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Test Code MISC2MAYOCKDGP Cystic Kidney Disease Gene Panel, Varies


Ordering Guidance


Targeted testing for familial variants (also called site-specific or known mutations/variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.

 

Customization of this panel and single gene analysis for any gene present on this panel are available. For more information, see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, 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 as this must be a different order number than the prenatal specimen.



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. For instructions for testing patients who have received a bone marrow transplant, call 800-533-1710.

 

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 whole blood specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

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.

 

Specimen Type: Amniotic fluid

Container/Tube: Amniotic fluid container

Specimen Volume: 20 mL

Specimen Stability Information: Refrigerated (preferred)/Ambient

Additional information:

1. If amniotic fluid or nonconfluent cultures are received, CULAF / Culture for Genetic Testing, Amniotic Fluid will be added at an additional charge.

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

 

Specimen Type: Chorionic villi

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

Specimen Volume: 20 mg

Specimen Stability Information: Refrigerated

Additional Information:

1. If nonconfluent cultures are received, CULFB / Fibroblast Culture for Biochemical or Molecular Testing will be added at an additional charge.

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

 

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

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


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:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Hereditary Renal Genetic Testing Patient Information (T918)

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

Secondary ID

618072

Useful For

Providing a genetic evaluation for patients with a personal or family history of cystic kidney disease

 

Establishing a diagnosis of hereditary cystic kidney disease

Reflex 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

For prenatal specimens only:

If an amniotic fluid specimen or nonconfluent cultures are received, amniotic fluid culture for a genetic test will be performed at an additional charge.

 

If a chorionic villi specimen is received, fibroblast culture for a genetic test will be performed at an additional charge.

 

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

Method Name

Sequence Capture and Amplicon-based Next-Generation Sequencing (NGS)

Reporting Name

Cystic Kidney Disease Gene Panel

Specimen Type

Varies

Specimen Minimum Volume

Blood: 1 mL; Amniotic fluid/CVS: See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Reject Due To

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

Clinical Information

Hereditary forms of cystic kidney disease have several underlying genetic etiologies and may present in childhood or adulthood, with or without extrarenal features. The two most common categories of hereditary cystic kidney disease are the ciliopathic disorders and the phakomatoses.(1)

 

Ciliopathic disorders causing cystic kidney disease include polycystic kidney disease (PKD), nephronophthisis (NPHP), and medullary cystic kidney disease (MCKD). The PKD1 and PKD2 genes cause the majority of autosomal dominant PKD (ADPKD), while the GANAB and DNAJB11 genes are implicated in a minority of cases.(2,3) The PKHD1 gene is the major gene associated with autosomal recessive PKD (ARPKD), while DZIP1L has been more recently identified as a secondary cause.(4) ARPKD is often diagnosed in utero due to oligohydramnios. NPHP is an autosomal recessive condition characterized by cystic kidney disease, inflammation, fibrosis, and progression to kidney failure. MCKD is an autosomal dominant condition characterized by cysts in the medullary region of the kidney, kidney tubule fibrosis, hyperuricemia, and slowly worsening kidney function. Genes included on this panel for MCKD include HNF1B, UMOD, and SEC61A1 (note the MUC1 gene is not included on this panel).

 

Phakomatoses, also known as neurocutaneous syndromes, are a broad group of hereditary disorders characterized by involvement of structures that arise from the embryonic ectoderm (central nervous system, skin, and eyes). Cystic renal lesions are common in these disorders. Phakomatoses genes included on this panel are the TSC1 and TSC2 tumor suppressor genes associated with tuberous sclerosis complex (TSC) and the VHL gene associated with von Hippel-Lindau syndrome.

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(5) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Method Description

Capture-based and amplicon-based next-generation sequencing (NGS is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions-insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.

 

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. See Targeted Genes and Methodology Details for Cystic Kidney Disease Gene Panel for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.(Unpublished Mayo method)

 

Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.

 

Genes analyzed: ALG8, ALG9, ANKS6, BICC1, CEP164, CEP290, CEP83, COL4A1, CRB2, DCDC2, DNAJB11, DZIP1L, GANAB, GLIS2, HNF1B, INVS, IQCB1, JAG1, LRP5, MAPKBP1, NEK8, NOTCH2, NPHP1, NPHP3, NPHP4, OFD1, PAX2, PKD1, PKD2, PKHD1, PRKCSH, RPGRIP1L, SDCCAG8, SEC61A1, SEC63, TMEM67, TRAF3IP1, TSC1, TSC2, TTC21B, UMOD, VHL, WDR19, WDR35, XPNPEP3

Day(s) Performed

Varies

Report Available

28 to 42 days

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

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

CPT Code Information

81404

81405

81406 x 6

81407 x 4

81408 x 3

81479

81265-Maternal cell contamination (if appropriate)

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

88235-Amniotic Fluid culture (if appropriate)

81479 (if appropriate for government payers)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
CKDGP Cystic Kidney Disease Gene Panel 51966-0

 

Result ID Test Result Name Result LOINC Value
618073 Test Description 62364-5
618074 Specimen 31208-2
618075 Source 31208-2
618076 Result Summary 50397-9
618077 Result 82939-0
618078 Interpretation 69047-9
618079 Additional Results 82939-0
618080 Resources 99622-3
618081 Additional Information 48767-8
618082 Method 85069-3
618083 Genes Analyzed 48018-6
618084 Disclaimer 62364-5
618085 Released By 18771-6