Cholestasis Panel

Updated
Summary
  • Is a 47 gene panel that includes assessment of non-coding variants.
  • Is ideal for patients who have any type of cholestasis including those with clinical suspicion of Alagille syndrome, citrullinemia type 2, Crigler-Najjar syndrome types 1 and 2, Dubin-Johnson syndrome, Gilbert syndrome, intrahepatic cholestasis of pregnancy type 3 or progressive familial intrahepatic cholestasis types 1-4.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

47

Test code

GA0501

Panel size

Large

CPT code *
81443(1)
* The CPT codes provided are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payer being billed.

Summary

The Blueprint Genetics Cholestasis Panel (test code GA0501):

ICD codes

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

ICD-10 Disease
K83.1 Progressive familial intrahepatic cholestasis types 1-4
E80.6 Dubin-Johnson syndrome
E80.5 Crigler-Najjar syndrome types 1 and 2
E80.4 Gilbert syndrome
Q44.7 Alagille syndrome
K83.1 Intrahepatic cholestasis of pregnancy type 3
E72.20 Citrullinemia type 2
K76.89 Congenital bile acid synthesis defect type 3
E88.01 Emphysema, related to alpha-1-antitrypsin deficiency
Q74.3 Arthrogryposis, renal dysfunction, and cholestasis 1
E70.21 Tyrosinemia type 1

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Please see Sample Requirements for accepted saliva kits)

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

We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.

Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.

Read more about our sample requirements here.

Cholestasis is characterized by jaundice and pruritus. It can present as the hallmark feature in progressive familial intrahepatic cholestasis (PFIC) or as a feature in other inherited disorders such as Alagille syndrome where cholestasis occur in 95% of cases in the neonatal period. PFIC is a group of autosomal recessive liver disorders caused by defects in bile secretion and is characterized by intrahepatic cholestasis with disease onset usually in infancy and childhood. PFIC patients usually develop fibrosis and end-stage liver disease before adulthood. Defects in PFIC-associated genes ATP8B1 and ABCB11 may also cause a milder disease called benign recurrent intrahepatic cholestasis. There are several other inherited disorders where cholestasis is frequent such as Alagille syndrome (JAG1 and NOTCH2), arthrogryposis, renal dysfunction, and cholestasis syndrome (ARC syndrome; VPS33B and VIPAS39), alpha-1-antitrypsin deficiency (SERPINA1), citrullinemia (SLC25A13), congenital defects of bile acid synthesis (HSD3B7 and AKR1D1), familial hypercholanemia (TJP2 and BAAT) and neonatal ichthyosis-sclerosing cholangitis syndrome (CLDN1). The prevalence of PFIC is unknown while the prevalence is as follows for other causes of cholestasis: Dubin-Johnson 1:1,300 in Iranian or Moroccan Jews, Alagille syndrome 1:30,000, Crigler-Najjar syndrome 1:1,000,000. The Gilbert syndrome prevalence is 3-7% but it does cause only abnormal laboratory findings but no clinical symptoms.

Genes in the Cholestasis Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCB11 Cholestasis, Cholestasis, benign recurrent intrahepatic, 2 AD/AR 35 299
ABCB4 Gallbladder disease, Low phospholipid-associated cholelithiasis, Cholestasis AD/AR 27 224
ABCC2 Dubin-Johnson syndrome AD/AR 29 46
AKR1D1 Bile acid synthesis defect, congenital, 2 AR 7 14
ATP8B1 Intrahepatic cholestasis of pregnancy, Familial intrahepatic cholestasis, recurrent, Cholestasis, progressive familial intrahepatic, Benign recurrent intrahepatic cholestasis AD/AR 18 131
BAAT Hypercholanemia, familial AR 3 7
CFTR Cystic fibrosis, Congenital bilateral absence of the vas deferens AD/AR 518 1803
CREB3L3 Hypertriglyceridaemia AD 9
CYP7B1 Bile acid synthesis defect, Spastic paraplegia 5A, autosomal recessive AR 18 60
DCDC2 Deafness, Nephronophthisis, Sclerosing cholangitis, neonatal AR 13 9
DGUOK Mitochondrial DNA depletion syndrome, Portal hypertension, noncirrhotic, Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 4 AR 23 62
EPCAM Diarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposis AD/AR 38 80
FAH Tyrosinemia AR 53 102
HSD3B7 Bile acid synthesis defect, congenital, 1 AR 8 25
JAG1 Alagille syndrome AD 131 610
LCT Lactase deficiency AR 11 15
LMF1 Combined lipase deficiency AR 4 14
MKS1 Bardet-Biedl syndrome, Meckel syndrome AR 50 52
MYO5B* Diarrhea, with microvillus atrophy AR 14 80
NEUROG3 Diarrhea, malabsorptive, congenital AR 3 8
NOTCH2* Alagille syndrome, Hajdu-Cheney syndrome AD 37 70
NPC1 Niemann-Pick disease AR 164 472
NPC2 Niemann-pick disease AR 21 27
NPHP1 Nephronophthisis, Joubert syndrome, Senior-Loken syndrome AR 19 76
NPHP3 Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndrome AR 38 75
NPHP4 Nephronophthisis, Senior-Loken syndrome AR 20 113
NR1H4 Cholestasis, progressive familial intrahepatic 5 AR 6 5
PEX1 Heimler syndrome, Peroxisome biogenesis factor disorder 1A, Peroxisome biogenesis factor disorder 1B AR 112 134
PEX10 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder, Ataxia AR 34 29
PEX12 Zellweger syndrome, Peroxisome biogenesis disorder AR 43 37
PEX2 Zellweger syndrome, Peroxisome biogenesis disorder AR 16 18
PEX26 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder AR 13 27
PEX5 Adrenoleukodystrophy, neonatal, Rhizomelic chondrodysplasia punctata, Zellweger syndrome, Peroxisome biogenesis disorder AR 8 14
PEX6 Heimler syndrome, Peroxisome biogenesis disorder 4A, Peroxisome biogenesis disorder 4B AR 58 107
SCYL1 Spinocerebellar ataxia, autosomal recessive 21 AR 12 6
SERPINA1 Alpha-1-antitrypsin deficiency AR 49 80
SLC25A13 Citrin deficiency AR 24 113
SLC26A3 Diarrhea, secretory chloride, congenital AR 55 88
SMPD1 Niemann-Pick disease AR 110 249
SPINT2 Diarrhea, secretory sodium, congenital AR 6 12
TJP2 Cholestasis, progressive familial intrahepatic, Hypercholanemia, familial, Deafness, autosomal dominant 51 AD/AR 25 27
TMEM216 Joubert syndrome, Meckel syndrome AR 17 8
TRMU Liver failure, infantile, Reversible infantile respiratory chain deficiency AR 20 21
TTC37 Trichohepatoenteric syndrome, Primary immunodeficiency AR 12 64
UGT1A1 Crigler-Najjar syndrome, Gilbert syndrome, Breast milk jaundice AD/AR 29 144
VIPAS39 Arthrogryposis, renal dysfunction, and cholestasis 2 AR 8 13
VPS33B Arthrogryposis - renal dysfunction - cholestasis AD/AR 17 58

* 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), mitochondrial (mi), 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 Mitomap databases.

Non-coding variants covered by Cholestasis Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ABCB11 Chr2:169873328 c.77-19T>A NM_003742.2
CFTR Chr7:117119654 c.-495C>T NM_000492.3 rs397507565
CFTR Chr7:117119797 NM_000492.3
CFTR Chr7:117119900 c.-249G>C NM_000492.3
CFTR Chr7:117119984 c.-165G>A NM_000492.3 rs145483167
CFTR Chr7:117120064 c.-85C>G NM_000492.3
CFTR Chr7:117120115 c.-34C>T NM_000492.3 rs756314710
CFTR Chr7:117120325 c.53+124T>C NM_000492.3
CFTR Chr7:117179040 c.870-1113_870-1110delGAAT NM_000492.3 rs397508809
CFTR Chr7:117182041 c.1117-26_1117-25delAT NM_000492.3 rs397508159
CFTR Chr7:117199500 c.1393-18G>A NM_000492.3 rs397508199
CFTR Chr7:117218381 c.1585-9412A>G NM_000492.3 rs397508229
CFTR Chr7:117227774 c.1585-19T>C NM_000492.3 rs778457306
CFTR Chr7:117227921 c.1679+34G>T NM_000492.3 rs767901668
CFTR Chr7:117229521 c.1680-886A>G NM_000492.3 rs397508266
CFTR Chr7:117229524 c.1680-883A>G NM_000492.3
CFTR Chr7:117229530 c.1680-877G>T NM_000492.3 rs397508261
CFTR Chr7:117243855 c.2908+19G>C NM_000492.3 rs370683572
CFTR Chr7:117246713 c.2909-15T>G NM_000492.3 rs397508455
CFTR Chr7:117246840 c.2988+33G>T NM_000492.3
CFTR Chr7:117251609 c.3140-26A>G NM_000492.3 rs76151804
CFTR Chr7:117251619 c.3140-16T>A NM_000492.3 rs767232138
CFTR Chr7:117251624 c.3140-11A>G NM_000492.3
CFTR Chr7:117266272 c.3469-1304C>G NM_000492.3
CFTR Chr7:117267864 c.3717+40A>G NM_000492.3 rs397508595
CFTR Chr7:117280015 c.3718-2477C>T NM_000492.3 rs75039782
CFTR Chr7:117282680 c.3873+33A>G NM_000492.3 rs397508622
CFTR Chr7:117288374 c.3874-4522A>G NM_000492.3
CFTR Chr7:117308395 c.*1233T>A NM_000492.3
DGUOK Chr2:74177650 c.444-62C>A NM_080916.2
DGUOK Chr2:74177701 c.444-11C>G NM_080916.2 rs536746349
EPCAM Chr2:47606078 c.556-14A>G NM_002354.2 rs376155665
JAG1 Chr20:10629767 c.1349-12T>G NM_000214.2
MYO5B Chr18:47365503 c.4852+11A>G NM_001080467.2
NPC1 Chr18:21132700 c.1554-1009G>A NM_000271.4
NPC1 Chr18:21137182 c.882-28A>G/T NM_000271.4
NPC1 Chr18:21137182 c.882-28A>G NM_000271.4
NPC1 Chr18:21137182 c.882-28A>T NM_000271.4
PEX6 Chr6:42933858 c.2301-15C>G NM_000287.3 rs267608236
PEX6 Chr6:42933952 c.2300+28G>A NM_000287.3 rs267608237
SERPINA1 Chr14:94854894 c.-5+2dupT NM_000295.4
SERPINA1 Chr14:94854896 c.-5+1G>A NM_000295.4 rs775786225
SMPD1 Chr11:6415102 c.1341-21_1341-18delAATG NM_000543.4 rs1312743513
UGT1A1 Chr2:234668848 c.-85_-83dupCAT NM_000463.2
UGT1A1 Chr2:234668879 c.-41_-40dupTA NM_000463.2 rs34983651
VPS33B Chr15:91550814 c.499-11G>A NM_018668.3

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
  • Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
  • 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
  • Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
  • 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 in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.

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%


Performance of Blueprint Genetics Mitochondrial Sequencing Assay.

Sensitivity % Specificity %
ANALYTIC VALIDATION (NA samples; n=4)
Single nucleotide variants
Heteroplasmic (45-100%) 100.0% (50/50) 100.0%
Heteroplasmic (35-45%) 100.0% (87/87) 100.0%
Heteroplasmic (25-35%) 100.0% (73/73) 100.0%
Heteroplasmic (15-25%) 100.0% (77/77) 100.0%
Heteroplasmic (10-15%) 100.0% (74/74) 100.0%
Heteroplasmic (5-10%) 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 50.0% (2/4) 100.0%
CLINICAL VALIDATION (n=76 samples)
All types
Single nucleotide variants n=2026 SNVs
Heteroplasmic (45-100%) 100.0% (1940/1940) 100.0%
Heteroplasmic (35-45%) 100.0% (4/4) 100.0%
Heteroplasmic (25-35%) 100.0% (3/3) 100.0%
Heteroplasmic (15-25%) 100.0% (3/3) 100.0%
Heteroplasmic (10-15%) 100.0% (9/9) 100.0%
Heteroplasmic (5-10%) 92.3% (12/13) 99.98%
Heteroplasmic (<5%) 88.9% (48/54) 99.93%
Insertions and deletions by sequence analysis n=40 indels
Heteroplasmic (45-100%) 1-10bp 100.0% (32/32) 100.0%
Heteroplasmic (5-45%) 1-10bp 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 1-10bp 100.0% (5/5) 99,997%
SIMULATION DATA /(mitomap mutations)
Insertions, and deletions 1-24 bps by sequence analysis; n=17
Homoplasmic (100%) 1-24bp 100.0% (17/17) 99.98%
Heteroplasmic (50%) 100.0% (17/17) 99.99%
Heteroplasmic (25%) 100.0% (17/17) 100.0%
Heteroplasmic (20%) 100.0% (17/17) 100.0%
Heteroplasmic (15%) 100.0% (17/17) 100.0%
Heteroplasmic (10%) 94.1% (16/17) 100.0%
Heteroplasmic (5%) 94.1% (16/17) 100.0%
Copy number variants (separate artifical mutations; n=1500)
Homoplasmic (100%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (50%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (30%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (20%) 500 bp, 1kb, 5 kb 99.7% 100.0%
Heteroplasmic (10%) 500 bp, 1kb, 5 kb 99.0% 100.0%
The performance presented above reached by following coverage metrics at assay level (n=66)
Mean of medians Median of medians
Mean sequencing depth MQ0 (clinical) 18224X 17366X
Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical) 100%
rho zero cell line (=no mtDNA), mean sequencing depth 12X

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. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. 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 suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) 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 and copy number variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.

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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