Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA and saliva are also acceptable.
Specimen Preparation
Please provide detailed clinical history and features. For more information contact the lab at 6-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
Unacceptable Conditions
Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.
Storage/Transport Temperature
For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day.
For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.
Please contact the lab (267-426-1447) with questions regarding non-blood specimens.
Volume Required
2-3 mL of blood or 3 ug of DNA with a concentration of at least 50 ng/ul
Minimum Required
1 mL of whole blood
Phlebotomy Draw
Yes
Clinical Features
Inflammatory bowel disease (IBD) is caused by defects in the intestinal mucosal barrier and inappropriate immune responses toward the intestinal bacterial microbiota which lead to chronic inflammation. This inflammation can result in diarrhea, bloody stools, abdominal pain, growth failure, and weight loss. Very early onset IBD (VEO-IBD), refers to disease onset in children less than 6 years of age and is commonly caused by highly penetrant monogenic variants in over 90 genes. These conditions can be caused by de novo alterations, or can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern. The CHOP VEO-IBD panel includes targeted analysis of sequencing and copy number data of genes known to cause monogenic forms of inflammatory bowel disease and listed in the 'Molecular Testing Notes' section.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
42 days
Detection Rate
The diagnostic yield for comprehensive next generation sequencing panels is not yet well-established, and depends on the panel’s gene content and the patient’s clinical features. However, in a study of 22 children with VEO-IBD, sequencing of 40 genes associated with this condition resulted in a positive rate of 18% [Kammermeier 2014, PMID: 25194001].
Utility
The clinical utility of the assay is to inform a clinical diagnosis of VEO-IBD, inform medical treatment decisions, facilitate genetic counseling, inform recurrence risk assessment, and support testing of at-risk family members.
Genomic DNA is extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing is performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis are based on the GRCh38 reference sequence. Sequencing data is processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants. Long-range polymerase chain reaction (LR-PCR) is performed for the IKBKG gene followed by next generation sequencing.
* Sequence analysis only is performed for this gene.
# Analysis of the pathogenic recurrent 253kb inversion in the UNC13D gene is included.
CPT Codes
81404x2, 81405, 81406x4, 81407, 81479
Collection
Collect
Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA and saliva are also acceptable.
Specimen Preparation
Please provide detailed clinical history and features. For more information contact the lab at 6-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
Unacceptable Conditions
Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.
Storage/Transport Temperature
For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day.
For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.
Please contact the lab (267-426-1447) with questions regarding non-blood specimens.
Volume Required
2-3 mL of blood or 3 ug of DNA with a concentration of at least 50 ng/ul
Minimum Required
1 mL of whole blood
Phlebotomy Draw
Yes
Ordering
Clinical Features
Inflammatory bowel disease (IBD) is caused by defects in the intestinal mucosal barrier and inappropriate immune responses toward the intestinal bacterial microbiota which lead to chronic inflammation. This inflammation can result in diarrhea, bloody stools, abdominal pain, growth failure, and weight loss. Very early onset IBD (VEO-IBD), refers to disease onset in children less than 6 years of age and is commonly caused by highly penetrant monogenic variants in over 90 genes. These conditions can be caused by de novo alterations, or can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern. The CHOP VEO-IBD panel includes targeted analysis of sequencing and copy number data of genes known to cause monogenic forms of inflammatory bowel disease and listed in the 'Molecular Testing Notes' section.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
42 days
Detection Rate
The diagnostic yield for comprehensive next generation sequencing panels is not yet well-established, and depends on the panel’s gene content and the patient’s clinical features. However, in a study of 22 children with VEO-IBD, sequencing of 40 genes associated with this condition resulted in a positive rate of 18% [Kammermeier 2014, PMID: 25194001].
Utility
The clinical utility of the assay is to inform a clinical diagnosis of VEO-IBD, inform medical treatment decisions, facilitate genetic counseling, inform recurrence risk assessment, and support testing of at-risk family members.
Genomic DNA is extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing is performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis are based on the GRCh38 reference sequence. Sequencing data is processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants. Long-range polymerase chain reaction (LR-PCR) is performed for the IKBKG gene followed by next generation sequencing.
