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Test ID: 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.

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.

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

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.

Clinical Reference

1. Uhlig HH, Schwerd T, Koletzko S, et al. The diagnostic approach to monogenic very early onset inflammatory bowel disease. Gastroenterology. 2014;147(5):990-1007

2. Uhlig HH, Schwerd T: From genes to mechanisms. The expanding spectrum of monogenic disorders associated with inflammatory bowel disease. Inflamm Bowel Dis. 2016;22(1):202-212

3. Kelsen JR, Baldassano RN, Artis D, Sonnenberg GF. Maintaining intestinal health: the genetics and immunology of very early-onset inflammatory bowel disease. Cell Mol Gastroenterol Hepatol. 20151;1(5):462-476

4. Ouahed J, Spencer E, Kotlarz D, et al. Very early onset inflammatory bowel disease: A clinical approach with a focus on the role genetics and underlying immune deficiencies. Inflamm Bowel Dis. 2020;26(6):820-842

5. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5)405-24

Day(s) Performed

Varies

Report Available

28 to 42 days

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
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
Mayo Clinic Laboratories | Genetics and Genomics Additional Information:

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