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Usher Syndrome Panel

Test code: D4308

Test Inquiry

Test code: D4308

Test Inquiry

Usher Syndrome Panel

This test analyzes genes associated with Usher syndrome.

View test information

Test Code	D4308
Test Summary	This test analyzes genes associated with Usher syndrome.
Turn Around Time	2 - 3 weeks
Acceptable Sample Types	DNA, Isolated , Dried Blood Spots , Saliva , Whole Blood (EDTA)
Acceptable Billing Types	Institutional Billing , Self (patient) Payment
NY Approved	No
CPT Codes**	81404(x2), 81406(x1), 81407(x3), 81408(x2), 81479(x2)

*TAT starts after the sample and all required sample information is received at the processing laboratory.

**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.

This testing service has not been cleared or approved by the U.S. Food and Drug Administration. Testing services may not be licensed in accordance with the laws in all countries. The availability of specific test offerings is dependent upon laboratory location.

Test code: D4308

Download PDF Version

Resources

Clinical Genomics Test Requisition Form

This test is not available in your region Japan, please select your nearest laboratory to request more information.

Test Inquiry

Test information

Test description

This gene sequencing panel includes both sequencing and deletion/duplication (CNV) analysis for all coding regions of the included genes (unless otherwise noted). All analysis is performed utilizing next-generation sequencing (NGS) technology. All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.

Condition description

Usher syndrome is characterized by the combination of sensorineural hearing loss and retinitis pigmentosa. Retinitis pigmentosa is a bilateral degeneration of the photoreceptors and leads to progressive vision loss. There are three types of Usher syndrome, which differ in disease onset and progression. Individuals with Usher syndrome type 1 have congenital, bilateral, profound sensorineural hearing loss, vestibular areflexia, and adolescent-onset retinitis pigmentosa. Usher syndrome type 2 is characterized by congenital, bilateral sensorineural hearing loss that is mild to moderate in the low frequencies and severe to profound in the higher frequencies and retinitis pigmentosa that begins with night blindness and tunnel vision with progression to decreased central visual acuity. Individuals with Usher syndrome type 3 have postlingual, progressive sensorineural hearing loss and late-onset retinitis pigmentosa. Types 1 and 2 are the most common, with certain mutations being more common among people of Ashkenazi Jewish or French Acadian heritage (NIH, genetics home reference). The estimated incidence of Usher syndrome is 1 in 10,000.

Genes

ABHD12, ADGRV1, CDH23, CEP250, CIB2, CLRN1, HARS1 MYO7A, PCDH15, PDZD7, USH1C, USH1G, USH2A, WHRN

Test methods and limitations

Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the exome. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on Illumina next generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. A list of these regions, if any, is available upon request. Alignment to the human reference genome (GRCh37) is performed and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indel and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at director discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA. Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be analyzed or may be difficult to detect. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics’ internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v6.1 software.

Detailed sample requirements

Saliva

Test Details Page
Collection Container(s)	Oragene™ Saliva Collection Kit or ORAcollect-Dx kit
Collection	Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer's instructions.
Sample Condition	Store at ambient temperature. Do not refrigerate or freeze.
Shipping	Ship overnight at ambient temperature.
SPECIAL SAMPLE INSTRUCTIONS	Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information.

Dried Blood Spots

Test Details Page
Collection Container(s)	Dried blood spot card
Collection	Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours. NBS: Please contact Revvity Omics to request the StepOne^® kit. Gene Sequencing: Please contact Revvity Omics to request the DBS collection kit. For pre-punched DBS: The required minimum is 6 punches
Sample Condition	Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer.
Shipping	Follow kit instructions. Double bag and ship overnight at ambient temperature.

DNA, Isolated

Test Details Page
Collection	Required DNA Quantity by Test Type: Next Generation Sequencing (NGS):* Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA. Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested). Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.
Sample Condition	* Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met.
Shipping	Ship overnight at ambient temperature.
SPECIAL SAMPLE INSTRUCTIONS	Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results. Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor before submitting a DNA sample from any non-CLIA-certified laboratory. Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.

Whole Blood (EDTA) (Preferred Sample)

Test Details Page
Collection Container(s)	EDTA (purple top)
Collection	Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.
Sample Condition	Store at ambient temperature. Do not refrigerate or freeze.
Shipping	Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
SPECIAL SAMPLE INSTRUCTIONS	Clotted or hemolyzed samples are not accepted.

Resources

Clinical Genomics Test Requisition Form

How To Order

Step 1

Choose Your Test

Select the correct test for your patient, and download and fill out the Clinical Genomics test requisition form.

Step 2

Collect Sample

Obtain a sample for testing from the patient using one of the provided Revvity Omics test packs.

Step 3

Send Samples

Send samples and all required forms back to Revvity for processing using pre-paid shipping label.

How can we help you?

We are here to answer your questions.

Revvity Sites Globally

Usher Syndrome Panel

Usher Syndrome Panel

Usher Syndrome Panel

About this test

Specifications

Test information

Test description

Condition description

Genes

Test methods and limitations

Detailed sample requirements

Saliva

Dried Blood Spots

DNA, Isolated

Whole Blood (EDTA) (Preferred Sample)

Resources

How To Order

Choose Your Test

Collect Sample

Send Samples

How can we help you?

Revvity Sites Globally

Usher Syndrome Panel

Usher Syndrome Panel

Usher Syndrome Panel

About this test

Specifications

Revvity Sites Globally

Test information

Test description

Condition description

Genes

Test methods and limitations

Detailed sample requirements

Saliva

Dried Blood Spots

DNA, Isolated

Whole Blood (EDTA) (Preferred Sample)

Resources

How To Order

Choose Your Test

Collect Sample

Send Samples

1. Build Your Custom Panel

2. Complete and print the test requisition

3. Collect and Send Patient Sample

How can we help you?