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Test ID: KVAR3 Known Variant Analysis-3+ Variants, Varies

Useful For

Diagnostic or predictive testing for specific conditions when 3 to 5 DNA sequence variants of interest have been previously identified in a family member, and follow-up testing for these specific variants in other family members is desired

 

Carrier screening for individuals at risk for having 3 to 5 DNA sequence variants that were previously identified in a family member

 

Segregation analysis for 3 to 5 familial DNA sequence variants

Testing Algorithm

For prenatal specimens only: If amniotic fluid (nonconfluent cultured cells) is received, CULAF / Amniotic Fluid Culture for Genetic Testing will be added and charged separately. If chorionic villus specimen (nonconfluent cultured cells) is received, CULFB / Fibroblast Culture for Genetic Testing will be added and charged separately. For any prenatal specimen that is received, MATCC / Maternal Cell Contamination, Molecular Analysis studies will be added.

For skin biopsy or cultured fibroblast specimens, FIBR / Fibroblast Culture and CRYOB / Cryopreservation for Biochemical Studies will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

Method Name

Polymerase Chain Reaction (PCR) Followed by DNA Sequencing Analysis

Reporting Name

Known Variant Analysis-3+ Variants

Specimen Type

Varies


Advisory Information


This test can only be performed if 3 to 5 variants need to be tested. If 2 variants need to be tested, order KVAR2 / Known Variant Analysis-2 Variants, Varies. If only 1 variant needs to be tested, order KVAR1 / Known Variant Analysis-1 Variant, Varies.



Additional Testing Requirements


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

 

If the familial variants were previously identified at an outside laboratory, sending DNA from a family member with a positive genetic test result to be used as a positive control is strongly recommended to ensure that the specific familial variant can be detected by our laboratory. Proband samples should be sent as a separate (KVAR3) order, under the proband's identifiers (ie, do not send the patient and proband samples under the same order). If a positive control is not provided, negative results will be reported with a stated limitation that the laboratory's ability to detect the familial variant has not been confirmed and a false-negative result cannot be ruled out.



Shipping Instructions


Prenatal specimens can be sent Monday through Thursday and must be received by 5 p.m. CST on Friday in order to be processed appropriately.



Necessary Information


The identification of 3 to 5 specific DNA sequence variants in an affected family member is required before this test can be performed for additional family members. If 3 to 5 familial variants have not been previously identified, call 800-533-1710 to discuss testing options.

 

Known Variant Analysis: Required Patient Information form (T768) with documentation of the specific familial variants is required. See Special Instructions. Testing will be held until information is received. If information is not received within 14 days of sample receipt, testing may be canceled.



Specimen Required


Submit only 1 of the following specimen types:

 

Preferred:

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 mL

Collection Instructions: Send specimen in original tube.

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

 

Specimen Type: Blood spot

Supplies: Card-Blood Spot Collection Filter Paper (T493)

Container/Tube:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: Whatman FTA Classic paper, Ahlstrom 226 filter paper, or Blood Spot Collection Card (T493)

Specimen Volume: 2 to 5 blood spots on collection card

Collection Instructions:

1. An alternative blood collection option for a patient <1 year of age is finger stick.

2. Let blood dry on the filter paper at ambient temperature in a horizontal position for 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

 

Specimen Type: Peripheral blood mononuclear cells (PBMCs)

Container/Tube: Cell pellet

Collection Instructions: Send as a suspension in freezing medium or cell pellet frozen on dry ice.

Specimen Stability Information: Frozen

 

Specimen Type: Cultured fibroblasts

Container/Tube: T-75 or T-25 flask

Specimen Volume: 1 Full T-75 or 2 full T-25 flasks

Additional Information: Indicate the tests to be performed on the fibroblast culture cells. A separate culture charge will be assessed under FIBR / Fibroblast Culture. An additional 4 weeks is required to culture fibroblasts before genetic testing can occur.

Specimen Stability Information: Ambient (preferred)/Refrigerated <24 hours

 

Specimen Type: Skin biopsy

Supplies: Fibroblast Biopsy Transport Media (T115)

Container/Tube: Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin. Tubes of culture media can be supplied upon request (Eagle's minimum essential medium with 1% penicillin and streptomycin [T115]).

Specimen Volume: 4-mm punch

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

Specimen Stability Information: Refrigerated (preferred)/Ambient

 

Specimen Type: Cord blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 mL

Collection Instructions:

1. Send specimen in original tube

2. Label specimen as cord blood

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

 

Specimen Type: DNA

Container/Tube: 2 mL screw top tube

Specimen Volume: 100 mcL (microliters)

Collection Instructions:

1. The preferred volume is 100 mcL at a concentration of 250 ng/mcL.

2. Include concentration and volume on tube.

Specimen Stability Information: Frozen (preferred)/Ambient/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

Additional Information: A separate culture charge will be assessed under CULAF / Amniotic Fluid Culture for Genetic Testing.

 

Specimen Type: Cultured amniocytes

Container/Tube: T-25 flask

Specimen Volume: 2 Full flasks

Collection Instructions: Submit confluent cultured cells from another laboratory.

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

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: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Genetic Testing.

 

Specimen Type: Cultured chorionic villi

Container/Tube: T-25 flasks

Specimen Volume: 2 Full flasks

Collection Instructions: Submit confluent cultured cells from another laboratory.

Specimen Stability Information: Ambient (preferred)/Refrigerated


Specimen Minimum Volume

Whole Blood: 1 mL
Cord Blood: 1 mL
Amniotic Fluid: 10 mL
Chorionic Villi: 5 mg

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies

Clinical Information

This test is for the analysis of the presence of 3 to 5 genetic variants (nucleotide substitution or small insertion or deletion of nucleotides) previously identified in a family member. This targeted testing can be used for diagnostic or predictive testing in cases in which variants have been previously identified in an affected family member. This testing may also be used for segregation analysis to determine whether a particular variant or variants are segregating with the phenotype in an affected family. This test is used for a specific subset of genes only. Refer to Genes Available for Known Variant Analysis Testing (KVAR1, KVAR2, or KVAR3) in Special Instructions.

 

Refer to the following resources for information regarding the listed gene targets. GeneReviews-NCBI Bookshelf, available at www.ncbi.nlm.nih.gov/books/NBK1116/ or OMIM, available at www.omim.org/.

 

If testing is needed for a gene not on the gene list [see Genetics Information or Genes Available for Known Variant Analysis Testing (KVAR1, KVAR2, or KVAR3) in Special Instructions], see FMTT / Familial Mutation, Targeted Testing, Varies which includes targeted/site-specific testing for additional genes.

 

Testing may be delayed if required documentation (ie, patient information sheet) is not received.

Reference Values

An interpretive report will be provided.

Interpretation

Evaluation and categorization of variants is performed using the most recent published American College of Medical Genetics and Genomics recommendations as a guideline.(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;17(5):405-424

Day(s) and Time(s) Performed

Varies

Analytic Time

10 days

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 U.S. Food and Drug Administration.

CPT Code Information

81403 x 3 (up to x 5)

81265 (if appropriate)

81266 (if appropriate)

 

88233-(if appropriate)

88240-(if appropriate)

 

88235-(if appropriate)

88240-(if appropriate)

88233-(if appropriate)

88240-(if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
KVAR3 Known Variant Analysis-3+ Variants In Process

 

Result ID Test Result Name Result LOINC Value
48265 Variant Tested 36908-2
43567 Result Summary 50397-9
43568 Result Details 82939-0
43569 Interpretation 69047-9
43570 Additional Information 48767-8
43571 Method 49549-9
43572 Disclaimer 62364-5
43573 Reviewed by 18771-6

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
MATCC Maternal Cell Contamination, B Yes No
CULFB Fibroblast Culture for Genetic Test Yes No
CULAF Amniotic Fluid Culture/Genetic Test Yes No
FIBR Fibroblast Culture Yes No
CRYOB Cryopreserve for Biochem Studies No No

Forms

1. Known Variant Analysis: Required Patient Information (T768) is required, see Special Instructions.

2. 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)

3. If not ordering electronically, complete, print, and send a Cardiovascular Test Request Form (T724) with the specimen.