

Preferred: Screw Cap Micro Tube, 2 mL with skirted conical base

Acceptable: Matrix tube, 1 mL

Collection Instructions:

1. The preferred volume is at least 100 mcL at a concentration of 75 ng/mcL.

2. Include concentration and volume on tube.

Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated

Additional Information: DNA must be extracted in a CLIA-certified laboratory, or equivalent, and must be extracted from a specimen type listed as acceptable for this test (including applicable anticoagulants). Our laboratory has experience with Chemagic, Puregene, Autopure, MagnaPure, and EZ1 extraction platforms and cannot guarantee that all extraction methods are compatible with this test. If testing fails, one repeat will be attempted, and if unsuccessful, the test will be reported as failed and a charge will be applied. If applicable, specific gene regions that were unable to be interrogated due to DNA quality will be noted in the report.

 

Specimen Type: Bone marrow aspirate

Container/Tube:

Preferred: Lavender top (EDTA)

Acceptable: Yellow top (ACD)

Specimen Volume: 2 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

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

3. Label specimen as bone marrow.

Specimen Stability: Ambient (preferred) 4 days/Refrigerate 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

 

Specimen Type: Cord blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Green top (sodium heparin)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

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

Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

3. While a properly collected cord blood sample may not be at risk for maternal cell contamination, unanticipated complications may occur during collection. Therefore, maternal cell contamination studies are recommended to ensure the test results reflect that of the patient tested and are available at an additional charge. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen

 

Specimen Type: Blood spot

Supplies: Card-Blood Spot Collection (Filter Paper) (T493)

Container/Tube:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: PerkinElmer 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 is a fingerstick. For detailed instructions, see How to Collect a Dried Blood Spot Sample.

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. Blood spot specimens are acceptable but not recommended. Multiple extractions will be required to obtain sufficient yield for supplemental analysis, and there is significant risk for test failure due to insufficient DNA.

2. Due to lower concentration of DNA yielded from blood spot, it is possible that additional specimen may be required to complete testing.

3. For collection instructions, see Blood Spot Collection Instructions.

4. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777)

5. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800)

 

Specimen Type: Saliva

Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.

Supplies: Saliva Swab Collection Kit (T786)

Specimen Volume: 2 Swabs, use 2 kits for collection

Collection Instructions: Collect and send specimen per kit instructions.

Specimen Stability Information: Ambient (preferred) 30 days, Refrigerated 30 days

Additional Information: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.

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

Forms

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. Combined Immunodeficiency, Severe Combined Immunodeficiency, and B-Cell/Antibody Deficiency Patient Information

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the testing laboratory. The minimum volume is sufficient for one attempt at testing.

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies 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 a hereditary combined humoral and cell-mediated immunodeficiency (CID)

 

Establishing a diagnosis of a combined immunodeficiency associated with known causal genes

 

Identifying variants within genes known to be associated with inherited CID, allowing for predictive testing of at-risk family members and/or determination of targeted management (anticipatory guidance, management changes, specific therapies)

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 117 genes associated with hereditary combined immunodeficiency: ADA, AK2, ARPC1B, ATM, BCL10, BCL11B, BLM, CARD11, CD247, CD28, CD3D, CD3E, CD3G, CD40, CD40LG, CD70, CD8A, CDCA7, CHD7, CIITA, CORO1A, CTLA4, DCLRE1C, DNMT3B, DOCK2, DOCK8, EPG5, ERCC6L2, EXTL3, FCHO1, FOXN1, GINS1, HELLS, ICOS, ICOSLG, IKBKB, IKBKG, IKZF1, IL21, IL21R, IL2RA, IL2RB, IL2RG, IL7R, ITK, ITPKB, JAK3, KDM6A, KMT2A, KMT2D, LAT, LCK, LCP2, LIG1, LIG4, LRBA, MAGT1, MALT1, MAP3K14, MCM10, MSN, MTHFD1, MYSM1, NBN, NFKBIA, NHEJ1, NSMCE3, ORAI1, PAX1, PGM3, PNP, POLD1, POLE, POLE2, PRKDC, PSMB9, PTPRC, RAC2, RAG1, RAG2, RASGRP1, RBCK1, REL, RELA, RELB, RFX5, RFXANK, RFXAP, RHOH, RMRP (NME1), RNF168, RNF31, RNU4ATAC, SEC61A1, SEMA3E, SH2D1A, SKIV2L (SKIC2), SMARCAL1, SP110, STAT3, STAT5B, STIM1, STK4, TAP1, TAP2, TAPBP, TAZ (TAFAZZIN), TBX1, TFRC, TNFRSF4, TRAC, TTC37 (SKIC3), TTC7A, WAS, WIPF1, ZAP70, and ZBTB24. See Targeted Genes and Methodology Details for Combined Humoral and Cell-Mediated Immunodeficiency Gene Panel and Method Description for additional details.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, recurrence risk assessment, familial screening, and genetic counseling for hereditary combined immunodeficiency.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Skin biopsy:

For skin biopsy or cultured fibroblast specimens, fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

 

Cord blood:

For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Combined immunodeficiencies (CIDs) comprise a group of disorders where the deficiency includes both the cellular and humoral component of the adaptive immune response, namely the T and B lymphocytes. As T lymphocyte function is required for most B lymphocyte functions, T-lymphocyte intrinsic genetic defects can lead to a CID. CIDs can be further grouped based on severity and based on presence or absence of syndromic features.

 

Severe combined immunodeficiency (SCID) is the most severe form of CID, where the T-cell deficiency is essentially complete. SCID requires immediate action as it is lethal if left untreated. SCID is now part of the recommended uniform newborn screening panel in the United States. SCID results from defects in the differentiation of hematopoietic stem cells into mature T lymphocytes, with additional lymphoid lineages affected in some forms. The defining feature of SCID is the absence of T cells, and it can be further divided into groups based on the presence or absence of the additional lymphoid (B cell and natural killer [NK] cell) lineages (eg, T-B+, T-B-, T- B- NK-, T-B-NK+). IL2RG deficiency causes X-linked SCID and leads to T-B+NK- SCID. Complete RAG1 and RAG2 deficiencies lead to T-B-NK+ SCID. Reticular dysgenesis (AK2 defect) presents with neutropenia together with lack of lymphocytes (T-B-NK-).

 

When the T-lymphocyte differentiation defect is less profound but still life threatening, the terminology of leaky/atypical SCID is often used. These are either due to hypomorphic disease-causing variants in the same genes responsible for typical SCID ("leaky SCID") or due to unidentified defects ("atypical SCID"). Omenn syndrome is a form of leaky SCID characterized by expanded oligoclonal memory T cells that infiltrate the skin and other tissues and produce a generalized erythematous rash. Defects in RAG1, RAG2, ADA, and RMRP genes are the most common cause of leaky SCID.

 

Less severe CIDs include many gene defects affecting T- and B-lymphocyte development or function. These defects are highly variable and extend from severe defects in cell counts to normal T- and B-lymphocyte counts but abnormal function. Major histocompatibility complex (MHC) class I deficiency (caused by TAP1, TAP2, TAPBP, B2M gene defects) lead low CD8 T-cell counts, whereas MHC class II defects (caused by CIITA, RFXANK, RFX5, RFXAP gene defects) lead to low CD4 T-cell counts. MALT1 deficiency presents with normal T- and B-cell counts but still leads to bacterial, fungal and viral infections. Similarly, calcium channel defects (ORAI1, STIM1, CRACR2A) lead to decreased T-cell activity with largely normal T-cell counts.

 

Ataxia-telangiectasia (ATM gene) presents with a progressive decrease in T-lymphocyte counts, poor proliferation to mitogens, normal B-cell counts, but often low IgA and IgE, in addition to ataxia, telangiectasia of sclerae, infections, and malignancies. Nijmegen breakage syndrome (due to variants in the NBS1 gene, also known as NBN) also shows a progressive decrease in T-lymphocyte counts with a decrease in B lymphocytes and immunoglobulins, as well as increased radiosensitivity and chromosomal instability, microcephaly, dysmorphic facies and malignancies. Hyper-IgE syndromes (eg, dominant negative STAT3 defects or autosomal recessive IL6ST defect can lead to normal T-cell counts, decrease in Th17 T cells, normal total B-cell counts with a decrease in switched memory B cells, and high IgE levels. Anhidrotic ectodermal dysplasia with immunodeficiency (EDAID1) can be caused by defects in IKBKG and NFKBIA. The T- and B-cell counts can be normal or low, but their function is decreased leading to decreased T-cell receptor (TCR) activation and decreased immunoglobulin production. Associated features include variable defects of skin, hair, and teeth.

 

Defects in thymus development can present essentially the same as SCID or CID, as T-cell maturation takes place in the thymus. However, thymic defects must be differentiated from SCID as the treatments are different. Hematopoietic stem cell (bone marrow) transplantation can correct SCID but not thymic stromal differentiation defects. Thymic transplant can correct developmental defects in the thymus but not in the hematopoietic stem cells. Biallelic FOXN1 deficiency leads to abnormal thymic epithelium, significantly decreased T-cell counts with congenital alopecia, and nail dystrophy. Heterozygous FOXN1 haploinsufficiency can also present with severe T-cell deficiency at birth but that mostly normalizes by adulthood. DiGeorge syndrome or velocardio-facial syndrome is caused by 22q11.2 deletions. 22q11.2 deletion syndrome may present from normal to significantly decreased T-cell counts in addition to hypoparathyroidism, cardiac malformations, abnormal facies, and intellectual disability. Autosomal dominant TBX1 deficiency is thought to be the cause of the main features in 22q11.2 deletion syndrome. CHARGE (coloboma of eye; heart anomaly; choanal atresia; restricted growth and development, genital and ear anomalies, intellectual disability; central nervous system malformation) syndrome can also present SCID-like with T-cell deficiency (autosomal dominant CHD7 and SENA3E defects).

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

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(1) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Clinical Correlations:

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.

 

To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact Mayo Clinic Laboratories genetic counselors at 800-533-1710.

 

Technical Limitations:

Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.

 

This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.

 

Deletion/Duplication Analysis:

This analysis targets single and multi-exon deletions/duplications; however, in some instances single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.

 

This test is not designed to detect low levels of mosaicism or to differentiate between somatic mutations and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.

 

Genes may be added or removed based on updated clinical relevance. For the most up to date list of genes included in this test and for detailed information regarding gene-specific performance and technical limitations, see Method Description or contact a laboratory genetic counselor.

 

If the patient has had an allogeneic hematopoietic stem cell transplant or a recent non-leukocyte reduced blood transfusion, results of tests performed on blood, bone marrow, or saliva specimens may be clinically inaccurate due to the presence of donor DNA. Test orders for blood, bone marrow, or saliva will be canceled by the laboratory if there is a history of an allogeneic hematopoietic stem cell transplant. Similarly, blood, bone marrow, and saliva results may be impacted by presence of active hematologic malignancy or hematologic disorder with clonal proliferation. Call Mayo Clinic Laboratories for instructions for testing a skin biopsy or fibroblast culture for patients who have received a bone marrow transplant or have an active hematologic disorder.

 

Reclassification of Variants:

Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages healthcare professionals to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time. Due to broadening genetic knowledge, it is possible that the laboratory may discover new information of relevance to the patient. Should that occur, the laboratory may issue an amended report.

 

Variant Evaluation:

Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline.(1) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.

 

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 periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.

 

Rarely, incidental or secondary findings may implicate another predisposition or presence of active disease. These findings will be carefully reviewed to determine whether they will be reported.

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

1. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-424

2. Tangye SG, Al-Herz W, Bousfiha A, et al. Human Inborn Errors of Immunity: 2022 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol. 2022;42(7):1473-1507. doi:10.1007/s10875-022-01289-3

3. Bousfiha A, Moundir A, Tangye SG, et al. The 2022 Update of IUIS Phenotypical Classification for Human Inborn Errors of Immunity. J Clin Immunol. 2022;42(7):1508-1520. doi:10.1007/s10875-022-01352-z

4. Bosticardo M, Yamazaki Y, Cowan J, et al. Heterozygous FOXN1 variants cause low TRECs and severe T cell lymphopenia, revealing a crucial role of FOXN1 in supporting early thymopoiesis. Am J Hum Genet. 2019;105(3):549-561. doi:10.1016/j.ajhg.2019.07.014

5. Dvorak CC, Haddad E, Heimall J, et al. The diagnosis of severe combined immunodeficiency (SCID): The Primary Immune Deficiency Treatment Consortium (PIDTC) 2022 Definitions. J Allergy Clin Immunol. 2023;151(2):539-546. doi:10.1016/j.jaci.2022.10.022

6. Yagi H, Furutani Y, Hamada H, et al. Role of TBX1 in human del22q11.2 syndrome. Lancet. 2003;362(9393):1366-1373. doi:10.1016/s0140-6736(03)14632-6

7. Verhagen JM, Diderich KE, Oudesluijs G, et al. Phenotypic variability of atypical 22q11.2 deletions not including TBX1. Am J Med Genet A. 2012;158A(10):2412-2420. doi:10.1002/ajmg.a.35517

Method Description
Describes how the test is performed and provides a method-specific reference

Next-generation sequencing (NGS) and/or Sanger sequencing is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions/insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. A supplemental PCR-based method is used to detect a large deletion in IKBKG.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. See Targeted Genes and Methodology Details for Combined Humoral and Cell-Mediated Immunodeficiency Gene Panel for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.(Unpublished Mayo method)

 

Genes analyzed: ADA, AK2, ARPC1B, ATM, BCL10, BCL11B, BLM, CARD11, CD247, CD28, CD3D, CD3E, CD3G, CD40, CD40LG, CD70, CD8A, CDCA7, CHD7, CIITA, CORO1A, CTLA4, DCLRE1C, DNMT3B, DOCK2, DOCK8, EPG5, ERCC6L2, EXTL3, FCHO1, FOXN1, GINS1, HELLS, ICOS, ICOSLG, IKBKB, IKBKG, IKZF1, IL21, IL21R, IL2RA, IL2RB, IL2RG, IL7R, ITK, ITPKB, JAK3, KDM6A, KMT2A, KMT2D, LAT, LCK, LCP2, LIG1, LIG4, LRBA, MAGT1, MALT1, MAP3K14, MCM10, MSN, MTHFD1, MYSM1, NBN, NFKBIA, NHEJ1, NSMCE3, ORAI1, PAX1, PGM3, PNP, POLD1, POLE, POLE2, PRKDC, PSMB9, PTPRC, RAC2, RAG1, RAG2, RASGRP1, RBCK1, REL, RELA, RELB, RFX5, RFXANK, RFXAP, RHOH, RMRP (NME1), RNF168, RNF31, RNU4ATAC, SEC61A1, SEMA3E, SH2D1A, SKIV2L (SKIC2), SMARCAL1, SP110, STAT3, STAT5B, STIM1, STK4, TAP1, TAP2, TAPBP, TAZ (TAFAZZIN), TBX1, TFRC, TNFRSF4, TRAC, TTC37 (SKIC3), TTC7A, WAS, WIPF1, ZAP70, and ZBTB24

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

Supplemental

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Varies

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

28 to 42 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Whole blood: 28 days (if available); Saliva: 30 days (if available); Extracted DNA: 3 months; Blood spots: 1 year (if available)

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Mayo Clinic Laboratories - Rochester Main Campus
CLIA Number: 24D0404292

Fees :
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

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  • Prospective clients should contact their account representative. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81443

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
COMID Combined Immunodeficiency GenePanel In Process
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
621534 Test Description 62364-5
621535 Specimen 31208-2
621536 Source 31208-2
621537 Result Summary 50397-9
621538 Result 82939-0
621539 Interpretation 69047-9
621540 Additional Results 82939-0
621541 Resources 99622-3
621542 Additional Information 48767-8
621543 Method 85069-3
621544 Genes Analyzed 82939-0
621545 Disclaimer 62364-5
621546 Released By 18771-6
MG148 Is this Bone Marrow 31208-2

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports

Test Update Resources

Change Type Effective Date
New Test 2025-07-08