Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies - Covenant HealthCare Laboratory Test Directory

Ordering Guidance

This test requires the creation of a unique Gene List ID that directs the laboratory to test the genes requested.

To create the required Gene List ID for your Custom Gene Panel, navigate to:

For answers to frequently asked questions, see Custom gene ordering on MayoClinicLabs.com.

Targeted testing for familial variants (also called site-specific or known mutation testing) is available under FMTT / Familial Variant, Targeted Testing, Varies. Call 800-533-1710 to obtain more information about this testing option.

Shipping Instructions

Specimen preferred to arrive within 96 hours of collection.

Necessary Information

Molecular Genetics: Hereditary Custom Gene Panel Patient Information is strongly recommended. Testing may proceed without the patient information; however, it aids in providing a more thorough interpretation. Ordering providers are strongly encouraged to complete the form and send it with the specimen.

Specimen Required

Specimen Type: Whole blood

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.

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 4 days/Refrigerated

Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy of the consent is on file.

-Informed Consent for Genetic Testing (T576)

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

2. Molecular Genetics: Hereditary Custom Gene Panel Patient Information

3. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Neurology Specialty Testing Client Test Request (T732)

-Renal Diagnostics Test Request (T830)

-Biochemical Genetics Test Request (T798)

Secondary ID

605198

Useful For

Customization of existing next-generation sequencing panels offered through Mayo Clinic Laboratories

Detection single nucleotide and copy number variants in a custom gene panel

Identification of a pathogenic variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for a hereditary condition

Testing Algorithm

Pricing for this test is based on the number of genes selected (1, 2-14, 15-49, 50-100, 101-500, and greater than 500) and their corresponding CPT codes. For more information see Custom Gene Ordering Pricing.

Special Instructions

Method Name

Sequence Capture and Next-Generation Sequencing (NGS)/Polymerase Chain Reaction (PCR), Sanger Sequencing or Multiplex Ligation-Dependent Probe Amplification (MLPA)

Reporting Name

Custom Gene Panel, Hereditary

Specimen Type

Varies

Specimen Minimum Volume

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

This test can be used to customize genetic testing panels offered at Mayo Clinic Laboratories. Individual genes can be added or removed to an existing genetic testing panel. Additionally, this test can be used to create your own custom single gene or multi-gene panel or to combine existing panels within the same disease state.

Note: Any genes added to the custom panel must be from the same disease state. Only one Gene List ID may be submitted per Custom Gene Panel, Hereditary order. The Gene List ID can be created using the Custom Gene Ordering tool (see Ordering Guidance).

Reference Values

An interpretive report will be provided.

Interpretation

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

Method Description

Next-generation sequencing (NGS) and/or Sanger sequencing are 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 is 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 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 amplified for sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high GC (guanine-cytosine) content, and repetitive sequences. Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.(Unpublished Mayo method)

For details regarding the specific gene regions not routinely covered, see the appropriate information:

-Targeted Genes and Methodology Details for Cardiovascular/Connective Tissue/Dyslipidemia/Cerebrovascular/Primary Ciliary Dyskinesia Custom Gene Panel

-Targeted Genes and Methodology Details for Epilepsy Custom Gene Panel

-Targeted Genes and Methodology Details for Hearing Loss Custom Gene Panel

-Targeted Genes and Methodology Details for Hereditary Cancer Custom Gene Panel

-Targeted Genes and Methodology Details for Inborn Errors of Metabolism Custom Gene Panel

-Targeted Genes and Methodology Details for Nephrology Custom Gene Panel

-Targeted Genes and Methodology Details for Neurologic Disorders Custom Gene Panel

-Targeted Genes and Methodology Details for the Nuclear Mitochondrial Disorders Custom Gene Panel

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

CPT codes are based on the gene content of the custom gene panel. Refer to the Custom Gene Ordering Tool for custom gene panel specific CPT code information.

81165 (if appropriate)

81166 (if appropriate)

81167 (if appropriate)

81162 (if appropriate)

81201 (if appropriate)

81216 (if appropriate)

81223 (if appropriate)

81249 (if appropriate)

81252 (if appropriate)

81286 (if appropriate)

81292 (if appropriate)

81295 (if appropriate)

81298 (if appropriate)

81307 (if appropriate)

81319 (if appropriate)

81321 (if appropriate)

81351 (if appropriate)

81403 (if appropriate)

81404 (if appropriate)

81405 (if appropriate)

81406 (if appropriate)

81407 (if appropriate)

81408 (if appropriate)

81430 (if appropriate)

81431 (if appropriate)

81440 (if appropriate)

81443 (if appropriate)

81448 (if appropriate)

81479 (if appropriate)

81189 (if appropriate)

81419 (if appropriate)

LOINC Code Information

Test ID	Test Order Name	Order LOINC Value
CGPH	Custom Gene Panel, Hereditary	105259-6

Result ID	Test Result Name	Result LOINC Value
MG135	Gene List ID	48018-6
610422	Test Description	62364-5
606046	Specimen	31208-2
606047	Source	31208-2
606040	Result Summary	50397-9
606041	Result	82939-0
606042	Interpretation	69047-9
620157	Additional Results	82939-0
610423	Resources	99622-3
606043	Additional Information	48767-8
606044	Method	85069-3
610424	Genes Analyzed	48018-6
606045	Disclaimer	62364-5
606048	Released By	18771-6

Day(s) Performed