2 purple-top (EDTA) tubes whole blood. Saliva is also acceptable.
Specimen Preparation
Please provide detailed clinical history and features. Parental samples can be submitted for DNA extraction at no-cost. For more information contact the lab at 6-1447 or by sending an email to DGDGeneticCounselor@email.chop.edu
Storage/Transport Temperature
Room temperature
Volume Required
5 mL in each tube
Minimum Required
3 mL
Phlebotomy Draw
Yes
Methodology
CHOP VEO-IBD Panel In is performed using the Agilent SureSelect XT Clinical Research Exome kit (per manufacturer’s protocol) followed by next generation sequencing on the Illumina HiSeq 2000 or 2500 platform with 100bp paired-end reads and an average sequencing depth of 100X. Mapping and analysis are based on the human genome build UCSC hg19 reference sequence. Variant calls, filtration and annotations are generated using an in-house custom-built bioinformatics pipeline. Sanger sequencing is used to fill in regions with insufficient coverage and to confirm all clinically significant variants, when appropriate. However, certain technically challenging, low coverage regions will not be filled in.
Detection of IKBKG variants utilizes Long-Range PCR Amplification (LR-PCR) followed by NGS sequencing. Deletion/duplication analysis is performed using a validated algorithm that utilizes coverage information from exome sequencing data to infer exon-level copy number variants, which when identified will be confirmed by custom digital droplet PCR (ddPCR) or another appropriate method before reporting.
Reported
42 days
Synonyms
IBDPN
VEOIBD
VEO-IBD
VEO
IBD
CHOP IBD panel
CHOP VEO panel
CHOP VEOIBD panel
LIS Mnemonic
IBDPN
Performed By
Division of Genomic Diagnostics
Available STAT
No
Test Notes
Exome-wide capture of the coding regions and splice sites (±10bp) of the genes on the CHOP VEO-IBD Panel In is performed using the Agilent SureSelect XT Clinical Research Exome kit (per manufacturer’s protocol) followed by next generation sequencing on the Illumina HiSeq 2000 or 2500 platform with 100bp paired-end reads and an average sequencing depth of 100X. Mapping and analysis are based on the human genome build UCSC hg19 reference sequence. Variant calls, filtration and annotations are generated using an in-house custom-built bioinformatics pipeline. Sanger sequencing is used to fill in regions with insufficient coverage and to confirm all clinically significant variants, when appropriate. However, certain technically challenging, low coverage regions will not be filled in.
Detection of IKBKG variants utilizes Long-Range PCR Amplification (LR-PCR) followed by NGS sequencing. Deletion/duplication analysis is performed using a validated algorithm that utilizes coverage information from exome sequencing data to infer exon-level copy number variants, which when identified will be confirmed by custom digital droplet PCR (ddPCR) or another appropriate method before reporting.
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 in age and is commonly caused by highly penetrant monogenic variants in over 50 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 very early onset inflammatory bowel disease (VEO-IBD) is indicated for any patient with IBD in whom:
1) A monogenetic cause is suspected but not yet identified
2) Children with disease onset before the age of 6 years
3) No other obvious and well-established complex genetic, environmental, or other non-genetic factors causative of IBD are present
4) No other major clinical features associated with specific known syndromes are present
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.
2 purple-top (EDTA) tubes whole blood. Saliva is also acceptable.
Specimen Preparation
Please provide detailed clinical history and features. Parental samples can be submitted for DNA extraction at no-cost. For more information contact the lab at 6-1447 or by sending an email to DGDGeneticCounselor@email.chop.edu
Storage/Transport Temperature
Room temperature
Volume Required
5 mL in each tube
Minimum Required
3 mL
Phlebotomy Draw
Yes
Ordering
Methodology
CHOP VEO-IBD Panel In is performed using the Agilent SureSelect XT Clinical Research Exome kit (per manufacturer’s protocol) followed by next generation sequencing on the Illumina HiSeq 2000 or 2500 platform with 100bp paired-end reads and an average sequencing depth of 100X. Mapping and analysis are based on the human genome build UCSC hg19 reference sequence. Variant calls, filtration and annotations are generated using an in-house custom-built bioinformatics pipeline. Sanger sequencing is used to fill in regions with insufficient coverage and to confirm all clinically significant variants, when appropriate. However, certain technically challenging, low coverage regions will not be filled in.
Detection of IKBKG variants utilizes Long-Range PCR Amplification (LR-PCR) followed by NGS sequencing. Deletion/duplication analysis is performed using a validated algorithm that utilizes coverage information from exome sequencing data to infer exon-level copy number variants, which when identified will be confirmed by custom digital droplet PCR (ddPCR) or another appropriate method before reporting.
Reported
42 days
Synonyms
IBDPN
VEOIBD
VEO-IBD
VEO
IBD
CHOP IBD panel
CHOP VEO panel
CHOP VEOIBD panel
LIS Mnemonic
IBDPN
Performed By
Division of Genomic Diagnostics
Available STAT
No
Test Notes
Exome-wide capture of the coding regions and splice sites (±10bp) of the genes on the CHOP VEO-IBD Panel In is performed using the Agilent SureSelect XT Clinical Research Exome kit (per manufacturer’s protocol) followed by next generation sequencing on the Illumina HiSeq 2000 or 2500 platform with 100bp paired-end reads and an average sequencing depth of 100X. Mapping and analysis are based on the human genome build UCSC hg19 reference sequence. Variant calls, filtration and annotations are generated using an in-house custom-built bioinformatics pipeline. Sanger sequencing is used to fill in regions with insufficient coverage and to confirm all clinically significant variants, when appropriate. However, certain technically challenging, low coverage regions will not be filled in.
Detection of IKBKG variants utilizes Long-Range PCR Amplification (LR-PCR) followed by NGS sequencing. Deletion/duplication analysis is performed using a validated algorithm that utilizes coverage information from exome sequencing data to infer exon-level copy number variants, which when identified will be confirmed by custom digital droplet PCR (ddPCR) or another appropriate method before reporting.
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 in age and is commonly caused by highly penetrant monogenic variants in over 50 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 very early onset inflammatory bowel disease (VEO-IBD) is indicated for any patient with IBD in whom:
1) A monogenetic cause is suspected but not yet identified
2) Children with disease onset before the age of 6 years
3) No other obvious and well-established complex genetic, environmental, or other non-genetic factors causative of IBD are present
4) No other major clinical features associated with specific known syndromes are present
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.
