Congenital Diarrhea Panel

Updated
Summary
  • Is a 29 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of early-onset chronic diarrhea, congenital tufting enteropathy / intestinal epithelial dysplasia or microvillus inclusion disease.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

29

Test code

GA0401

Panel size

Small

CPT codes
81479

Summary

The Blueprint Genetics Congenital Diarrhea Panel (test code GA0401):

ICD codes

Commonly used ICD-10 code(s) when ordering the Congenital Diarrhea Panel

ICD-10 Disease
P78.3 Congenital tufting enteropathy / intestinal epithelial dysplasia
Q43.8 Microvillus inclusion disease
P78.3 Early-onset chronic diarrhea
E73.0 Congenital lactase deficiency
P78.3 Congenital secretory sodium diarrhea
P78.3 Malabsorptive congenital diarrhea
P78.3 Neonatal-onset chronic diarrhea
P78.3 Congenital Finnish type chloride diarrhea

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.

Persistent diarrhea and failure to thrive may be caused by inherited diarrheas. Congenital diarrheas represent a group of rare autosomal recessive enteropathies with often severe outcomes. They may present prenatally with intrauterine growth restriction but disease onset generally occurs soon after delivery and in rare occasions at up to 3-4 months. Diarrhea is generally frequent and depending on the diarrhea subtype, the stool may contain high levels of sodium or chloride resulting in dehydration and electrolyte imbalance. Affected infants often have failure to thrive, developmental delay, liver and kidney problems and osteoporosis. Genetic defects have been described quite recently, thus the clinical utility of multigene NGS panels in this disease group remains unknown. Tufting enteropathy or intestinal epithelial dysplasia is caused by recessive EPCAM mutations and is the most common disease in this category with an estimated prevalence of 1:50,000-100,000. It causes ‘intractable’ diarrheas starting in early childhood and resulting in failure to thrive, total dependence on parenteral nutrition and eventually requiring transplantation for treatment. Congenital diarrhea type 6 is the only autosomal dominant condition targeted by this panel. The prevalence of congenital diarrheas is highest in regions with higher numbers of consanguineous marriages.

Genes in the Congenital Diarrhea Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ADAM17 Inflammatory skin and bowel disease, neonatal 1 AR 1 7
ALPI Inflammatory bowel disease AR 5
CYP27A1 Cerebrotendinous xanthomatosis AR 69 110
DGAT1 Diarrhea AR 7 11
EPCAM Diarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposis AD/AR 38 80
FOXP3 Immunodysregulation, polyendocrinopathy, and enteropathy XL 28 93
GUCY2C Diarrhea, Meconium ileus AD/AR 7 10
IL10 Graft vs. host disease AD 1 5
IL10RA Inflammatory bowel disease AR 4 43
IL10RB Inflammatory bowel disease AR 2 19
IL21 Immunodeficiency, common variable, 11 AR 1 1
LCT Lactase deficiency AR 11 15
LIPA Wolman disease, Cholesterol ester storage disease AR 27 93
MVK Mevalonic aciduria, Hyper-IgD syndrome, Porokeratosis 3, multiple types AD/AR 35 181
MYO5B* Diarrhea, with microvillus atrophy AR 14 80
NCF2 Chronic granulomatous disease AR 19 72
NEUROG3 Diarrhea, malabsorptive, congenital AR 3 8
SAR1B Chylomicron retention disease (Anderson disease) AR 8 16
SI Sucrase-isomaltase deficiency, congenital AR 12 23
SKIV2L Trichohepatoenteric syndrome 2 AR 6 33
SLC10A2 Bile acid malabsorption, primary AD 2 4
SLC26A3 Diarrhea, secretory chloride, congenital AR 55 88
SLC5A1 Glucose/galactose malabsorption AR 3 58
SLC9A3 Diarrhea, secretory sodium, congenital AR 6 12
SPINT2 Diarrhea, secretory sodium, congenital AR 6 12
STX3 Microvillus inclusion disease AR 3
TTC37 Trichohepatoenteric syndrome, Primary immunodeficiency AR 12 64
TTC7A Gastrointestinal defects and immunodeficiency syndrome AR 21 46
XIAP* Lymphoproliferative syndrome XL 14 96

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by Congenital Diarrhea Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
EPCAM Chr2:47606078 c.556-14A>G NM_002354.2 rs376155665
FOXP3 ChrX:49106917 c.*878A>G NM_014009.3
FOXP3 ChrX:49106919 c.*876A>G NM_014009.3
FOXP3 ChrX:49121118 c.-23+5G>A NM_014009.3
FOXP3 ChrX:49121121 c.-23+2T>G NM_014009.3
FOXP3 ChrX:49121122 c.-23+1G>A NM_014009.3
FOXP3 ChrX:49121122 c.-23+1G>T NM_014009.3
IL10RB Chr21:34668714 c.*52C>T NM_000628.4
MVK Chr12:110029032 c.769-7dupT NM_000431.2 rs104895348
MYO5B Chr18:47365503 c.4852+11A>G NM_001080467.2

Added and removed genes from the panel

Genes added Genes removed
ALPI

Test Strengths

The strengths of this test include:
  • CAP accredited laboratory
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publicly available analytic validation demonstrating complete details of test performance
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
  • Our rigorous variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test Limitations

Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
This test may not reliably detect the following:
  • Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999%
11-50 bps 99.13% (2,524/2,546) >99.9999%
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
     
Mean sequencing depth 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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