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STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

Test code: D4718F

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Test code: D4718F

Order Tests

STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

This test analyzes genes associated with premature ovarian failure.

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Test Code	D4718F
Test Summary	This test analyzes genes associated with premature ovarian failure.
Turn Around Time	7 - 10 days
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**	81479(x2), 81244(x1), 81443(x1)

Self (patient) Price	$1,550.00
Institutional Price	$2,400.00

*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: D4718F

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Clinical Genomics Test Requisition Form

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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, withthe exception of FMR1 repeat testing, is performed utilizing next-generation sequencing (NGS) technology. All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.

The number of CGG repeats in the FMR1 gene is determined by PCR. Normal: Approximately 5-44 CGG repeats. Intermediate: Approximately 54-45 unmethylated CGG repeats. Premutation: Approximately 55-200 CGG repeats and methylation of expanded allele. Affected: Over 200 CGG repeats and methylation of expanded allele.

Condition description

Primary ovarian failure is the depletion of ovarian follicles with cessation of menses before age 40. It is associated with hypoestrogenism and loss of residual follicles. These changes lead to menstrual abnormalities and pregnancy failures. The prevalence of this condition is estimated at 1% in the general population. Genetic causes are responsible for 10% of cases of primary ovarian failure.

Genes

BMP15, CYP17A1, CYP19A1, DIAPH2, EIF2B2 EIF2B3, EIF2B5, FIGLA, FMR1, FOXL2, FSHR, GALT, GDF9, HFM1, LHCGR, LMNA, NOBOX, NR5A1, POF1B, POR, PSMC3IP

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. For FMR1 CGG repeat analysis, the size of the repeat region is determined by polymerase chain reaction (PCR).

Detailed sample requirements

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.

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.

Resources

Clinical Genomics Test Requisition Form

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Step 1

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

Step 2

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

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STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

About this test

Specifications

Price

Test information

Test description

Condition description

Genes

Test methods and limitations

Detailed sample requirements

Whole Blood (EDTA) (Preferred Sample)

Saliva

Dried Blood Spots

DNA, Isolated

Resources

How To Order

Choose Your Test

Collect Sample

Send Samples

How can we help you?

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STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

STAT Premature Ovarian Failure: Sequencing Panel and FMR1 CGG Repeat Analysis

About this test

Specifications

Price

Test information

Test description

Condition description

Genes

Test methods and limitations

Detailed sample requirements

Whole Blood (EDTA) (Preferred Sample)

Saliva

Dried Blood Spots

DNA, Isolated

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?