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Test Code VIRID Viral Susceptibility, Defects in Intrinsic and Innate Immunity, Gene Panel, Varies


Ordering Guidance


For patients with Epstein-Barr virus (EBV) susceptibility or a heritable predisposition to lymphoproliferative diseases, see EBLPD / Epstein-Barr Virus (EBV) Susceptibility and Lymphoproliferative Disorders Gene Panel, Varies.

 

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, please 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 testing option, call 800-533-1710.



Shipping Instructions


 



Specimen Required


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

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

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

3. Whole blood collected postnatal from an umbilical cord is also acceptable. See Additional Information

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 are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

3. For postnatal umbilical cord whole blood specimens, maternal cell contamination studies are recommended to ensure test results reflect that of the patient tested. A maternal blood specimen is required to complete maternal cell contamination studies. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on both the cord blood and maternal blood specimens under separate order numbers.

 

Specimen Type: Saliva

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

Supplies:

DNA Saliva Kit High Yield (T1007)

Saliva Swab Collection Kit (T786)

Container/Tube:

Preferred: High-yield DNA saliva kit

Acceptable: Saliva swab

Specimen Volume: 1 Tube if using T1007 or 2 swabs if using T786

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.

 

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. Due to lower quantity/quality of DNA yielded from blood spots, 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.

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: 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 or Molecular Testing. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Cultured fibroblasts

Source: Skin or tissue

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured fibroblast cells from a biopsy. 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 or Molecular Testing. 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, 2mL with skirted conical base

Acceptable: Matrix tube, 1mL

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.


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. Molecular Genetics: Congenital Inherited Diseases Patient Information (T521)

3. Viral Susceptibility, Lymphoproliferation, and Hemophagocytic Lymphohistiocytosis Patient Information

Useful For

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of an inborn error of immunity causing a hereditary form of severe viral susceptibility

 

Establishing a diagnosis of hereditary form of viral susceptibility, allowing for appropriate management and surveillance for disease features based on the gene and/or variant involved

 

Identifying variants within genes known to be associated with a hereditary form of viral susceptibility, allowing for predictive testing of at-risk family members

Genetics Test Information

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 30 genes associated with a hereditary form of viral susceptibility: CARMIL2, CD27, CD70, CIB1, CTPS1, CXCR4, DBR1, IFIH1, IFNAR1, IFNAR2, IRF3, IRF7, IRF9, MAGT1, POLR3A, POLR3C, PRKCD, RASGRP1, SH2D1A, STAT1, STAT2, TLR3, TLR7, TLR8, TMC6, TMC8, TNFRSF9, TRAF3, UNC93B1, and XIAP. See Targeted Genes and Methodology Details for Viral Susceptibility, Defects in Intrinsic and Innate Immunity, 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 a hereditary form of viral susceptibility.

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
CULFB Fibroblast Culture for Genetic Test Yes No
MATCC Maternal Cell Contamination, B Yes No

Testing Algorithm

Skin biopsy or cultured fibroblast specimens:

For skin biopsy or cultured fibroblast specimens, a 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

Sequence Capture and Targeted Next-Generation Sequencing (NGS)

Reporting Name

Viral Susceptibility Gene Panel

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies

Reject Due To

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

Clinical Information

Viral infections are common in otherwise healthy individuals, but they may also present clinically due to a primary (genetic) immunodeficiency (ie, inborn error of immunity: IEI). Alternatively, secondary immunodeficiencies may have a similar presentation but result from immunosuppressive medication or illness, such as HIV infection.(1) IEIs may cause a susceptibility to an entire group of pathogens (bacteria, fungi, or viruses), a subset of pathogens (eg, RNA viruses), or can cause susceptibility specific to a single pathogen (eg, Epstein-Barr virus [EBV], human papillomavirus [HPV]). IEIs may also lead to a more severe presentation, including fatal infection caused by a pathogen that usually causes only mild or non-fatal disease (eg, influenza).(2) This panel targets IEIs that lead to susceptibility to viruses or to a subset of viruses, severe viral pneumonia, or a specific virus. Examples of infections where this gene panel is useful include EBV, skin-tropic beta-HPV, influenza, and SARS-CoV-2. IEIs that lead to systemic immune deficiencies and susceptibility to a large variety of pathogens (eg, T-cell deficiencies) are not included in this panel.

 

Epstein-Barr virus is the cause of infectious mononucleosis and persists asymptomatically for life in nearly all adults. It is also associated with the development of T- and B-cell lymphomas, nasopharyngeal and gastric carcinomas, and other malignancies. EBV infection in IEIs can present with fulminant infectious mononucleosis, hemophagocytosis, B-cell proliferative disease (including lymphoma), and hypogammaglobulinemia.(3)

 

Beta-HPVs circulate silently in the general population and cause no visible lesions in most people. Genetic susceptibility to beta-HPVs leads to warts, pityriasis-like lesions, epidermodysplasia verruciformis, and increased risk of non-melanoma skin cancers.(4)

 

Seasonal influenza viruses are common RNA viruses that infect the respiratory tract, causing a benign illness in most infected individuals. Influenza pneumonia or acute respiratory distress syndrome are rare, and the case fatality ratio is less than 1%.(1) Children with severe influenza have been found to carry defects in IRF7, IRF9, STAT1, STAT2, and TLR3.(2) Similarly, the COVID-19 pandemic has revealed that SARS-CoV-2 infection can lead to asymptomatic infection as well as fatal pneumonia. Genetic studies showed that approximately 2 to 3% of cases of severe life-threatening SARS-CoV-2 infection resulted from IEI, mainly genetic defects in the TLR3- or TLR7-dependent type 1 interferon pathway (eg, TLR3, TLR7, IFNAR1/2, STAT2, and IRF7), overlapping with that of severe pneumonia susceptibility in influenza infections.(5)

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(6) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Day(s) Performed

Varies

Report Available

28 to 42 days

Specimen Retention Time

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

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

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

81443

88233-Tissue culture, skin, solid tissue biopsy (if appropriate)

88240-Cryopreservation (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
VIRID Viral Susceptibility Gene Panel 103742-3

 

Result ID Test Result Name Result LOINC Value
619901 Test Description 62364-5
619902 Specimen 31208-2
619903 Source 31208-2
619904 Result Summary 50397-9
619905 Result 82939-0
619906 Interpretation 69047-9
619907 Additional Results 82939-0
619908 Resources 99622-3
619909 Additional Information 48767-8
619910 Method 85069-3
619911 Genes Analyzed 82939-0
619912 Disclaimer 62364-5
619913 Released By 18771-6