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Test ID CHLGP Cholestasis Gene Panel, Varies


Ordering Guidance


Customization of this panel and single gene analysis for any gene present on this panel is available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Specimen Required


Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 14 days

 

Specimen Type: Cultured fibroblast

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)/Refrigerated (<24 hours)

Additional Information: A separate culture charge will be assessed under FIBR / Fibroblast Culture, Tissue. An additional 4 weeks is required to culture fibroblasts before genetic testing can occur.

 

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 (formerly Ahlstrom 226) filter paper or blood spot collection card

Specimen Volume: 5 Blood spots

Collection Instructions:

1. An alternative blood collection option for a patient older than 1 year of age is fingerstick. See Dried Blood Spot Collection Tutorial for how to collect blood spots via fingerstick: https://vimeo.com/508490782 .

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. For collection instructions, see Blood Spot Collection Instructions in Special Instructions.

2. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777) in Special Instructions.

3. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800) in Special Instructions.

4. Due to lower concentration of DNA yielded from blood spot, it is possible that additional specimen may be required to complete testing.

 

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: 1 Swab

Collection Instructions: Collect and send specimen per kit instructions.

Specimen Stability Information: Ambient 30 days

Additional Information: Due to lower concentration of DNA yielded from saliva, it is possible that 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 Special Instructions:

-Informed Consent for Genetic Testing  (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

2. Molecular Genetics: Biochemical Disorders Patient Information (T527) in Special Instructions

Useful For

Establishing a molecular diagnosis for patients with monogenic cholestasis

 

Identifying variants within genes known to be associated with primary, monogenic cholestasis, allowing for predictive testing of at-risk family members

Method Name

Sequence Capture and Targeted Next-Generation Sequencing followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing.

Reporting Name

Cholestasis Gene Panel

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Clinical Information

Cholestasis is a decrease in or obstruction of bile flow that results in jaundice, pruritus, hepatomegaly, and splenomegaly. Cholestasis can be the primary clinical symptom due to progressive familial intrahepatic cholestasis (PFIC) or one of a number of symptoms due to a variety of genetic disorders that cause multisystem disease. Many forms of cholestasis are multifactorial in origin occurring due to the presence of both risk-associated alleles and environmental circumstances. This panel is not intended to diagnose multifactorial cholestasis and risk-associated alleles will not be reported unless requested.

 

PFIC is a group of disorders caused by bile secretion or transport defects that result in intrahepatic cholestasis in infancy or childhood. There are 5 types of PFIC that are molecularly defined: FIC1 (ATP8B1 gene), PFIC2 (ABCB11 gene), PFIC3 (ABCB4 gene), PFIC4 (TJP2 gene), and PFIC5 (NR1H4 gene). PFICs 1, 2, and 4 have normal to mild elevations of gamma-glutamyltransferase (GGT). PFIC 3 results in significantly elevated serum GGT, whereas PFIC5 causes low to normal GGT levels.

 

PFIC can present with cholestasis in neonates, but most commonly manifests around 3 months of age for those with PFIC2, the most common type. Studies of infants and children with cholestasis have shown that 12% to 13% have molecularly confirmed PFIC. Disease progression results in liver failure and hepatocellular carcinoma. Liver transplantation is an effective treatment, though less effective for multisystemic PFIC1 than for other types. However, there is significant mortality, as 87% of patients with untreated PFIC will not survive.

 

A variety of other genetic disorders can also result in cholestasis, such as Alagille syndrome (JAG1 and NOTCH2 genes), alpha-1-antitrypsin deficiency (SERPINA1 gene), arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome (VPS33B and VIPAS39 genes), citrullinemia (SLC25A13 gene), congenital defects of bile acid synthesis (HSD3B7 and AKR1D1 genes), familial hypercholanemia (BAAT gene), neonatal ichthyosis-sclerosing cholangitis syndrome (CLDN1 gene), and Crigler-Najjar syndrome types I or II or Gilbert syndrome (UGT1A1). In addition, peroxisomal disorders (PEX genes) and mitochondrial disorders can include cholestatic liver disease among other features.

 

A comprehensive gene panel is a rapid and reliable first-tier test to establish a diagnosis for patients with monogenic cholestasis

Reference Values

An interpretive report will be provided.

Interpretation

All detected alterations are evaluated according to American College of Medical Genetics and Genomics (ACMG) recommendations.(1) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Clinical Reference

1. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424

2. Baker A, Kerkar N, Todorova L, et al: Systematic review of progressive familial intrahepatic cholestasis. Clin Res Hepatol Gastroenterol. 2019;43(1):20-36

3. Chowdhury J, Wolkoff AW, Chowdhury N, Arias IM: Hereditary jaundice and disorders of bilirubin metabolism. In: Valle D, Antonarakis S, Ballabio A, Beaudet A, Mitchell GA, eds. The Online Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill; 2019 Accessed January 07, 2020. Available at http://ommbid.mhmedical.com/content.aspx?bookid=2709&sectionid=225541453

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

81443

88233-Tissue culture, skin, solid tissue biopsy (if appropriate)

88240-Cryopreservation (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
CHLGP Cholestasis Gene Panel In Process

 

Result ID Test Result Name Result LOINC Value
608620 Test Description 62364-5
608621 Specimen 31208-2
608622 Source 31208-2
608623 Result Summary 50397-9
608624 Result 82939-0
608625 Interpretation 69047-9
608626 Resources 99622-3
608627 Additional Information 48767-8
608628 Method 85069-3
608629 Genes Analyzed 48018-6
608630 Disclaimer 62364-5
608631 Released By 18771-6

Day(s) Performed

Varies

Report Available

4 to 6 weeks

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
FIBR Fibroblast Culture Yes No
CRYOB Cryopreserve for Biochem Studies No No

Testing Algorithm

If skin biopsy is received, fibroblast culture and cryopreservation for biochemical studies will be added at an additional charge.