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HelpOrder Code LABGOR, EOIBD Early Onset Monogenic Inflammatory Bowel Disease (IBD) Gene Panel, Varies
Additional Codes
Mayo Test Code:EOIBD
Ordering Guidance
Patients who have had a previous bone marrow transplant from an allogenic donor should not have testing performed on blood, bone marrow, or saliva because any results generated will reflect the genome of the donor rather than the recipient. Testing on patients who have an active hematologic malignancy or hematologic disorder with clonal proliferation may identify both somatic mutations and germline variants, which may result in test failure or necessitate follow-up testing to determine whether the detected variant is germline or somatic. For these patients, testing a skin biopsy or cultured fibroblasts is recommended. For instructions for testing patients who have received a bone marrow transplant or have an active hematologic disorder, call 800-533-1710. For more information see Cautions.
Customization of this panel and single gene analysis for any gene present on this panel are available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies. To modify this panel via CGPH, use the Inborn Errors of Immunity/Bone Marrow Failure/Telomeropathy/Pulmonary Fibrosis/Very Early Onset IBD/Pancreatitis disease state for step 1 on the Custom Gene Ordering Tool.
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.
Additional Testing Requirements
For cord blood specimens: Maternal cell contamination (MCC) studies are available. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on both the cord blood and maternal specimens under separate order numbers. Cord blood testing will proceed without MCC studies, but results may be compromised if MCC is present.
Shipping Instructions
Specimen Required
Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor will interfere with testing. For information about testing patients who have received a hematopoietic stem cell transplant, call 800-533-1710.
Submit only 1 of the following specimens:
Specimen Type: Whole blood
Container/Tube: Lavender top (EDTA) or yellow top (ACD)
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 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.
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: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information:
1.Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2.A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks are 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) <24 hours/Refrigerated <24 hours
Additional Information:
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical and Molecular Testing, Tissue. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.
Specimen Type: Extracted DNA
Container/Tube:
Preferred: Screw Cap Micro Tube, 2 mL with skirted conical base
Acceptable: Matrix tube, 1 mL
Collection Instructions:
1. The preferred volume is at least 100 mcL at a concentration of 75 ng/mcL.
2. Include concentration and volume on tube.
Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated
Additional Information: DNA must be extracted in a CLIA-certified laboratory, or equivalent, and must be extracted from a specimen type listed as acceptable for this test (including applicable anticoagulants). Our laboratory has experience with Chemagic, Puregene, Autopure, MagnaPure, and EZ1 extraction platforms and cannot guarantee that all extraction methods are compatible with this test. If testing fails, one repeat will be attempted, and if unsuccessful, the test will be reported as failed and a charge will be applied. If applicable, specific gene regions that were unable to be interrogated due to DNA quality will be noted in the report.
Specimen Type: Cord blood
Container/Tube: Lavender top (EDTA) or yellow top (ACD)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send cord blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.
3. While a properly collected cord blood sample may not be at risk for maternal cell contamination, unanticipated complications may occur during collection. Therefore, maternal cell contamination studies are recommended to ensure the test results reflect that of the patient tested and are available at an additional charge. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Blood spot
Supplies: Card-Blood Spot Collection (Filter Paper) (T493)
Container/Tube:
Preferred: Collection card (Whatman Protein Saver 903 Paper)
Acceptable: PerkinElmer 226 filter paper or blood spot collection card
Specimen Volume: 2 to 5 Blood spots
Collection Instructions:
1. An alternative blood collection option for a patient older than 1 year is a fingerstick. For detailed instructions, see How to Collect a Dried Blood Spot Sample.
2. Let blood dry on the filter paper at ambient temperature in a horizontal position for a minimum of 3 hours.
3. Do not expose specimen to heat or direct sunlight.
4. Do not stack wet specimens.
5. Keep specimen dry.
Specimen Stability Information: Ambient (preferred)/Refrigerated
Additional Information:
1. Blood spot specimens are acceptable but not recommended. Multiple extractions will be required to obtain sufficient yield for supplemental analysis, and there is significant risk for test failure due to insufficient DNA.
2. Due to lower concentration of DNA yielded from blood spot, it is possible that additional specimen may be required to complete testing.
3. For collection instructions, see Blood Spot Collection Instructions.
4. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777).
5. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800).
Specimen Type: Saliva
Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.
Supplies: Saliva Swab Collection Kit (T786)
Specimen Volume: 2 Swabs, use 2 kits for collection
Collection Instructions: Collect and send specimen per kit instructions.
Specimen Stability Information: Ambient (preferred) 30 days, Refrigerated; 30 days
Additional Information: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.
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 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 108 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, NCF1, NCF2, NCF4, NEUROG3, NFKBIA, NLRC4, PAX1, PCSK1, PIK3CD, PIK3R1, PLCG2, PLVAP, POLA1, RAG1, RAG2, RIPK1, RTEL1, SH2D1A, SI, SKIV2L (SKIC2), SLC10A2, SLC26A3, SLC37A4, SLC39A4, SLC51B, SLC5A1, SLC9A3, SPINT2, STAT1, STAT3, STAT5B, STIM1, STX3, STXBP2, TGFB1, TGFBR1, TGFBR2, TLR3, TNFAIP3, TRIM22, TRNT1, TTC37 (SKIC3), 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 |
| MATCC | Maternal Cell Contamination, B | Yes | No |
Testing Algorithm
Skin biopsy:
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.
Cord blood:
For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.
For more information see Inflammatory Bowel Disease Diagnostic Testing Algorithm.
Special Instructions
- Informed Consent for Genetic Testing
- Blood Spot Collection Card-Spanish Instructions
- Blood Spot Collection Card-Chinese Instructions
- Informed Consent for Genetic Testing (Spanish)
- Blood Spot Collection Instructions
- 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), Polymerase Chain Reaction (PCR), and Droplet Digital Polymerase Chain Reaction (ddPCR)/Quantitative Real-Time Polymerase Chain Reaction (qPCR) and Sanger Sequencing as needed
Reporting Name
Early Onset IBD Gene PanelSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| 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 (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. A supplemental PCR-based method is used to detect a large deletion in IKBKG, and a supplemental droplet digital PCR method is used to detect the c.75_76del;p.Tyr26Hisfs*26 (delta GT) disease-causing variant in NCF1.
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)
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, NCF1, NCF2, NCF4, NEUROG3, NFKBIA, NLRC4, PAX1, PCSK1, PIK3CD, PIK3R1, PLCG2, PLVAP, POLA1, RAG1, RAG2, RIPK1, RTEL1, SH2D1A, SI, SKIV2L (SKIC2), SLC10A2, SLC26A3, SLC37A4, SLC39A4, SLC51B, SLC5A1, SLC9A3, SPINT2, STAT1, STAT3, STAT5B, STIM1, STX3, STXBP2, TGFB1, TGFBR1, TGFBR2, TLR3, TNFAIP3, TRIM22, TRNT1, TTC37 (SKIC3), TTC7A, UNC45A, WAS, WIPF1, XIAP, ZAP70, and ZBTB24
Day(s) Performed
Varies
Performing Laboratory
Mayo Clinic Laboratories in Rochester
CPT Code Information
81443
88233- Tissue culture, skin, solid tissue biopsy (if appropriate)
88240- Cryopreservation (if appropriate)