Test Code AUTOG Autoinflammatory Disorders Gene Panel, Varies
Ordering Guidance
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.
Shipping Instructions
Specimen preferred to arrive within 96 hours of collection.
Specimen Required
Patient Preparation: A previous bone marrow transplant from an allogenic donor 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:
Specimen Type: Whole blood
Container/Tube:
Preferred: Lavender top (EDTA) or yellow top (ACD)
Acceptable: Any anticoagulant
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
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: 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: Cultured fibroblasts
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)/Refrigerated (<24 hours)
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.
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. Inborn Errors of Immunity, Autoimmunity and Autoinflammatory Disease Patient Information
Secondary ID
620092Useful For
Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of an inherited autoinflammatory disorder
Establishing a diagnosis of a monogenic autoinflammatory disorder, allowing for appropriate management and surveillance for disease features based on the gene or variant involved
Identifying variants within genes known to be associated with monogenic autoinflammatory disorders, allowing for predictive testing of at-risk family members
Reflex Tests
Test ID | Reporting Name | Available Separately | Always Performed |
---|---|---|---|
CULFB | Fibroblast Culture for Genetic Test | Yes | No |
Testing Algorithm
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.
Special Instructions
Method Name
Sequence Capture and Amplicon-Based Next-Generation Sequencing (NGS)/Quantitative Real-Time Polymerase Chain Reaction (qPCR) and Sanger Sequencing as needed.
Reporting Name
Autoinflammatory Gene PanelSpecimen Type
VariesSpecimen Minimum Volume
Blood: 1 mL; Skin biopsy or cultured fibroblasts: See Specimen Required
Specimen Stability Information
Specimen Type | Temperature | Time | Special Container |
---|---|---|---|
Varies | Varies |
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.Clinical Information
Systemic autoinflammatory disorders result from dysregulation of the innate immune system and are characterized by a hyperinflammatory state with elevated acute phase reactants. These disorders may present at any age, but symptoms often begin in childhood with unexplained fever that may be accompanied by a rash. While these features can mimic infections or hematological neoplasias, the inflammatory lesions are noncancerous and sterile. Additional features may be present and highly variable, depending on the organ or organs impacted by cytokine amplification loops and sterile inflammation. Symptoms may involve the gastrointestinal (GI) tract (eg, serositis, abdominal pain, early-onset inflammatory bowel disease), bone, eyes (eg, uveitis), musculoskeletal system (eg, arthritis and arthralgias), central nervous system (eg, meningitis), or other tissues. Some autoinflammatory disorders are also associated with an increased risk of developing AA amyloidosis. These disorders include familial Mediterranean fever (FMF), tumor necrosis factor receptor-associated periodic syndrome (TRAPS), cryopyrin-associated autoinflammatory syndrome (CAPS), and hyper-IgD syndrome/mevalonate kinase deficiency (HIDS/MKD).
Autoinflammatory disorders are classified by molecular pathogenesis or clinical features. Pathophysiologic classification is based on the pathway or cytokine that drives disease, such as interleukin (IL)-1, interferon, nuclear factor kappa B, and IL-18. Disease classification based on clinical features often focuses on skin involvement or fever duration and frequency. Age of onset, triggers, and additional organ system involvement are also used to classify these disorders and aid clinical diagnosis.
The genetic basis of many heritable autoinflammatory disorders has been identified. Autoinflammatory disorders may be inherited in an autosomal recessive, autosomal dominant, or X-linked manner. Disease-causing variants may also arise de novo. The inheritance pattern appears more complicated for some disorders. For example, FMF is typically inherited in an autosomal recessive manner. However, some affected individuals appear to have only one disease-causing alteration. For other autoinflammatory disorders, cases of digenic and oligogenic inheritance have also been described. Inheritance may also be multifactorial, requiring an environmental component along with low-penetrance variants. One example is Yao syndrome, a recently described clinical entity characterized by recurrent fever, dermatitis, inflammatory arthritis, and GI symptoms in most affected individuals. While some variants in NOD2 have been reported in association with Yao syndrome, they are relatively common among the general population. They may confer an increased risk for developing Yao syndrome but are not diagnostic and appear insufficient to cause disease by themselves. Some disorders such as PFAPA (periodic fever, aphthous stomatitis, pharyngitis, adenitis) syndrome, systemic juvenile idiopathic arthritis, adult-onset Still disease, and Behcet disease have significant phenotypic overlap with monogenic autoinflammatory conditions, but a genetic cause of these disorders has not been identified.
Finally, several examples of post-zygotic (mosaic or somatic) genetic alterations causing autoinflammatory disorders have been described. While it may be possible to identify mosaic variants, this test is primarily intended for the identification of germline variants and the diagnosis of inherited monogenic autoinflammatory disorders.
Determining the underlying genetic cause of an autoinflammatory condition may help guide treatment decisions. For example, colchicine is an effective therapy for many patients with FMF, but some patients may not respond. Instead, these individuals, and others affected by a subset of autoinflammatory disorders, may respond to IL-1 blocking therapies. Anakinra, rilonacept, and canakinumab are several examples of medications that target IL-1. However, another subset of autoinflammatory disorders is not responsive to IL-1 blockade, such as proteasome-associated autoinflammatory syndromes (PRAAS), CANDLE (chronic atypical neutrophilic dermatosis with lipodystrophy), deficiency of IL-36 receptor antagonist, and CAMPS (CARD14-mediated psoriasis). Medications that target other components of the IL-1 pathway are under development. In addition, medications that target other pathways (eg, anti-tumor necrosis factor, anti-IL-6, and JAK-inhibitors) have demonstrated efficacy in some patients.
Reference Values
An interpretive report will be provided.
Interpretation
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.
Method Description
Next-generation sequencing (NGS) and/or Sanger sequencing are 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), and above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.
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 Autoinflammatory Disorders Gene Panel for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method)
Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.
Genes analyzed:
ACP5, ADA, ADA2, ADAM17, ADAR, AIRE, ALPI, AP3B1, AP3D1, ARPC1B, ASAH1, C1QA, C1QB, C1QC, C1R, C1S, C2, CARD11, CARD14, CASP10, CASP8, CD3G, CD40LG, CD48, CD55, CDC42, COPA, CTLA4, DDX58, DNASE1, DNASE1L3, DNASE2, DOCK8, FADD, FOXP3, GATA2, HAVCR2, ICOS, IFIH1, IKBKG, IL10, IL10RA, IL10RB, IL1RN, IL2RA, IL2RB, IL2RG, IL36RN, ISG15, ITCH, ITGB2, ITK, JAK1, LACC1, LIG4, LPIN2, LRBA, LSM11, LYN, LYST, MEFV, MVK, NLRC4, NLRP1, NLRP12, NLRP3, NOD2, OAS1, OTULIN, PIK3CD, PIK3R1, PLCG2, POLA1, POMP, PRF1, PRKCD, PSMA3, PSMB10, PSMB4, PSMB8, PSMB9, PSMG2, PSTPIP1, RAB27A, RBCK1, RIPK1, RNASEH2A, RNASEH2B, RNASEH2C, RNF31, RNU7-1, SAMD9L, SAMHD1, SH2D1A, SH3BP2, SKIV2L, SLC29A3, SLC37A4, STAT1, STAT2, STAT3, STIM1, STING1, STX11, STXBP2, TLR7, TNFAIP3, TNFRSF1A, TPP2, TREX1, TRNT1, UNC13D, USP18, WAS, WDR1, XIAP, and ZAP70
Day(s) Performed
Varies
Performing Laboratory
Mayo Clinic Laboratories in RochesterTest 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 |
---|---|---|
AUTOG | Autoinflammatory Gene Panel | In Process |
Result ID | Test Result Name | Result LOINC Value |
---|---|---|
620093 | Test Description | 62364-5 |
620094 | Specimen | 31208-2 |
620095 | Source | 31208-2 |
620096 | Result Summary | 50397-9 |
620097 | Result | 82939-0 |
620098 | Interpretation | 69047-9 |
620099 | Additional Results | 82939-0 |
620100 | Resources | 99622-3 |
620101 | Additional Information | 48767-8 |
620102 | Method | 85069-3 |
620103 | Genes Analyzed | 82939-0 |
620104 | Disclaimer | 62364-5 |
620105 | Released By | 18771-6 |