Test Catalog

Test Id : ARPKZ

Autosomal Recessive Polycystic Kidney Disease, Full Gene Analysis, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Diagnosis of individuals suspected of having autosomal recessive polycystic kidney disease (ARPKD)

 

Prenatal diagnosis if there is a high suspicion of ARPKD based on ultrasound findings

 

Carrier testing of individuals with a family history of ARPKD, but an affected individual is not available for testing or disease-causing variants have not been identified

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test includes next-generation sequencing to evaluate for variants in the PKHD1 gene. Sanger sequencing may be performed to confirm detected variants.

Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial tests.

Test Id Reporting Name Available Separately Always Performed
CULFB Fibroblast Culture for Genetic Test Yes No
CULAF Amniotic Fluid Culture/Genetic Test Yes No
MATCC Maternal Cell Contamination, B Yes No

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For prenatal specimens only: If amniotic fluid (nonconfluent cultured cells) is received, amniotic fluid culture/genetic test will be added and charged separately. If chorionic villus specimen (nonconfluent cultured cells) is received, fibroblast culture for genetic test will be added and charged separately. For any prenatal specimen that is received, maternal cell contamination studies will be added.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Custom Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing when appropriate

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

ARPKD Full Gene Analysis

Aliases
Lists additional common names for a test, as an aid in searching

ARPKD

PKHD1

Polycystic Kidney Disease (PKD)

Next Gen Sequencing Test

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For prenatal specimens only: If amniotic fluid (nonconfluent cultured cells) is received, amniotic fluid culture/genetic test will be added and charged separately. If chorionic villus specimen (nonconfluent cultured cells) is received, fibroblast culture for genetic test will be added and charged separately. For any prenatal specimen that is received, maternal cell contamination studies will be added.

Specimen Type
Describes the specimen type validated for testing

Varies

Additional Testing Requirements

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

Shipping Instructions

Whole blood specimens preferred to arrive within 96 hours of collection.

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

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.

Additional Information: To ensure minimum volume and concentration of DNA is met, the preferred volume of specimen must be submitted. Testing may be canceled if DNA requirements are inadequate.

 

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)/Refrigerated

 

Prenatal Specimens

Due to the complexity of prenatal testing, consultation with the laboratory is required for all prenatal testing.

 

Specimen Type: Amniotic fluid

Container/Tube: Amniotic fluid container

Specimen Volume: 20 mL

Specimen Stability Information: Refrigerated (preferred)/Ambient

 

Specimen Type: Chorionic villi

Container/Tube: 15-mL tube containing 15 mL of transport media

Specimen Volume: 20 mg

Specimen Stability Information: Refrigerated

 

Acceptable:

Specimen Type: Confluent cultured cells

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured cells from another laboratory.

Specimen Stability Information: Ambient (preferred)/Refrigerated

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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: Congenital Inherited Diseases Patient Information (T521) in Special Instructions

3. If not ordering electronically, complete, print, and send a Renal Diagnostics Test Request (T830) with the specimen.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

Blood: 1 mL

Amniotic Fluid: 10 mL

Chorionic Villi: 5 mg

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Varies (preferred)

Useful For
Suggests clinical disorders or settings where the test may be helpful

Diagnosis of individuals suspected of having autosomal recessive polycystic kidney disease (ARPKD)

 

Prenatal diagnosis if there is a high suspicion of ARPKD based on ultrasound findings

 

Carrier testing of individuals with a family history of ARPKD, but an affected individual is not available for testing or disease-causing variants have not been identified

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test includes next-generation sequencing to evaluate for variants in the PKHD1 gene. Sanger sequencing may be performed to confirm detected variants.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For prenatal specimens only: If amniotic fluid (nonconfluent cultured cells) is received, amniotic fluid culture/genetic test will be added and charged separately. If chorionic villus specimen (nonconfluent cultured cells) is received, fibroblast culture for genetic test will be added and charged separately. For any prenatal specimen that is received, maternal cell contamination studies will be added.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Autosomal recessive polycystic kidney disease (ARPKD) is a disorder caused by variants in the polycystic kidney and hepatic disease 1 (PKHD1) gene. The incidence of ARPKD is approximately 1:20,000 and the estimated carrier frequency in the general population is 1:70. ARPKD is characterized by enlarged echogenic kidneys, congenital hepatic fibrosis, and pulmonary hypoplasia (secondary to oligohydramnios [insufficient volume of amniotic fluid] in utero). Most individuals with ARPKD present during the neonatal period and, of those, nearly one-third die of respiratory insufficiency. Early diagnosis, in addition to initiation of renal replacement therapy (dialysis or transplantation) and respiratory support, increases the 10-year survival rate significantly. Presenting symptoms include bilateral palpable flank masses in infants and subsequent observation of typical findings on renal ultrasound, often within the clinical context of hypertension and prenatal oligohydramnios. In rarer cases, individuals may present during childhood or adulthood with hepatosplenomegaly. Of those who survive the neonatal period, one-third progress to end-stage kidney disease and up to one-half develop chronic kidney insufficiency.

 

The PKHD1 gene maps to 6p12 and includes 67 exons. The PKHD1 gene encodes a protein called fibrocystin, which is localized to the primary cilia and basal body of renal tubular and biliary epithelial cells. Because ARPKD is an autosomal recessive disease, affected individuals must carry 2 deleterious variants within the PKHD1 gene. Although disease penetrance is 100%, intrafamilial variation in disease severity has been observed. Variant detection is often difficult due to the large gene size and the prevalence of private variants that span the entire length of the gene.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

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.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

A small percentage of individuals who are carriers or have a diagnosis of autosomal recessive polycystic kidney disease (ARPKD) may have a variant that is not identified by this method (eg, large genomic deletions/duplications, promoter alterations, deep intronic variants). The absence of a variant, therefore, does not eliminate the possibility of positive carrier status or the diagnosis of ARPKD. For carrier testing, it is important to first document the presence of a polycystic kidney and hepatic disease 1 (PKHD1) gene variant in an affected family member.

 

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

 

Technical Limitations:

In some cases, DNA variants of undetermined significance may be identified.

 

Rare alterations (ie, polymorphisms) exist that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, additional testing should be considered.

 

Evaluation Tools:

Multiple in-silico evaluation tools were used to assist in the interpretation of these results. These tools are updated regularly; therefore, changes to these algorithms may result in different predictions for a given alteration. Additionally, the predictability of these tools for the determination of pathogenicity is currently unvalidated.

 

Unless reported or predicted to cause disease, alterations in protein coding genes that do not result in an amino acid substitution are not reported. These and common alterations identified for this patient are available upon request.

 

Reclassification of Variants-Policy:

At this time, it is not standard practice for the laboratory to systematically review likely pathogenic alterations or variants of uncertain significance that have been previously detected and reported. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

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. doi: 10.1038/gim.2015.30

2. Guay-Woodford LM, Desmond RA: Autosomal recessive polycystic kidney disease: the clinical experience in North America. Pediatrics. 2003;111:1072-1080. doi: 10.1542/peds.111.5.1072

3. Guay-Woodford LM, Bissler JJ, Braun MC, et al: Consensus expert recommendations for the diagnosis and management of autosomal recessive polycystic kidney disease: Report of an international conference. J Pediatr. 2014 Sep;165(3):611-617. doi: 10.1016/j.jpeds.2014.06.015

4. Gunay-Aygun M, Avner E, Bacallao RL, et al: Autosomal recessive polycystic kidney disease and congenital hepatic fibrosis: summary of a first National Institutes of Health/Office of Rare Diseases conference. J Pediatr. 2006;149:159-164. doi: 10.1016/j.jpeds.2006.03.014

5. Harris PC, Rossetti S: Molecular genetics of autosomal recessive polycystic kidney disease. Mol Genet Metab. 2004;81:75-85. doi: 10.1016/j.ymgme.2003.10.010

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Next-generation sequencing is performed to test for the presence of variants in 66 exons (exon 2-67) of the polycystic kidney and hepatic disease 1 (PKHD1) gene. Sanger sequencing is used to confirm alterations detected by next-generation sequencing when appropriate.(Unpublished Mayo method)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Varies

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

14 to 20 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Whole Blood: 2 weeks (if available); Extracted DNA: 3 months

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81408

Fibroblast Culture for Genetic Test

88233-(if appropriate)

88240-(if appropriate)

 

Amniotic Fluid Culture/Genetic Test

88235-(if appropriate)

88240-(if appropriate)

 

Maternal Cell Contamination, B

81265-(if appropriate)

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
ARPKZ ARPKD Full Gene Analysis 94226-8
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
53449 Result Summary 50397-9
53450 Result 82939-0
53451 Interpretation 69047-9
53452 Additional Information 48767-8
53453 Specimen 31208-2
53454 Source 31208-2
53455 Released By 18771-6

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Create a PDF

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports