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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

620092

Useful 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.

Method Name

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

Specimen Type

Varies

Specimen 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.

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

Report Available

28 to 42 days

Specimen Retention Time

Whole blood: 2 weeks (if available); Extracted DNA: 3 months; Cultured fibroblasts, skin biopsy: 1 month

Performing Laboratory

Mayo Clinic Laboratories in Rochester

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