Test Code EOIBD Early Onset Monogenic Inflammatory Bowel Disease (IBD) 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 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.
Secondary ID
620120Useful 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
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
- Informed Consent for Genetic Testing
- Informed Consent for Genetic Testing (Spanish)
- Early Onset Inflammatory Bowel Disease Patient Information
- Targeted Genes and Methodology Details for Early Onset Monogenic Inflammatory Bowel Disease (IBD) Gene Panel
- Inflammatory Bowel Disease Diagnostic Testing Algorithm
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 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
Inflammatory bowel disease (IBD) is a term encompassing numerous disorders featuring chronic intestinal inflammation. These conditions are typically classified as either Crohn disease or ulcerative colitis based on clinical features, colonoscopy findings, histologic changes, and the anatomical distribution of disease. However, some cases are not readily classified or may have overlapping features and are classified as IBD-unspecified (IBD-U). The incidence of IBD has rapidly increased in children and adults over the past few decades. Common symptoms include diarrhea, abdominal pain, fatigue, and failure to thrive or unintentional weight loss.
IBD is caused by a combination of dysregulated immune response, microbial dysbiosis, and environmental triggers and occurs in individuals with genetic susceptibility. Most IBD is thought to be either polygenic or multifactorial. However, in rare cases, IBD or IBD-like intestinal inflammation can be attributed to disease-causing variants in a single gene (ie, monogenic inheritance) that result in a highly penetrant condition that presents early in life. Many monogenic forms of IBD are disorders of immune deficiency or dysregulation. Genes associated with IBD continue to be identified with advances in sequencing technology. However, 70% to 80% of patients have IBD without a known genetic etiology.
While the peak age of onset of IBD is between the ages of 20 and 40 years, the incidence of IBD in pediatric patients is increasing. When IBD presents in children younger than 6 years old, it is described as very early onset IBD (VEO-IBD). IBD that presents in children younger than 2 years old is described as infantile-onset IBD. VEO-IBD differs from IBD in older patients in that it is more likely to be IBD-U and have a monogenic cause, particularly among those with infantile-onset IBD.
Conditions associated with VEO-IBD can be grouped into the following broad, sometimes overlapping categories: disorders of general immune dysregulation (eg,. IL-10 signaling defects, IPEX syndrome, STAT3 gain-of-function); T- and B-cell defects (eg,. LRBA deficiency, CTLA4 deficiency, Wiskott Aldrich syndrome, severe combined immunodeficiency [SCID]/Omenn syndrome); phagocytic defects (eg,. chronic granulomatous disease); hyper- or auto-inflammatory disorders (eg,. familial Mediterranean fever, familial hemophagocytic lymphohistiocytosis); epithelial barrier dysfunction (eg, TTC7A deficiency, nuclear factor kappa B essential modulator [NEMO] deficiency); and syndromic conditions (eg, trichohepatoenteric syndrome, CHAPLE [CD55 deficiency with hyper-activation of complement, angiopathic thrombosis, and severe protein-losing enteropathy] syndrome).
Previous reports indicate patients with a monogenic form of IBD may not respond as well to conventional treatment modalities. Identification of the genetic cause of disease in these individuals is important as it may change their treatment plan. Depending on the genetic cause, targeted therapies or allogeneic hematopoietic stem cell transplantation may be beneficial. Therefore, early diagnosis and identification of the specific underlying genetic alteration is important in order to inform treatment, such as medical therapy, surgery, and stem cell transplant and to reduce the high morbidity and mortality associated with these conditions.
Individuals with polygenic or monogenic IBD may have other family members affected with IBD. A family history of IBD is more common among those with VEO-IBD. If a monogenic cause is identified in an individual, family members may be tested for the genetic variant to assess their risk of developing IBD or to guide therapy for those who are affected.
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 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
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 |
---|---|---|
EOIBD | Early Onset IBD Gene Panel | 105196-0 |
Result ID | Test Result Name | Result LOINC Value |
---|---|---|
620121 | Test Description | 62364-5 |
620122 | Specimen | 31208-2 |
620123 | Source | 31208-2 |
620124 | Result Summary | 50397-9 |
620125 | Result | 82939-0 |
620126 | Interpretation | 69047-9 |
620127 | Additional Results | 48767-8 |
620128 | Resources | 99622-3 |
620129 | Additional Information | 48767-8 |
620130 | Method | 85069-3 |
620131 | Genes Analyzed | 82939-0 |
620132 | Disclaimer | 62364-5 |
620133 | Released By | 18771-6 |