Wilson Disease, ATP7B Full Gene Sequencing with Deletion/Duplication, Varies

Marshfield Lab Public WebSite

Marshfield Clinic Public WebSite

Test Code: WNDZSO

Overview
Ordering
Specimen
Performing
Clinical/Interpretive
Contacts
Coding

Synonyms/Keywords

ATP7B gene

NextGen Sequencing Test

Wilsons Disease

WDZ

Useful For

Confirming the diagnosis of Wilson disease.

Specimen Requirements

Specimen Type	Preferred Container/Tube	Acceptable Container/Tube	Specimen Volume	Specimen Minimum Volume (allows for 1 repeat)
Submit only 1 of the following specimens:
Whole Blood	EDTA Lavender Top Tube (LTT) or (YTT) ACD	Sodium Heparin Green Top Tube (GTT)	3 mL	1 mL
Saliva	DNA Saliva Kit High Yield (T1007) Saliva Swab Collection Kit (T786)		1 Swab if using T1007 or 2 swabs if using T786
Skin Biopsy	Fibroblast Biopsy Transport Media (T115)	Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin.	4-mm Punch
Amniotic Fluid	Amniotic fluid container		20 mL
**For specimen requirement information on other acceptable specimen types please refer to the Mayo Clinic Laboratories Website

Collection Processing Instructions

Specimen preferred to arrive within 96 hours of collection.

Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor will interfere with testing. For information about testing patients who have received a hematopoietic stem cell transplant, call 800-533-1710.

Whole Blood:

1. Invert several times to mix blood.

2. Send specimen in original tube. DO NOT aliquot.

3. Whole blood collected postnatal from an umbilical cord is also acceptable.

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

3. For postnatal umbilical cord whole blood specimens, maternal cell contamination studies are recommended to ensure test results reflect that of the patient tested. A maternal blood specimen is required to complete maternal cell contamination studies. Order MATCC / Maternal Cell contamination, Molecular Analysis, Varies on both the cord blood and maternal blood specimens under separate order numbers.

Saliva:

Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.

Collect and send specimen per kit instructions.

Note: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.

Skin biopsy specimens:
For skin biopsy, a fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

Specimens are preferred to be received within 24 hours of collection. Culture and/or extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.

A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.

PRENATAL SPECIMENS
Due to its complexity, consultation with the laboratory is required for all prenatal testing; call 800- 533-1710 to speak to a genetic counselor.

Prenatal specimens:

If an amniotic fluid specimen is received, an amniotic fluid culture will be performed at an additional charge.

For any prenatal specimen that is received, maternal cell contamination testing will be performed at an additional charge.

Cord blood:

For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.

Amniotic Fluid:

Specimen will only be tested after culture.

Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
A separate culture charge will be assessed under CULAF / Culture for Genetic Testing, Amniotic Fluid. An additional 2 to 3 weeks are required to culture amniotic fluid before genetic testing can occur.

All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.

Specimen Stability Information

Specimen Type	Temperature	Time
Whole Blood	Ambient	4 days
	Refrigerated	4 days
	Frozen	4 days
Saliva	Ambient	30 days
Saliva	Refrigerated	30 days
Skin Biopsy	Ambient (preferred)	<24 hours
Skin Biopsy	Refrigerated	<24 hours
Amniotic Fluid	Ambient (preferred)	<24 hours
Amniotic Fluid	Refrigerated	<24 hours

Interference

Clinical Correlations:

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

If testing was performed because of clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.

To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact the Mayo Clinic Laboratories genetic counselors at 800-533-1710.

Technical Limitations:

Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.

This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.

Deletion/Duplication Analysis:

This analysis targets single and multi-exon deletions/duplications; however, in some instances, single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.
This test is not designed to detect low levels of mosaicism or to differentiate between somatic and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.
For detailed information regarding gene-specific performance and technical limitations, see Method Description or contact a laboratory genetic counselor.
If the patient has had an allogeneic hematopoietic stem cell transplant or a recent blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant.

Reclassification of Variants:
Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages healthcare providers to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time. Due to broadening genetic knowledge, it is possible that the laboratory may discover new information of relevance to the patient. Should that occur, the laboratory may issue an amended report.

Variant Evaluation:
Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline. Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.
Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.
Rarely, incidental or secondary findings may implicate another predisposition or presence of active disease. Incidental findings may include, but are not limited to, results related to the sex chromosomes. These findings will be carefully reviewed to determine whether they will be reported.

Performing Laboratory Information

Performing Location	Day(s) Test Performed	Report Available	Methodology/Instrumentation
Mayo Clinic Laboratories	Varies	14 -21 days	Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing

Reference Lab

Mayo Clinic Laboratories

Test Information

Wilson disease (WD) is an autosomal recessive disorder that results from the body's inability to excrete excess copper. Typically, the liver releases excess copper into the bile. Individuals with WD lack the necessary enzyme that facilitates clearance of copper from the liver to bile. As a result, copper accumulates first in the liver and gradually in other organs. The brain, kidneys, bones, and corneas can also be affected. WD affects approximately 1 in 30,000 people worldwide, with a carrier frequency of approximately 1 in 90 individuals.

The primary clinical manifestations of WD are hepatic and neurologic. Hepatic disease can be quite variable, ranging from hepatomegaly or other nonspecific symptoms that mimic viral hepatitis to severe liver damage, such as cirrhosis. Neurologic symptoms of WD can include poor fine-motor coordination, ataxia, and dysphagia. Psychiatric manifestations are reported in approximately 20% of individuals with WD. A characteristic ophthalmologic finding is the Kayser-Fleischer ring. Individuals with WD typically begin to show symptoms of liver dysfunction or neurologic disease in the first or second decade of life. If not treated, WD can cause liver failure, severe brain damage, and even death.

A variety of laboratory tests are recommended in the initial evaluation for WD. In approximately 95% of cases, serum ceruloplasmin is below normal. Additionally, patients with WD show decreased copper in serum, increased copper in urine, and significantly elevated copper on liver biopsy. While liver biopsy is not recommended as a first-tier screening test for WD, it can be useful to help interpret discrepant biochemical or molecular results. Analyte screening tests should be considered prior to molecular analysis. WD is caused by disease-causing variants in the ATP7B gene. More than 300 disease-causing variants have been identified in the ATP7B gene. Most disease-causing variants are family-specific, with the exception of the H1069Q variant, which accounts for greater than 50% of identified disease alleles in the Northern European population.

Reference Range Information

An interpretive report will be provided.

Interpretation

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

Outreach CPTs

CPT	Modifier (if needed)	Quantity	Description	Comments
81406		1

Classification