Order Code LABGOR, EOIBD Early Onset Monogenic Inflammatory Bowel Disease (IBD) Gene Panel, Varies

Additional Codes

Mayo Test Code:EOIBD

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)

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 in:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

2. Early Onset Inflammatory Bowel Disease Patient Information

3. If not ordering electronically, complete, print, and send a Gastroenterology and Hepatology Test Request (T728) with the specimen.

Useful For

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of an inherited inflammatory bowel disorder

Establishing a diagnosis of a monogenic early onset inflammatory bowel disease, 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 monogenic early onset inflammatory bowel disease, 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 107 genes associated with monogenic early onset inflammatory bowel disease: ADA, ADAM17, AICDA, AIRE, ALPI, ANKZF1, ARPC1B, ASAH1, BACH2, BTK, CARMIL2, CASP8, CD3G, CD40LG, CD55, COL7A1, CTLA4, CYBA, CYBB, CYBC1, DCLRE1C, DEF6, DGAT1, DKC1, DOCK8, DUOX2, EPCAM, FCHO1, FERMT1, FOXP3, G6PC(G6PC1), G6PC3, GUCY2C, HPS1, HPS3, HPS4, HPS6, ICOS, IFIH1, IKBKG, IL10, IL10RA, IL10RB, IL21, IL21R, IL2RA, IL2RB, IL2RG, IL7R, ITCH, ITGB2, JAK1, LCT, LIG4, LRBA, MALT1, MEFV, MVK, MYO5B, NCF2, NCF4, NEUROG3, NFKBIA, NLRC4, PAX1, PCSK1, PIK3CD, PIK3R1, PLCG2, PLVAP, POLA1, RAG1, RAG2, RIPK1, RTEL1, SH2D1A, SI, SKIV2L, SLC10A2, SLC26A3, SLC37A4, SLC39A4, SLC51B, SLC5A1, SLC9A3, SPINT2, STAT1, STAT3, STAT5B, STIM1, STX3, STXBP2, TGFB1, TGFBR1, TGFBR2, TLR3, TNFAIP3, TRIM22, TRNT1, TTC37, TTC7A, UNC45A, WAS, WIPF1, XIAP, ZAP70, and ZBTB24. See Targeted Genes and Methodology Details for Early Onset Monogenic Inflammatory Bowel Disease (IBD) Gene Panel for details regarding the targeted gene regions evaluated by this test.

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, recurrence risk assessment, familial screening, and genetic counseling for monogenic early onset inflammatory bowel disease.

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.

For more information see Inflammatory Bowel Disease Diagnostic Testing Algorithm.

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

Early Onset IBD Gene Panel

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.

Method Description

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-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 Early Onset Monogenic Inflammatory Bowel Disease (IBD) Gene Panel for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method) (Unpublished Mayo method)

Genes analyzed: ADA, ADAM17, AICDA, AIRE, ALPI, ANKZF1, ARPC1B, ASAH1, BACH2, BTK, CARMIL2, CASP8, CD3G, CD40LG, CD55, COL7A1, CTLA4, CYBA, CYBB, CYBC1, DCLRE1C, DEF6, DGAT1, DKC1, DOCK8, DUOX2, EPCAM, FCHO1, FERMT1, FOXP3, G6PC(G6PC1), G6PC3, GUCY2C, HPS1, HPS3, HPS4, HPS6, ICOS, IFIH1, IKBKG, IL10, IL10RA, IL10RB, IL21, IL21R, IL2RA, IL2RB, IL2RG, IL7R, ITCH, ITGB2, JAK1, LCT, LIG4, LRBA, MALT1, MEFV, MVK, MYO5B, NCF2, NCF4, NEUROG3, NFKBIA, NLRC4, PAX1, PCSK1, PIK3CD, PIK3R1, PLCG2, PLVAP, POLA1, RAG1, RAG2, RIPK1, RTEL1, SH2D1A, SI, SKIV2L, SLC10A2, SLC26A3, SLC37A4, SLC39A4, SLC51B, SLC5A1, SLC9A3, SPINT2, STAT1, STAT3, STAT5B, STIM1, STX3, STXBP2, TGFB1, TGFBR1, TGFBR2, TLR3, TNFAIP3, TRIM22, TRNT1, TTC37, TTC7A, UNC45A, WAS, WIPF1, XIAP, ZAP70, and ZBTB24

Day(s) Performed