Test Catalog

Test Id : CGPH

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Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies

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Overview

Test Catalog

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

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

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

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
G145 Hereditary Custom Gene Panel Tier 1 No, (Bill Only) No
G146 Hereditary Custom Gene Panel Tier 2 No, (Bill Only) No
G147 Hereditary Custom Gene Panel Tier 3 No, (Bill Only) No
G148 Hereditary Custom Gene Panel Tier 4 No, (Bill Only) No
G149 Hereditary Custom Gene Panel Tier 5 No, (Bill Only) No
G150 Hereditary Custom Gene Panel Tier 6 No, (Bill Only) No

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

Pricing for this test will be 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.

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

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

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

Custom Gene Panel, Hereditary

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

3-MCC deficiency

Acylglycerol disorders

Alexander disease (GFAP)

AMT

Biotin disorders

Biotinidase Deficiency (BTD)

Carnitine Palmitoyltransferase II Deficiency (CPT2)

Carnitine-Acylcarnitine Translocase Deficiency (SLC25A20)

CCM2

CDKL5

Cerebral Cavernous Malformation

COL4A1

Congenital Disorders of Glycosylation (CDG)

Copper disorders

Creatine Deficiency Disorder

CSTB

Custom Gene Ordering

Custom Gene Panel

Custom NGS Panel

Custom ordering

Custom Panels

Custom Sequencing Panels

Custom sequencing test

Customizable Hereditary Panels

Customizable Panels

Cystinuria

Fabry disease (GLA)

Familial adenomatous polyposis

FAP

Fructose disorders

GABA disorders

GAMT

Gastric cancer

GATM

Gaucher disease (GBA)

Glucose Transporter Deficiency

Glutaric aciduria

Glycogen Storage Disease (GSD)

HBOC

HDGC

Hereditary Breast and Ovarian Cancer syndrome

Hereditary Diffuse Gastric Cancer

Hereditary paraganglioma and pheochromocytoma

HNPCC

Hyperammonemia

Inborn errors of metabolism

Juvenile polyposis syndrome

Krabbe Disease (GALC)

KRIT1

LGI1

Li Fraumeni syndrome

Lung cancer

Lynch Syndrome

Lysosomal acid lipase deficiency (Wolman, LIPA)

Lysosomal Storage Disease (LSD)

MAP

Medium-Chain Acyl-CoA Dehydrogenase (MCAD) Deficiency (ACADM)

Melanoma

MEN1

MEN2

Metabolic/biochemical disorders

Metachromatic leukodystrophy (ARSA)

Methionine disorder

Methylmalonic aciduria and homocystinuria

Mucopolysaccharidosis Type II (Hunter, IDS)

Mucopolysaccharidosis Type I (Hurler, IDUA)

Mucopolysaccharidosis

Multiple endocrine neoplasia syndrome type 1

Multiple endocrine neoplasia syndrome type 2

MUTYH Associated Polyposis

Neuronal Ceroid Lipofuscinosis (NCL, Batten Disease)

NextGen Sequencing Test

Niemann-Pick disease

Ornithine Transcarbamylase deficiency (OTC)

Ovarian cancer

Pancreatic cancer

Paraganglioma

PDCD10

Peutz Jeghers syndrome

PGL/PCC

Pheochromocytoma

Polyposis

Pompe disease (GAA)

porphyria

Propionic acidemia

Prostate cancer

PRRT2

PSAP

PTEN Hamartoma Tumor Syndrome

Purine/pyrimidine disorders

Sanfilippo syndrome (SGSH, NAGLU, HGSNAT, GNS)

Short-Chain Acyl-CoA Dehydrogenase (SCAD) Deficiency (ACADS)

Skin cancer

SLC2A1

SLC6A8

Tay-Sachs Disease (HEXA)

TCF4

Thiamine disorders

Thyroid cancer

Tuberous sclerosis

UBE3A

Uterine cancer

Very Long Chain Acyl-Coenzyme A Dehydrogenase Deficiency (ACADVL)

Wilms tumor

Wolfram (WFS1, CISD2)

X-linked adrenoleukodystrophy (ABCD1)

ZEB2

Zellweger syndrome

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

Pricing for this test will be 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.

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

This test can only be utilized to modify genetic testing panels for biochemical and hereditary oncology disease states at this time.

 

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:

-Custom Gene Ordering Tool

-Custom Gene Ordering tutorial

 

See Frequently Asked Questions: Custom Gene Ordering Tool

 

Targeted testing for familial variants (also called site-specific or known mutation testing) is available under FMTT / Familial Mutation, 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 required. 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.

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
MG135 Gene List ID

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

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/Refrigerated

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

Forms

1. Molecular Genetics: Hereditary Custom Gene Panel Patient Information is required.

2. 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)

3. If not ordering electronically, complete, print, and send a Neurology Specialty Testing Client Test Request (T732) with the specimen.

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

See Specimen Required

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

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

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

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

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

Pricing for this test will be 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.

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

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
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 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.

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

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 a 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 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 will be performed by alternate methodologies based on internal laboratory criteria.

 

The test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) greater or equal to 40 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 the Targeted Genes and Methodology Details for Hearing Loss Custom Gene Panel and the appropriate Targeted Gene and Methodology details in 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-Policy:

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.

 

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.(1) 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.

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

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 (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 Epilepsy Custom Gene Panel

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

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

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

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

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

Supplemental

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.

28 to 35 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 account representative. 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.

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)

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)

81440 (if appropriate)

81443 (if appropriate)

81479 (if appropriate)

81188 (if appropriate)

81419 (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
CGPH Custom Gene Panel, Hereditary In Process
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.
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
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

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 | 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

Test Update Resources

Change Type Effective Date
New Test 2021-04-27