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Test Code #6000
We are pleased to offer PGxomeTM Custom Sequencing Panels, which are whole exome based and completely customizable to fit your patients’ specific needs. The automatic inclusion of copy number variant (CNV) analysis via NGS data increases clinical utility, and our Enhance feature offers complete coverage as needed. Our test menu also offers >200 defined gene sequencing panels to choose from, so before you start a custom panel order, be sure to search our existing menu.Full Guide
- Use our PGxome Custom Panel Tool. There are three easy ways to build your panel:
- Search by Phenotype Cluster or Gene: enter in HUGO gene name or a phenotype to get started
- Search by Category: to see our phenotype clusters of grouped genes
- Select Full Phenotype Cluster List: to see all of our preset phenotype clusters
- Add a list of genes: click the "Add a list of genes here" link under the search bar to add a list of genes to your order
WHOLE BLOOD: Collect 3 ml-5 ml of whole blood in EDTA (purple top tube) or ACD (yellow top tube), minimum 1 ml for small infants.
SALIVA: OrageneTM Saliva Collection kit used according to manufacturer instructions.
FRESH, FROZEN TISSUE: Collect 2mm x 2mm x 2mm tissue and flash freeze. Tissue to be sent frozen (preferably dry ice). Please contact us for additional details.
DNA: Send in screw cap tube at least 10 μg of purified DNA at a concentration of at least 50 μg/ml (indicate concentration on tube label).
CULTURED CELLS: Specimen requirements: Ship at least two T25 flasks of confluent cells. Storage and shipping: T25 flasks need to be shipped in appropriate complete culture medium filled to the brim. Ship T25 flasks at room temperature in an insulated container once 90% confluency is reached and by overnight delivery.
Pricing & Billing Details
Pricing is determined by the number of genes ordered and the number of Enhance options selected. Pricing calculator is subject to change over time.
|PGxome Custom Panels|
|Number of Genes Ordered||Total Price (before Enhance)||Reflex to Exome|
|>500||$2,490* call for price||$890|
Cost for Enhance option varies by gene, depending on amount of laboratory work needed to achieve full coverage or address paralogy issues.
As your custom panel is being built, the cost of the panel will be updated in real-time in the bottom right corner of the screen as you are adding genes to your cart. If pricing reaches cost of PGxome test, you will be prompted to decide whether to proceed with the current custom panel or convert the order to a PGxome test request.
Once you select "Proceed to Reviewing Order," CPT codes and final pricing details will be displayed. If you desire insurance billing and investigation of benefits prior to sending the patient’s specimen, this order form can be printed and faxed to us with a completed Benefit Investigation Request Form. Otherwise, for general information about our billing policy, click here.
If results are negative, can I reflex to PGxome Diagnostic if desired?
Our custom panel allows for reflex to PGxome Diagnostic WES if the custom panel does not yield a diagnosis. See table above for the cost to reflex to PGxome Diagnostic after custom panel testing for an individual; each comparative exome is $990. If reflex PGxome Diagnostic test is needed, please complete the PGxome Test Requisition Form.
The great majority of PGxome Custom Panels are completed within 26 days.
Our Phenotype Clusters
Phenotype-driven starter panels are intended to simplify the ordering process. The genes in these panels will be updated periodically by our laboratory. Please review and customize your panel as indicated (adding or deleting genes) to meet your patient’s diagnostic needs. Don’t see what you are looking for? Build the phenotype cluster panel you desire and then email it to our team.
If testing is for a fetus in an ongoing pregnancy please Contact Us.
Note: If testing is for an ongoing pregnancy the reflex option to a PGxome is not currently available.
Enhance Option Details
- Our Enhance option utilizes Sanger sequencing to approach 100% coverage of coding regions and ~10bp of flanking sequence.
- Sanger sequencing is used for regions that may not perform well with NextGen sequencing technology.
- Enhance option is available for many genes and forced for genes that may have non-unique coding sequence (paralogy).
- For genes whose average % of bp covered at 20X is already listed at 100%, selecting Enhance option will offer necessary backfill (with Sanger sequencing) in the event individual results deviate from average coverage performance.
- Cost for Enhance option varies by gene, depending on amount of laboratory work needed to achieve full coverage.
- Our custom panel does include CNV analysis via NGS data. However, aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region. Balanced translocations or inversions within a targeted gene are not detected. In nearly all cases, our ability to determine the exact copy number change within a targeted gene is limited. Our ability to detect CNVs due to somatic mosaicism is limited. The sensitivity of this test is dependent on DNA quality.
- Where desired, del/dup testing is available also via gene-centric aCGH for many genes on our menu. Del/dup testing can be ordered via Test Code 600 for genes that are available. This can be offered concurrently or as a reflex from PGxome Custom Panels.
- For some disorders the common disease mechanism is repeat expansions. While the gene may be available via sequencing, this does not generally include repeat expansion testing.
- Mitochondrial genome is currently not available.
- Some genes with significant paralogy may not be available.
- Over time, more gene specific notes will be added to our PGxome Custom Panel Tool. Current notes are not all inclusive.
- Our custom panels do not generally cover pathogenic variants outside of +/- 10bp of coding regions.
Contact us with any questions. Our client services team, comprised of client service representatives, genetic counseling assistants, and genetic counselors, are happy to assist you with your custom panel questions.